FTIR, FT-Raman spectra and ab initio, DFT vibrational analysis of 2,4-dinitrophenylhydrazine

NASA Astrophysics Data System (ADS)

Sundaraganesan, N.; Ayyappan, S.; Umamaheswari, H.; Dominic Joshua, B.

2007-01-01

The FTIR and FT-Raman spectra of 2,4-dinitrophenylhydrazine (2,4-DNPH) has been recorded in the region 4000-400 and 3500-50 cm -1, respectively. The optimized geometry, frequency and intensity of the vibrational bands of 2,4-DNPH were obtained by the ab initio and density functional theory (DFT) levels of theory with complete relaxation in the potential energy surface using 6-31G(d,p) and 6-311G(d,p) basis sets. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically constructed bar type spectrograms.

An ab-initio study of the relative stability of the ggg and the gtg conformer in hexane

NASA Astrophysics Data System (ADS)

Koglin, Eckhard; Meier, Robert J.

1999-10-01

Earlier ab-initio work suggested, on the basis of MP2 level calculations, that the hexane ggg conformer is more stable than the gtg conformer. Because this is unexpected and if true might have a significant impact on force field parametrisations, we have applied Hartree-Fock and post-HF methods to evaluate the relative stability of these conformers. We find that at levels higher than MP2 the gtg conformer is more stable than the ggg conformer, in agreement with the conventional idea that each additional gauche bond causes a further decrease in stability of the conformer. DFT methods were also applied, but although DFT methods including gradient corrections show correct qualitative behaviour, quantitatively the relative energies are far off compared to the post-HF results.

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

Structure and gas phase stability of complexes L . .. M, where M = Li+, Na+, Mg2+ and L is formaldehyde, formic acid, formate anion, formamide and their sila derivatives

NASA Astrophysics Data System (ADS)

Remko, Milan

Ab initio SCF and DFT methods were used to characterize the gas-phase complexes of selected carbonyl and silacarbonyl bases with Li+ , Na+ and Mg2+ . Geometries were optimized at the Hartree-Fock ab initio and Becke 3LYP DFT levels with the 6-31G* basis set. Frequency computations were performed at the RHF/6-31G* level of theory. Interaction energies of the cation-coordinated systems also were determined with the MP2/6-31G* method. The effect of extension of basis set (to the 6-31+ G* basis) on the computed properties of anion-metal cation complexes was investigated. Calculated energies of formation vary as Mg2+ > Li+ > Na+ . The Becke 3LYP DFT binding energies were comparable with those obtained at the correlated MP2 level and are in good agreement with available experimental data.

Ab initio study of the alkaline hydrolysis of a thio-β-lactam structure

NASA Astrophysics Data System (ADS)

Coll, Miguel; Frau, Juan; Vilanova, Bartolomé; Donoso, Josefa; Muñoz, Francisco

2000-08-01

The alkaline hydrolysis of a thio-β-lactam in the gas phase was examined in the light of RHF and DFT ab initio calculations. The solvent effect was considered via IPCM computations. The tetrahedral intermediate for the thio-β-lactam studied is unstable, so the compound evolves directly to the corresponding thio-azethidin-2-one open ring with cleavage of the C-S bond. The end-products obtained bear a carbamate group, which suggests that the thio-β-lactam might be an effective inhibitor for β-lactamases.

Elastic and Photoelastic Properties of M(NO3)2, MO (M = Mg, Ca, Sr, Ba)

NASA Astrophysics Data System (ADS)

Zhuravlev, Yu. N.; Korabel'nikov, D. V.

2017-05-01

The paper deals with ab initio investigations of elastic and photoelastic properties of oxides and nitrates of alkaline-earth metals. In gradient approximation of the density functional theory (DFT), these properties are studied with the use of the linear combination of the atomic orbital technique. DFT calculations are done with the CRYSTAL 14 software package. The paper introduces the elastic and photoelastic constants, anisotropy parameters for single-crystalline phases and the elastic modules, hardness, Poisson ratio for polycrystalline phases. Such parameters as sonic speed, Debye temperature, thermal conductivity, and Gruneisen parameter are estimated herein. For the fist time, mechanical stability, anisotropy of elastic and photoelastic properties and their dependences are investigated ab initio in this paper. Experimental results on elastic and photoelastic properties of oxides and nitrates are in good agreement with theoretical calculations.

Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

NASA Astrophysics Data System (ADS)

Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

2013-06-01

The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

Large-Scale Hybrid Density Functional Theory Calculations in the Condensed-Phase: Ab Initio Molecular Dynamics in the Isobaric-Isothermal Ensemble

NASA Astrophysics Data System (ADS)

Ko, Hsin-Yu; Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto

Hybrid functionals are known to alleviate the self-interaction error in density functional theory (DFT) and provide a more accurate description of the electronic structure of molecules and materials. However, hybrid DFT in the condensed-phase has a prohibitively high associated computational cost which limits their applicability to large systems of interest. In this work, we present a general-purpose order(N) implementation of hybrid DFT in the condensed-phase using Maximally localized Wannier function; this implementation is optimized for massively parallel computing architectures. This algorithm is used to perform large-scale ab initio molecular dynamics simulations of liquid water, ice, and aqueous ionic solutions. We have performed simulations in the isothermal-isobaric ensemble to quantify the effects of exact exchange on the equilibrium density properties of water at different thermodynamic conditions. We find that the anomalous density difference between ice I h and liquid water at ambient conditions as well as the enthalpy differences between ice I h, II, and III phases at the experimental triple point (238 K and 20 Kbar) are significantly improved using hybrid DFT over previous estimates using the lower rungs of DFT This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.

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.

Computation of geometries and frequencies of singlet and triplet nitromethane with density functional theory byusing gaussian type orbitals

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

Jursic, B.S.

1996-12-31

The results of the computational study of the structures, energies, dipole moments and IR spectra for a singlet and a triplet nitromethane are presented. Five different hybrids (BHandH, BHandHLYP, B3LYP, B3P86 and B3PW91), local (SVWN), and nonlocal (BLYP) DFT methods are used with various sizes of the gaussian type of basis set. The obtained results are compared to the HF, MP2, and MCSCF ab initio calculations, as well as, to the experimental results. Becke`s three functional based hybrid DFT methods outperform the following: the ab initio (HF, MP2 and MCSCF), the Becke`s half-and-half based DFT methods, and the local (SVWNmore » or LSDA) and nonlocal (BLYP) DFT methods. The computed nitromethane geometry, the dipole moment, the energy difference, and the IR frequency are in extraordinary agreement with the experimental results. Thus, we are recommending the B3LYP and the B3PW91 as the methods of choice when the computational study of small {open_quotes}difficult{close_quotes} molecules is considered.« less

The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking.

PubMed

Cerný, Jirí; Hobza, Pavel

2005-04-21

The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.

Diffusion Monte Carlo calculations of Xenon and Krypton at High Pressure

NASA Astrophysics Data System (ADS)

Shulenburger, Luke; Mattsson, Thomas R.

2011-06-01

Ab initio calculations based on density functional theory (DFT) have proven a valuable tool in understanding the properties of materials at extreme conditions. However, there are entire classes of materials where the current limitations of DFT cast doubt upon the predictive power of the method. These include so called strongly correlated systems and materials where van der Waals forces are important. Diffusion Monte Carlo (DMC) can treat materials with a different class of approximations that have generally proven to be more accurate. The use of DMC together with DFT may therefore improve the predictive capability of the ab initio calculation of materials at extreme conditions. We present two examples of this approach. In the first we use DMC total energies to address the discrepancy between DFT and diamond anvil cell melt curves of Xe. In the second, DMC is used to address the choice of density functional used in calculations of the Kr hugoniot. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract No. DE-AC04-94AL85000. Belonoshko et al. PRB 74, 054114 (2006).

DFT-based ab initio MD simulation of the ionic conduction in doped ZrO₂ systems under epitaxial strain.

PubMed

Oka, M; Kamisaka, H; Fukumura, T; Hasegawa, T

2015-11-21

The oxygen ionic conduction in ZrO2 systems under tensile epitaxial strain was investigated by performing ab initio molecular dynamics (MD) calculations based on density functional theory (DFT) to elucidate the essential factors in the colossal ionic conductivity observed in the yttria stabilized ZrO2 (YSZ)/SrTiO3 heterostructure. Three factors were evaluated: lattice strain, oxygen vacancies, and dopants. Phonon calculations based on density functional perturbation theory (DFPT) were used to obtain the most stable structure for nondoped ZrO2 under 7% tensile strain along the a- and b-axes. This structure has the space group Pbcn, which is entirely different from that of cubic ZrO2, suggesting that previous ab initio MD calculations assuming cubic ZrO2 may have overestimated the ionic conductivity due to relaxation from the initial structure to the stable structure (Pbcn). Our MD calculations revealed that the ionic conductivity is enhanced only when tensile strain and oxygen vacancies are incorporated, although the presently obtained diffusion constant is far below the range for the colossal ionic conduction experimentally observed. The enhanced ionic conductivity is due to the combined effects of oxygen sublattice formation induced by strain and deformation of this sublattice by oxygen vacancies.

Ab-initio Electronic, Transport and Related Properties of Zinc Blende Boron Arsenide (zb-BAs)

NASA Astrophysics Data System (ADS)

Nwigboji, Ifeanyi H.; Malozovsky, Yuriy; Bagayoko, Diola

We present results from ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of zinc blende boron arsenide (zb-BAs). We utilized a local density approximation (LDA) potential and the linear combination of atomic orbital (LCAO) formalism. Our computational technique follows the Bagayoko, Zhao, and Williams method, as enhanced by Ekuma and Franklin. Our results include electronic energy bands, densities of states, and effective masses. We explain the agreement between these findings, including the indirect band gap, and available, corresponding, experimental ones. This work confirms the capability of DFT to describe accurately properties of materials, provided the computations adhere to the conditions of validity of DFT [AIP Advances, 4, 127104 (2014)]. 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 No. DE- NA0002630), LaSPACE, and LONI-SUBR.

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.

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.

Site occupancy trend of Co in Ni{sub 2}MnIn: Ab initio approach

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

Pal, Soumyadipta, E-mail: soumyadipta.pal@gmail.com; Mahadevan, Priya; Biswas, C.

2015-06-24

The trend of site occupation of Co at Ni sites of Ni{sub 2}MnIn system is studied in austenitic phase having L2{sub 1} structure by ab initio density functional theory (DFT) calculation. The Co atoms prefer to be at Ni sites rather than Mn site and are ferromagetically coupled with Ni and Mn. The ground state has tetragonal structure for Ni{sub 1.5}Co{sub 0.5}MnIn and Ni{sub 1.25}Co{sub 0.75}MnIn. The Co tends to form cluster.

Stabilization of flat aromatic Si6 rings analogous to benzene: ab initio theoretical prediction.

PubMed

Zdetsis, Aristides D

2007-12-07

It is shown by ab initio calculations, based on density functional (DFT/B3LYP), and high level coupled-cluster [CCSD(T)] and quadratic CI [QCISD(T)] methods, that flat aromatic silicon structures analogous to benzene (C6H6) can be stabilized in the presence of lithium. The resulting planar Si6Li6 structure is both stable and aromatic, sharing many key characteristics with benzene. To facilitate possible synthesis and characterization of these species, routes of formation with high exothermicity are suggested and several spectral properties (including optical absorption, infrared, and Raman) are calculated.

Electron transport in all-Heusler Co2CrSi/Cu2CrAl/Co2CrSi device, based on ab-initio NEGF calculations

NASA Astrophysics Data System (ADS)

Mikaeilzadeh, L.; Pirgholi, M.; Tavana, A.

2018-05-01

Based on the ab-initio non-equilibrium Green's function (NEGF) formalism based on the density functional theory (DFT), we have studied the electron transport in the all-Heusler device Co2CrSi/Cu2CrAl/Co2CrSi. Results show that the calculated transmission spectra is very sensitive to the structural parameters and the interface. Also, we obtain a range for the thickness of the spacer layer for which the MR effect is optimum. Calculations also show a perfect GMR effect in this device.

Molecular structures of Se(SCH3)2 and Te(SCH3)2 using gas-phase electron diffraction and ab initio and DFT geometry optimisations.

PubMed

Fleischer, Holger; Wann, Derek A; Hinchley, Sarah L; Borisenko, Konstantin B; Lewis, James R; Mawhorter, Richard J; Robertson, Heather E; Rankin, David W H

2005-10-07

The molecular structures of Se(SCH(3))(2) and Te(SCH(3))(2) were investigated using gas-phase electron diffraction (GED) and ab initio and DFT geometry optimisations. While parameters involving H atoms were refined using flexible restraints according to the SARACEN method, parameters that depended only on heavy atoms could be refined without restraints. The GED-determined geometric parameters (r(h1)) are: rSe-S 219.1(1), rS-C 183.2(1), rC-H 109.6(4) pm; angleS-Se-S 102.9(3), angleSe-S-C 100.6(2), angleS-C-H (mean) 107.4(5), phiS-Se-S-C 87.9(20), phiSe-S-C-H 178.8(19) degrees for Se(SCH(3))(2), and rTe-S 238.1(2), rS-C 184.1(3), rC-H 110.0(6) pm; angleS-Te-S 98.9(6), angleTe-S-C 99.7(4), angleS-C-H (mean) 109.2(9), phiS-Te-S-C 73.0(48), phiTe-S-C-H 180.1(19) degrees for Te(SCH(3))(2). Ab initio and DFT calculations were performed at the HF, MP2 and B3LYP levels, employing either full-electron basis sets [3-21G(d) or 6-31G(d)] or an effective core potential with a valence basis set [LanL2DZ(d)]. The best fit to the GED structures was achieved at the MP2 level. Differences between GED and MP2 results for rS-C and angleS-Te-S were explained by the thermal population of excited vibrational states under the experimental conditions. All theoretical models agreed that each compound exists as two stable conformers, one in which the methyl groups are on the same side (g(+)g(-) conformer) and one in which they are on different sides (g(+)g(+) conformer) of the S-Y-S plane (Y = Se, Te). The conformational composition under the experimental conditions could not be resolved from the GED data. Despite GED R-factors and ab initio and DFT energies favouring the g(+)g(+) conformer, it is likely that both conformers are present, for Se(SCH(3))(2) as well as for Te(SCH(3))(2).

Mesoscale models for stacking faults, deformation twins and martensitic transformations: Linking atomistics to continuum

NASA Astrophysics Data System (ADS)

Kibey, Sandeep A.

We present a hierarchical approach that spans multiple length scales to describe defect formation---in particular, formation of stacking faults (SFs) and deformation twins---in fcc crystals. We link the energy pathways (calculated here via ab initio density functional theory, DFT) associated with formation of stacking faults and twins to corresponding heterogeneous defect nucleation models (described through mesoscale dislocation mechanics). Through the generalized Peieirls-Nabarro model, we first correlate the width of intrinsic SFs in fcc alloy systems to their nucleation pathways called generalized stacking fault energies (GSFE). We then establish a qualitative dependence of twinning tendency in fee metals and alloys---specifically, in pure Cu and dilute Cu-xAl (x= 5.0 and 8.3 at.%)---on their twin-energy pathways called the generalized planar fault energies (GPFE). We also link the twinning behavior of Cu-Al alloys to their electronic structure by determining the effect of solute Al on the valence charge density redistribution at the SF through ab initio DFT. Further, while several efforts have been undertaken to incorporate twinning for predicting stress-strain response of fcc materials, a fundamental law for critical twinning stress has not yet emerged. We resolve this long-standing issue by linking quantitatively the twin-energy pathways (GPFE) obtained via ab initio DFT to heterogeneous, dislocation-based twin nucleation models. We establish an analytical expression that quantitatively predicts the critical twinning stress in fcc metals in agreement with experiments without requiring any empiricism at any length scale. Our theory connects twinning stress to twin-energy pathways and predicts a monotonic relation between stress and unstable twin stacking fault energy revealing the physics of twinning. We further demonstrate that the theory holds for fcc alloys as well. Our theory inherently accounts for directional nature of twinning which available qualitative models do not necessarily account for. Finally, we extend the present work to martensitic transformations and determine the energy pathway for B2→B19 transformation in NiTi. Based on our ab initio DFT calculations, we propose a combined distortion-shuffle pathway for B2→B19 transformation in NiTi. Our results indicate that in NiTi, a barrier of 0.48 mRyd/atom (relative to B2 phase) must be overcome to transform the parent B2 into orthorhombic B19 phase.

Assessment of Ab Initio and Density Functional Theory Methods for the Excitations of Donor-Acceptor Complexes: The Case of the Benzene-Tetracyanoethylene Model.

PubMed

Xu, Peng; Zhang, Cai-Rong; Wang, Wei; Gong, Ji-Jun; Liu, Zi-Jiang; Chen, Hong-Shan

2018-04-10

The understanding of the excited-state properties of electron donors, acceptors and their interfaces in organic optoelectronic devices is a fundamental issue for their performance optimization. In order to obtain a balanced description of the different excitation types for electron-donor-acceptor systems, including the singlet charge transfer (CT), local excitations, and triplet excited states, several ab initio and density functional theory (DFT) methods for excited-state calculations were evaluated based upon the selected model system of benzene-tetracyanoethylene (B-TCNE) complexes. On the basis of benchmark calculations of the equation-of-motion coupled-cluster with single and double excitations method, the arithmetic mean of the absolute errors and standard errors of the electronic excitation energies for the different computational methods suggest that the M11 functional in DFT is superior to the other tested DFT functionals, and time-dependent DFT (TDDFT) with the Tamm-Dancoff approximation improves the accuracy of the calculated excitation energies relative to that of the full TDDFT. The performance of the M11 functional underlines the importance of kinetic energy density, spin-density gradient, and range separation in the development of novel DFT functionals. According to the TDDFT results, the performances of the different TDDFT methods on the CT properties of the B-TCNE complexes were also analyzed.

Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

2017-02-01

The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

Assessment of TD-DFT and LF-DFT for study of d − d transitions in first row transition metal hexaaqua complexes

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

Vlahović, Filip; Perić, Marko; Zlatar, Matija, E-mail: matijaz@chem.bg.ac.rs

2015-06-07

Herein, we present the systematic, comparative computational study of the d − d transitions in a series of first row transition metal hexaaqua complexes, [M(H{sub 2}O){sub 6}]{sup n+} (M{sup 2+/3+} = V {sup 2+/3+}, Cr{sup 2+/3+}, Mn{sup 2+/3+}, Fe{sup 2+/3+}, Co{sup 2+/3+}, Ni{sup 2+}) by the means of Time-dependent Density Functional Theory (TD-DFT) and Ligand Field Density Functional Theory (LF-DFT). Influence of various exchange-correlation (XC) approximations have been studied, and results have been compared to the experimental transition energies, as well as, to the previous high-level ab initio calculations. TD-DFT gives satisfactory results in the cases of d{sup 2}, d{supmore » 4}, and low-spin d{sup 6} complexes, but fails in the cases when transitions depend only on the ligand field splitting, and for states with strong character of double excitation. LF-DFT, as a non-empirical approach to the ligand field theory, takes into account in a balanced way both dynamic and non-dynamic correlation effects and hence accurately describes the multiplets of transition metal complexes, even in difficult cases such as sextet-quartet splitting in d{sup 5} complexes. Use of the XC functionals designed for the accurate description of the spin-state splitting, e.g., OPBE, OPBE0, or SSB-D, is found to be crucial for proper prediction of the spin-forbidden excitations by LF-DFT. It is shown that LF-DFT is a valuable alternative to both TD-DFT and ab initio methods.« less

E2 and SN2 Reactions of X(-) + CH3CH2X (X = F, Cl); an ab Initio and DFT Benchmark Study.

PubMed

Bento, A Patrícia; Solà, Miquel; Bickelhaupt, F Matthias

2008-06-01

We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X(-) + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) < SN2 (X = F) < SN2 (X = Cl) ∼ syn-E2 (X = F) < anti-E2 (X = Cl) < syn-E2 (X = Cl). Thus, anti-E2 dominates for F(-) + CH3CH2F, and SN2 dominates for Cl(-) + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for SN2 over the anti-E2 in the case of F(-) + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.

The molecular structure and conformation of tetrabromoformaldazine: ab initio and DFT calculations

NASA Astrophysics Data System (ADS)

Jeong, Myongho; Kwon, Younghi

2000-06-01

Ab initio and density functional theory methods are applied to investigate the molecular structure and conformational nature of tetrabromoformaldazine. The calculations including the effects of the electron correlation at the B3LYP and MP2 levels with the basis set 6-311+G(d) can reproduce the experimental geometrical parameters at the skew conformation. The N-N bond torsional angle φ calculated at the MP2/6-311+G(d) level is found to be closest to the observed angle. The scanning of the potential energy surface suggests that the anti-conformation is at a saddle point corresponding to the transition state.

High-throughput ab-initio dilute solute diffusion database.

PubMed

Wu, Henry; Mayeshiba, Tam; Morgan, Dane

2016-07-19

We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.

Towards an ab initio description of correlated materials

NASA Astrophysics Data System (ADS)

Yee, Chuck-Hou

Strongly-correlated materials are a rich playground for physical phenomena, exhibiting complex phase diagrams with many competing orders. Ab initio insights into materials combined with physical ideas provide the ability to identify the organizing principles driving the correlated electronic behavior and pursue first-principles design of new compounds. Realistic modeling of correlated materials is an active area of research, especially with the recent merger of density functional theory (DFT) with dynamical mean-field theory (DMFT). This thesis is structured in two parts. The first describes the methods and algorithmic developments which drive advances in DFT+DMFT. In Ch. 2 and 3, we provide an overview of the two foundational theories, DMFT and DFT. In the second half of Ch. 3, we describe some of the principles guiding the combination of the two theories to form DFT+DMFT. In Ch. 4, we describe the algorithm lying at the heart of modern DFT+DMFT implementations, the hybridization expansion formulation of continuous-time quantum monte carlo (CTQMC) for the general Anderson impurity problem, as well as a fast rejection algorithm for speeding-up the local trace evaluation. The final chapter in the methods section describes an algorithm for direct sampling of the partition function, and thus the free energy and entropy, of simple Anderson impurity models within CTQMC. The second part of the thesis is a collection of applications of our ab initio approach to key correlated materials. We first apply our method to plutonium binary alloys (Ch. 6), which when supplemented with slave-boson mean-field theory, allows us to understand the observed photoemission spectra. Ch. 7 describes the computation of spectra and optical conductivity for rare-earth nickelates grown as epitaxial thin films. In the final two chapters, we turn our attention to the high-temperature superconductors. In the first, we show that the charge-transfer energy is a key chemical variable which controls the superconducting transition temperatures across the cuprate families. In the second, we extend this idea towards first-principles design of cuprates by exploring a new family of copper oxysulfides.

Potential-Energy and Free-Energy Surfaces of Glycyl-Phenylalanyl-Alanine (GFA) Tripeptide. Experiment and Theory

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

Valdes, Haydee; Spiwok, Vojtech; Rezac, Jan

2008-04-17

The free-energy surface (FES) of glycyl-phenylalanyl-alanine (GFA) tripeptide was explored by molecular dynamics (MD) simulations in combination with high-level correlated ab initio quantum chemical calculations and metadynamics. Both the MD and metadynamics employed the tightbinding DFT-D method instead of the AMBER force field, which yielded inaccurate results. We classified the minima localised in the FESs as follows: a) the backbone-conformational arrangement; and b) the existence of a COOH---OC intramolecular H-bond (families CO₂Hfree and CO₂Hbonded). Comparison with experimental results showed that the most stable minima in the FES correspond to the experimentally observed structures. Remarkably, however, we did not observe experimentallymore » the CO₂Hbonded family (also predicted by metadynamics), although its stability is comparable to that of the CO₂Hfree structures. This fact was explained by the former’s short excited state lifetime. We also carried out ab initio calculations using DFT-D and the M06-2X functional. The importance of the dispersion energy in stabilizing peptide conformers is well reflected by our pioneer analysis using the DFT-SAPT method to explore the nature of the backbone/side-chain interactions.« less

High-Level Ab Initio Calculations of Intermolecular Interactions: Heavy Main-Group Element π-Interactions.

PubMed

Krasowska, Małgorzata; Schneider, Wolfgang B; Mehring, Michael; Auer, Alexander A

2018-05-02

This work reports high-level ab initio calculations and a detailed analysis on the nature of intermolecular interactions of heavy main-group element compounds and π systems. For this purpose we have chosen a set of benchmark molecules of the form MR 3 , in which M=As, Sb, or Bi, and R=CH 3 , OCH 3 , or Cl. Several methods for the description of weak intermolecular interactions are benchmarked including DFT-D, DFT-SAPT, MP2, and high-level coupled cluster methods in the DLPNO-CCSD(T) approximation. Using local energy decomposition (LED) and an analysis of the electron density, details of the nature of this interaction are unraveled. The results yield insight into the nature of dispersion and donor-acceptor interactions in this type of system, including systematic trends in the periodic table, and also provide a benchmark for dispersion interactions in heavy main-group element compounds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

NASA Astrophysics Data System (ADS)

Chen, Yi; Zhang, Hui; Liu, Qing

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

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.

Ab initio study of the structural properties of acetonitrile-water mixtures

NASA Astrophysics Data System (ADS)

Chen, Jinfan; Sit, Patrick H.-L.

2015-08-01

Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.

High-throughput ab-initio dilute solute diffusion database

PubMed Central

Wu, Henry; Mayeshiba, Tam; Morgan, Dane

2016-01-01

We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

The molecular structures and conformation of o-selenobenzyl fluoride derivatives, ArSeX (Ar=C 6H 4CH 2F; X=CN, Cl, Me): ab initio and DFT calculations

NASA Astrophysics Data System (ADS)

Jeong, Myongho; Kwon, Younghi

2000-10-01

Ab initio and density functional theory methods are applied to investigate the molecular structures, intramolecular orbital interactions, and 19F and 77Se NMR chemical shifts of o-selenobenzyl fluoride derivatives, ArSeX ( Ar= C6H4CH2F; X= CN, Cl, Me) , at both RHF and B3LYP levels with the basis sets 6-311G ∗∗ and 6-311+G ∗∗. There are two stable rotational conformers for ArSeX. The energy differences between both conformers for each compound are small (within 2 kcal/mol) at various levels.

Unexpected carboxylate like CO adsorption at the Sr3Ru2O7 (001) surface

NASA Astrophysics Data System (ADS)

Hieckel, Marcel; Mittendorfer, Florian; Redinger, Josef; Stoeger, Bernhard; Wang, Zhiming; Schmid, Michael; Diebold, Ulrike

2014-03-01

Oxide perovskite materials have attracted enormous attention because of a variety of intriguing physical properties ranging from catalysis to multiferroicity. We present a combined experimental and ab-initio (DFT) study with the Vienna Ab initio Simulation Package (VASP) on the adsorption of CO at the Sr3Ru2O7 (001) surface. We identify both a physisorbed and a chemisorbed CO configuraton. Unexpectedly, in the latter case adsorption occurs in a carboxylate (COO) like state. Both configurations have been confirmed by detailed STM experiments and simulations. In addition we find only a small barrier for the carboxylate formation on the surface. Work supported by the Austrian FWF, SFB F45 (FOXSI).

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

Strubbe, David

Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.

Multi-Paradigm Multi-Scale Simulations for Fuel Cell Catalysts and Membranes

DTIC Science & Technology

2006-01-01

transfer studies on model systems. . Applying newly developed density functionals QM ( X3LYP ) for estimating the thermodynamics and kinetic energy...Density functional theory methods We have used many QM methods to probe chemical reaction mechanisms and find that the B3LYP and X3LYP [6] flavors of DFT...carried out QM calculations on the surface reactivity of the Pt and PtRu anode catalysts. This QM uses a new ab initio DFT-GGA method ( X3LYP ) [6

Mechanical and magneto-opto-electronic investigation of transition metal based fluoro-perovskites: An ab-initio DFT study

NASA Astrophysics Data System (ADS)

Erum, Nazia; Azhar Iqbal, Muhammad

2017-09-01

Detailed ab-initio calculations are performed to investigate structural, elastic, mechanical, magneto-electronic and optical properties of the KXF3 (X = V, Fe, Co, Ni) fluoro-perovskites using Full Potential Linearized Augmented Plane Wave (FP-LAPW) method within the framework of density functional theory (DFT). The calculated structural parameters by DFT and analytical methods are found consistent with the experimental results. From the elastic and mechanical properties, it can be inferred that these compounds are elastically stable and anisotropic while KCoF3 is harder than rest of the compounds. Furthermore, thermal behavior of these compounds is analyzed by calculating Debye temperature (θD). The calculated spin dependent magneto-electronic properties in these compounds reveal that exchange splitting is dominated by N-3d orbital. The stable magnetic phase optimizations verify the experimental observations at low temperature. Type of chemical bonding is analyzed with the help of variations in electron density difference distribution that is induced due to changes of the second cation. The linear optical properties are also discussed in terms of optical spectra. The present methodology represents an influential approach to calculate the whole set of mechanical and magneto-opto-electronic parameters, which would support to understand various physical phenomena and empower device engineers for implementing these materials in spintronic applications.

DFT energy optimization of a large carbohydrate: cyclomaltohexaicosaose (CA-26)

USDA-ARS?s Scientific Manuscript database

CA-26 is the largest cyclodextrin (546 atoms) for which refined X-ray structural data is available. Because of its size, 26 D-glucose residues, it is beyond the scope of study of most ab initio or density functional methods, and to date has only been computationally examined using empirical force fi...

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

Starrett, C. E.; Saumon, D.

Here, we present an approximation for calculating the equation of state (EOS) of warm and hot dense matter that is built on the previously published pseudoatom molecular dynamics (PAMD) model of dense plasmas [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. And while the EOS calculation with PAMD was previously limited to orbital-free density functional theory (DFT), the new approximation presented here allows a Kohn-Sham DFT treatment of the electrons. The resulting EOS thus includes a quantum mechanical treatment of the electrons with a self-consistent model of the ionic structure, while remaining tractable at high temperatures. The method ismore » validated by comparisons with pressures from ab initio simulations of Be, Al, Si, and Fe. The EOS in the Thomas-Fermi approximation shows remarkable thermodynamic consistency over a wide range of temperatures for aluminum. We also calculate the principal Hugoniots of aluminum and silicon up to 500 eV. We find that the ionic structure of the plasma has a modest effect that peaks at temperatures of a few eV and that the features arising from the electronic structure agree well with ab initio simulations.« less

Derivation of force field parameters for SnO2-H2O surface systems from plane-wave density functional theory calculations.

PubMed

Bandura, A V; Sofo, J O; Kubicki, J D

2006-04-27

Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO2 (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H2O present. A classical interatomic force field has been developed to describe bulk SnO2 and SnO2-H2O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO2 are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H2O molecules agree well between the ab initio and force field predictions. H2O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well.

An ab initio study of the molecular properties of the propyne water hydrogen-bonded complex

NASA Astrophysics Data System (ADS)

Lopes, Kelson C.; Araújo, Regiane C. M. U.; Rusu, Victor H.; Ramos, Mozart N.

2007-05-01

We have employed ab initio MP2 and DFT/B3LYP calculations with the 6-31++G(d,p) basis set to obtain structural, electronic and vibrational properties of the H-bonded complex between propyne and water. This study has revealed that H 2O can doubly complex with propyne forming a quasi five-membered ring. The first complexation occurs through the hydrogen bond between the acid hydrogen of H 2O and the C tbnd C triple bond, whereas the second complexation involves the oxygen atom of H 2O and the in-plane hydrogen atom of the methyl group in propyne. Our calculations have shown that the H-bond lengths between H⋯π and O⋯HC) are 2.419 and 2.707 Å, respectively, employing the DFT/B3LYP calculation whereas the corresponding MP2 values are 2.373 and 2.651 Å. The binding energies including both BSSE and ZPE corrections are -6.16 and -6.72 kJ mol -1, respectively, using the DFT/B3LYP and MP2 calculations. For example, the O-H stretching frequencies of water are decreased by -60 and -29 cm -1 using the DFT/B3LYP calculation, whereas the bending frequency is increased by +15 cm -1. As expected, the infrared intensities for the stretching modes are increased after complexation, especially involving the O-H b bond forming the hydrogen bond with the C tbnd C triple bond.

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.

Comparative semiempirical and ab initio study of the structural and chemical properties of uric acid and its anions

NASA Astrophysics Data System (ADS)

Altarsha, Muhannad; Monard, Gérald; Castro, Bertrand

Semiempirical, density functional theory (DFT), and ab initio calculations have been performed to assess the relative stabilities of 15 possible tautomer forms of neutral uric acid, and of the different urate mono- and dianion forms. These methods have also been used to compute ionization potentials (IPs) for uric acid and its derived anions. Overall, we have found that semiempirical calculations, in particular PM3, perform well as compared with B3LYP or MP2 computations toward these different structural and chemical properties of uric acid: the triketo form of uric acid is the most stable tautomer form of neutral uric acid. Three other tautomer forms are relatively close in energy, within the range 2-6 kcal/mol above the triketo form, with a mean energy deviation of only 1.3 kcal/mol between PM3 and DFT or ab initio results; the monoanion form of uric acid obtained by abstracting one proton in position 3 (denoted UAN3-) is the most stable form among all four possible urate monoanions both in gas phase and in solution; the dianion form of uric acid obtained by abstracting two protons, respectively, in positions 3 and 9 of uric acid (denoted UAN3-N9-) is the most stable urate dianion form both in gas phase and in solution. However, these two most stable species do not have the lowest IPs in solution: among monoanions and dianions, respectively, the species with the lowest IPs are UAN7- and UAN7-N9-.

On the structural and electronic properties of Ir-silicide nanowires on Si(001) surface

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

Fatima,; Hossain, Sehtab; Mohottige, Rasika

Iridium (Ir) modified Silicon (Si) (001) surface is studied with Scanning Tunneling Microscopy/Spectroscopy (STM/STS) and Density Functional Theory (DFT). A model for Ir-silicide nanowires based on STM images and ab-initio calculations is proposed. According to our model, the Ir adatom is on the top of the substrate dimer row and directly binds to the dimer atoms. I-V curves measured at 77 K shows that the nanowires are metallic. DFT calculations confirm strong metallic nature of the nanowires.

Ab initio perspective on the Mollwo-Ivey relation for F centers in alkali halides

NASA Astrophysics Data System (ADS)

Tiwald, Paul; Karsai, Ferenc; Laskowski, Robert; Gräfe, Stefanie; Blaha, Peter; Burgdörfer, Joachim; Wirtz, Ludger

2015-10-01

We revisit the well-known Mollwo-Ivey relation that describes the "universal" dependence of the absorption energies of F-type color centers on the lattice constant a of alkali-halide crystals, Eabs∝a-n. We perform both state-of-the-art ab initio quantum chemistry and post-DFT calculations of F-center absorption spectra. By "tuning" independently the lattice constant and the atomic species we show that the scaling with the lattice constant alone (keeping the elements fixed) would yield n =2 in agreement with the "particle-in-the-box" model. Keeping the lattice constant fixed and changing the atomic species enables us to quantify the ion-size effects which are shown to be responsible for the exponent n ≈1.8 .

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

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

Genova, Alessandro, E-mail: alessandro.genova@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Ceresoli, Davide, E-mail: davide.ceresoli@cnr.it

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange–correlation potentials that aremore » linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH{sup •} radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH{sup •} radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.« less

Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}] as model system

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

Ulian, Gianfranco; Valdrè, Giovanni, E-mail: giovanni.valdre@unibo.it; Tosoni, Sergio

2013-11-28

The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, andmore » phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.« less

Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical.

PubMed

Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

2016-06-21

In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH(•) radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH(•) radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

PubMed

Hafner, Jürgen

2010-09-29

During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

Ab-initio and DFT methodologies for computing hyperpolarizabilities and susceptibilities of highly conjugated organic compounds for nonlinear optical applications

NASA Astrophysics Data System (ADS)

Karakas, A.; Karakaya, M.; Ceylan, Y.; El Kouari, Y.; Taboukhat, S.; Boughaleb, Y.; Sofiani, Z.

2016-06-01

In this talk, after a short introduction on the methodologies used for computing dipole polarizability (α), second and third-order hyperpolarizability and susceptibility; the results of theoretical studies performed on density functional theory (DFT) and ab-initio quantum mechanical calculations of nonlinear optical (NLO) properties for a few selected organic compounds and polymers will be explained. The electric dipole moments (μ) and dispersion-free first hyperpolarizabilities (β) for a family of azo-azulenes and a styrylquinolinium dye have been determined by DFT at B3LYP level. To reveal the frequency-dependent NLO behavior, the dynamic α, second hyperpolarizabilities (γ), second (χ(2)) and third-order (χ(3)) susceptibilites have been evaluated using time-dependent HartreeFock (TDHF) procedure. To provide an insight into the third-order NLO phenomena of a series of pyrrolo-tetrathiafulvalene-based molecules and pushpull azobenzene polymers, two-photon absorption (TPA) characterizations have been also investigated by means of TDHF. All computed results of the examined compounds are compared with their previous experimental findings and the measured data for similar structures in the literature. The one-photon absorption (OPA) characterizations of the title molecules have been theoretically obtained by configuration interaction (CI) method. The highest occupied molecular orbitals (HOMO), the lowest unoccupied molecular orbitals (LUMO) and the HOMO-LUMO band gaps have been revealed by DFT at B3LYP level for azo-azulenes, styrylquinolinium dye, push-pull azobenzene polymers and by parametrization method 6 (PM6) for pyrrolo-tetrathiafulvalene-based molecules.

Equation of state of dense plasmas with pseudoatom molecular dynamics

DOE PAGES

Starrett, C. E.; Saumon, D.

2016-06-14

Here, we present an approximation for calculating the equation of state (EOS) of warm and hot dense matter that is built on the previously published pseudoatom molecular dynamics (PAMD) model of dense plasmas [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. And while the EOS calculation with PAMD was previously limited to orbital-free density functional theory (DFT), the new approximation presented here allows a Kohn-Sham DFT treatment of the electrons. The resulting EOS thus includes a quantum mechanical treatment of the electrons with a self-consistent model of the ionic structure, while remaining tractable at high temperatures. The method ismore » validated by comparisons with pressures from ab initio simulations of Be, Al, Si, and Fe. The EOS in the Thomas-Fermi approximation shows remarkable thermodynamic consistency over a wide range of temperatures for aluminum. We also calculate the principal Hugoniots of aluminum and silicon up to 500 eV. We find that the ionic structure of the plasma has a modest effect that peaks at temperatures of a few eV and that the features arising from the electronic structure agree well with ab initio simulations.« less

Application of ab initio many-body perturbation theory with Gaussian basis sets to the singlet and triplet excitations of organic molecules

NASA Astrophysics Data System (ADS)

Hamed, Samia; Rangel, Tonatiuh; Bruneval, Fabien; Neaton, Jeffrey B.

Quantitative understanding of charged and neutral excitations of organic molecules is critical in diverse areas of study that include astrophysics and the development of energy technologies that are clean and efficient. The recent use of local basis sets with ab initio many-body perturbation theory in the GW approximation and the Bethe-Saltpeter equation approach (BSE), methods traditionally applied to periodic condensed phases with a plane-wave basis, has opened the door to detailed study of such excitations for molecules, as well as accurate numerical benchmarks. Here, through a series of systematic benchmarks with a Gaussian basis, we report on the extent to which the predictive power and utility of this approach depend critically on interdependent underlying approximations and choices for molecules, including the mean-field starting point (eg optimally-tuned range separated hybrids, pure DFT functionals, and untuned hybrids), the GW scheme, and the Tamm Dancoff approximation. We demonstrate the effects of these choices in the context of Thiels' set while drawing analogies to linear-response time-dependent DFT and making comparisons to best theoretical estimates from higher-order wavefunction-based theories.

Combined ab initio and density functional study on polaron to bipolaron transitions in oligophenyls and oligothiophenes

NASA Astrophysics Data System (ADS)

Irle, Stephan; Lischka, Hans

1997-08-01

Ab initio self-consistent-field (SCF), two-configuration SCF (TCSCF), and density functional theory (DFT) calculations on the charge-transfer complexes of doubly Li/Cl-doped oligothiophenes and oligo(p-phenyls) and on respective charged systems without counterions have been carried out in order to study polaron to bipolaron transitions. Oligomer chains up to octamers and the ring structures cyclo-dodecathiophene and cyclo-dodeca(p-phenyl) have been investigated. Special attention is paid to the open-shell biradical character of two isolated polaronic defects. It is found that the TCSCF and the spin-unrestricted DFT methods can be successfully applied. A bipolaron structure is obtained when the doping atoms are located on neighboring rings and when there is one undoped ring separating the two doped ones. If there are two or more undoped rings in between a two-polaron configuration (biradical) is found. The bipolaron system is calculated to be more stable than the two-polaron case when counterions are taken into account. The stabilities are reversed if the bare, doubly-charged systems are considered. A theoretical estimate for the barrier height of the polaron to bipolaron transition is given using model reaction coordinates.

Ab initio quasiparticle bandstructure of ABA and ABC-stacked graphene trilayers

NASA Astrophysics Data System (ADS)

Menezes, Marcos; Capaz, Rodrigo; Louie, Steven

2013-03-01

We obtain the quasiparticle band structure of ABA and ABC-stacked graphene trilayers through ab initio density functional theory (DFT) and many-body quasiparticle calculations within the GW approximation. To interpret our results, we fit the DFT and GW π bands to a low energy tight-binding model, which is found to reproduce very well the observed features near the K point. The values of the extracted hopping parameters are reported and compared with available theoretical and experimental data. For both stackings, the quasiparticle corrections lead to a renormalization of the Fermi velocity, an effect also observed in previous calculations on monolayer graphene. They also increase the separation between the higher energy bands, which is proportional to the nearest neighbor interlayer hopping parameter γ1. Both features are brought to closer agreement with experiment through the quasiparticle corrections. Finally, other effects, such as trigonal warping, electron-hole assymetry and energy gaps are discussed in terms of the associated parameters. This work was supported by the Brazilian funding agencies: CAPES, CNPq, FAPERJ and INCT-Nanomateriais de Carbono. It was also supported by NSF grant No. DMR10-1006184 and U.S. DOE under Contract No. DE-AC02-05CH11231.

Development of a machine learning potential for graphene

NASA Astrophysics Data System (ADS)

Rowe, Patrick; Csányi, Gábor; Alfè, Dario; Michaelides, Angelos

2018-02-01

We present an accurate interatomic potential for graphene, constructed using the Gaussian approximation potential (GAP) machine learning methodology. This GAP model obtains a faithful representation of a density functional theory (DFT) potential energy surface, facilitating highly accurate (approaching the accuracy of ab initio methods) molecular dynamics simulations. This is achieved at a computational cost which is orders of magnitude lower than that of comparable calculations which directly invoke electronic structure methods. We evaluate the accuracy of our machine learning model alongside that of a number of popular empirical and bond-order potentials, using both experimental and ab initio data as references. We find that whilst significant discrepancies exist between the empirical interatomic potentials and the reference data—and amongst the empirical potentials themselves—the machine learning model introduced here provides exemplary performance in all of the tested areas. The calculated properties include: graphene phonon dispersion curves at 0 K (which we predict with sub-meV accuracy), phonon spectra at finite temperature, in-plane thermal expansion up to 2500 K as compared to NPT ab initio molecular dynamics simulations and a comparison of the thermally induced dispersion of graphene Raman bands to experimental observations. We have made our potential freely available online at [http://www.libatoms.org].

Explicitly correlated benchmark calculations on C8H8 isomer energy separations: how accurate are DFT, double-hybrid, and composite ab initio procedures?

NASA Astrophysics Data System (ADS)

Karton, Amir; Martin, Jan M. L.

2012-10-01

Accurate isomerization energies are obtained for a set of 45 C8H8 isomers by means of the high-level, ab initio W1-F12 thermochemical protocol. The 45 isomers involve a range of hydrocarbon functional groups, including (linear and cyclic) polyacetylene, polyyne, and cumulene moieties, as well as aromatic, anti-aromatic, and highly-strained rings. Performance of a variety of DFT functionals for the isomerization energies is evaluated. This proves to be a challenging test: only six of the 56 tested functionals attain root mean square deviations (RMSDs) below 3 kcal mol-1 (the performance of MP2), namely: 2.9 (B972-D), 2.8 (PW6B95), 2.7 (B3PW91-D), 2.2 (PWPB95-D3), 2.1 (ωB97X-D), and 1.2 (DSD-PBEP86) kcal mol-1. Isomers involving highly-strained fused rings or long cumulenic chains provide a 'torture test' for most functionals. Finally, we evaluate the performance of composite procedures (e.g. G4, G4(MP2), CBS-QB3, and CBS-APNO), as well as that of standard ab initio procedures (e.g. MP2, SCS-MP2, MP4, CCSD, and SCS-CCSD). Both connected triples and post-MP4 singles and doubles are important for accurate results. SCS-MP2 actually outperforms MP4(SDQ) for this problem, while SCS-MP3 yields similar performance as CCSD and slightly bests MP4. All the tested empirical composite procedures show excellent performance with RMSDs below 1 kcal mol-1.

Ab initio calculations, structure, NBO and NCI analyses of Xsbnd H⋯π interactions

NASA Astrophysics Data System (ADS)

Wu, Qiyang; Su, He; Wang, Hongyan; Wang, Hui

2018-02-01

The performance of ab initio methods (MP2, DFT/B3LYP, random-phase approximation (RPA), CCSD(T) and QCISD(T)) in predicting interaction energy of Xsbnd H⋯π (Xsbnd H = HCCH, HCl, HF; π = C2H2, C2H4, C6H6) hydrogen complexes are assessed systematically. The CCSD(T)/CBS benchmarks of interaction energy are reported. It is found that RPA agrees well with CCSD(T)/CBS benchmarks and experimental results. CCSD(T) and QCISD(T) perform the best only when compared with CCSD(T)/CBS benchmarks, MP2 performs well only for experimental data. B3LYP provides the worst accuracy. Additionally, the equilibrium structure, interaction type of Xsbnd H⋯π hydrogen complexes are investigated by the natural bond orbital (NBO) and the non-covalent interaction index (NCI).

Computer modeling of adsorption and decomposition pathways of boundary-layer lubricants on clean aluminum(111) surface, and adhesive metal transfer at the aluminum/steel interface: The ab-initio study

NASA Astrophysics Data System (ADS)

Zhong, Jun

Density functional theory (DFT) is employed to study lubricant adsorption and decomposition pathways, and adhesive metal transfer on clean aluminum surfaces. In this dissertation, density functional theory (DFT-GGA) is used to investigate the optimal adsorption geometries and binding energies of vinyl-phosphonic and ethanoic acids on an A1(111) surface. Tri-bridged, bi-bridged and uni-dentate coordinations for adsorbates are examined to determine the optimal binding sites on the surface. An analysis of the charge density of states (DOS) of oxygen involved in reacting with aluminum ions reveals changes in the atomic bonding configuration. For these acid molecules, the favorable decomposition pathways lead to fragments of vinyl- and alkylchains bonding to the Al(111) surface with phosphorous and carbon ions. Final optimal decomposition geometries and binding energies for various decomposition stages are also discussed. In addition, ab-initio molecular dynamics (AIMD) is carried out to explore collisions of aliphatic lubricants like butanol-alcohol and butanoic-acid with the Al(111) surface. Simulation results indicate that functional oxygen groups on these molecules could react with the "islands of nascent aluminum" and oxidize the surface. Favorable decomposition pieces on the surface, which were corroborated with experiment and DFT calculations, are found to contribute to the effectiveness of a particular molecule for boundary thinfilm lubrication to reduce the wear of aluminum. Finally, ab-initio molecular dynamics is also applied to investigations of the interaction between aluminum and hematite surfaces with and without a vinyl-phosphonic acid (VPA) lubricant. Without the lubricant, hematite is found to react with Al strongly (thermit reaction). This removes relatively large fragments from the surface of the aluminum substrate when this substrate is rubbed with a harder steel-roller under an external shock contact-load exceeding the ability of the substrate to support the aluminum-oxide film. Adhesive wear is found to significantly raise the temperature of system. Addition of VPA lubricant is found to retard the reaction of hematite with aluminum by forming an effective barrier between the two surfaces.

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

Cyclic density functional theory: A route to the first principles simulation of bending in nanostructures

NASA Astrophysics Data System (ADS)

Banerjee, Amartya S.; Suryanarayana, Phanish

2016-11-01

We formulate and implement Cyclic Density Functional Theory (Cyclic DFT) - a self-consistent first principles simulation method for nanostructures with cyclic symmetries. Using arguments based on Group Representation Theory, we rigorously demonstrate that the Kohn-Sham eigenvalue problem for such systems can be reduced to a fundamental domain (or cyclic unit cell) augmented with cyclic-Bloch boundary conditions. Analogously, the equations of electrostatics appearing in Kohn-Sham theory can be reduced to the fundamental domain augmented with cyclic boundary conditions. By making use of this symmetry cell reduction, we show that the electronic ground-state energy and the Hellmann-Feynman forces on the atoms can be calculated using quantities defined over the fundamental domain. We develop a symmetry-adapted finite-difference discretization scheme to obtain a fully functional numerical realization of the proposed approach. We verify that our formulation and implementation of Cyclic DFT is both accurate and efficient through selected examples. The connection of cyclic symmetries with uniform bending deformations provides an elegant route to the ab-initio study of bending in nanostructures using Cyclic DFT. As a demonstration of this capability, we simulate the uniform bending of a silicene nanoribbon and obtain its energy-curvature relationship from first principles. A self-consistent ab-initio simulation of this nature is unprecedented and well outside the scope of any other systematic first principles method in existence. Our simulations reveal that the bending stiffness of the silicene nanoribbon is intermediate between that of graphene and molybdenum disulphide - a trend which can be ascribed to the variation in effective thickness of these materials. We describe several future avenues and applications of Cyclic DFT, including its extension to the study of non-uniform bending deformations and its possible use in the study of the nanoscale flexoelectric effect.

Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).

PubMed

Hafner, Jürgen

2008-02-13

The development of modern materials science has led to a growing need to understand the phenomena determining the properties of materials on an atomistic level. As the behavior of atoms and electrons is governed by the laws of quantum mechanics, accurate and efficient techniques for solving the basic quantum-mechanical equations for very complex many-atom, many-electron systems are required. The development of density-functional theory (DFT) represents a decisive step forwards in our efforts to develop tools for ab initio atomistic simulations of complex materials, preparing the way towards computational materials design. The development of these ab initio simulation methods, whose aim is to model processes in materials by solving the coupled Newtonian equations of motion of the atoms and the Schrödinger equation for the electrons from first principles without any other input than the atomic numbers of the constituents, is part of fundamental research. Hence, for a long time the development and application of DFT methods has been a domain of academic research. Only during the past decade, based on the development of increasingly sophisticated codes and better computer performance, has the impact of DFT-based simulation methods has spread from academia to industry. New opportunities are opening for innovative materials research across physics, chemistry, surface science and nanotechnology extending even to earth sciences and molecular biology. In 1998 we organized, at the Vienna University of Technology, a first workshop entitled 'Electronic Structure Calculations for Industry and Basic Sciences' (short title 'Theory meets Industry') to celebrate the start of the European Science Foundation (ESF) research program 'Electronic Structure Calculations for Elucidating the Complex Atomistic Behavior of Solids and Surfaces', known as the Ψ(k)-network. At this workshop, researchers from academia presented recent results in the development of ab initio simulation methods and their application to key areas of condensed matter physics. Researchers from industry mainly focused on challenges arising from applied industrial research; contributions describing successful applications of DFT techniques to industrial problems were more scarce. Progress during the last decade has been very fast. The ESF research program has been renewed under the much bolder title 'Towards Computational Materials Design' and is now approaching the end of this second funding period. Due to the development of accurate, efficient and stable software packages for ab initio simulations, DFT-based techniques are now routinely used in many industrial laboratories worldwide. It was therefore considered timely to organize a second 'Theory meets Industry' workshop. The meeting took place between 12-14 June 2007 at the Erwin-Schrödinger-Institute (ESI) for Mathematical Physics in Vienna (Austria). It was sponsored by the Universität Wien through the VASP (Vienna Ab-initio Simulation Program) project, the Center for Computational Materials Science Vienna, the Erwin-Schrödinger-Institute and the ESF Program 'Towards Computational Materials Design'. The program of the workshop was decided by an international advisory board consisting of Ryoji Asahi (Toyota Central Research and Development Laboratory), Risto Nieminen (Helsinki University of Technology), Herve Toulhoat (Institut Français du Pétrole), Erich Wimmer (Materials Design Inc.), Chris Wolverton (Ford Motor Co. and Northwestern University) and Jürgen Hafner (Universität Wien). The 35 invited talks presented at the meeting were divided equally between researchers from academia and from industry. The contributions from academia concentrated on a wide range of new developments in DFT and post-DFT simulations (with contributions from the developers of leading software packages for ab initio simulations), as well as on applications in front-line materials research. In contrast to the first workshop nine years ago, all industrial speakers presented results of extensive ab initio studies in key areas of modern technology, concentrating on catalysis and chemical processing, information technologies, automotive engineering and energy. The proceedings assemble full papers summarizing 23 of the invited talks, abstracts of the remaining invited talks and abstracts of all the poster contributions. It is complemented by a conference summary written by Erich Wimmer. Erich is certainly excellently qualified for this task, because for many years he has played the role of mediator between academia and industry. I shall not anticipate his summary here, but I think that it is fair to say that tremendous progress has been made since the first workshop. Ab initio DFT simulations are now a well established tool for industrial research and, due to the availability of cheap high-performance server clusters, their use is no longer the reserve of large corporate laboratories equipped with supercomputers, but are also accessible to medium-sized enterprises. The basic methodology is still developed by the leading academic research groups. These groups urgently need support from funding agencies and/or industry not only for the basic code development, but also to bring their research codes up to industrial standards of programming, stability, user-friendliness and documentation. The fundamental challenge to theory, however, remains the same: more accurate total energies, application to larger and even more complex systems, and access to new materials properties. Responding to these challenges will require substantial effort at various levels. Achieving greatly improved accuracy of calculated total energies demands an improved description of electronic exchange and correlation. Possible routes (hybrid functionals for solids, dynamical mean field theory (DMFT), many-body perturbation theory (GW), quantum Monte-Carlo) have been presented at this meeting. Access to larger systems could be realized either by codes achieving O (N)-scaling or by adopting a strategy of multi-scale simulations. At least two different O (N)-codes have been discussed at the workshop. But even if these approaches allow ab initio calculations to be performed for ten times as many atoms as before, in terms of linear dimensions, the accessible systems size increases only by a factor of two. Therefore, multi-scale simulations strategies remain a very important issue. Access to new materials properties requires adding new routines to the basic codes. Again, this meeting has highlighted important new developments: evolutionary crystal structure predictions, transport properties of semiconductors and insulators, and calculations of free-energy reaction barriers to name only a few. The task of providing a full 'tool-box' of routines for fast and efficient calculation of many different materials properties evidently exceeds the capacity of a single group of developers. Here, collaboration is necessary between the developers of the basic DFT codes and the expert users of these codes pushing the application of the methodology to new frontiers. Again, it will be important to bring the newly developed routines into a stable, well documented form and to make them accessible to a wide range of users, both in academia and industry. Supporting these efforts is also a challenge to industry. The academic research needs industry's support in many ways. Industry has to make governmental and funding agencies aware of the vital role of our research for future technological development-and a very persuasive way to do that is to invest directly into leading academic groups. As the workshop organizer and editor of the proceedings, I would like to thank all contributors (especially those who accepted the burden of writing a full paper), the members of the Advisory Board for helping to organize such a good program, and the Institute of Physics for their help in the preparation of the proceedings.

FOREWORD: Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12 14 June 2007)

NASA Astrophysics Data System (ADS)

Hafner, Jürgen

2008-02-01

The development of modern materials science has led to a growing need to understand the phenomena determining the properties of materials on an atomistic level. As the behavior of atoms and electrons is governed by the laws of quantum mechanics, accurate and efficient techniques for solving the basic quantum-mechanical equations for very complex many-atom, many-electron systems are required. The development of density-functional theory (DFT) represents a decisive step forwards in our efforts to develop tools for ab initio atomistic simulations of complex materials, preparing the way towards computational materials design. The development of these ab initio simulation methods, whose aim is to model processes in materials by solving the coupled Newtonian equations of motion of the atoms and the Schrödinger equation for the electrons from first principles without any other input than the atomic numbers of the constituents, is part of fundamental research. Hence, for a long time the development and application of DFT methods has been a domain of academic research. Only during the past decade, based on the development of increasingly sophisticated codes and better computer performance, has the impact of DFT-based simulation methods has spread from academia to industry. New opportunities are opening for innovative materials research across physics, chemistry, surface science and nanotechnology extending even to earth sciences and molecular biology. In 1998 we organized, at the Vienna University of Technology, a first workshop entitled 'Electronic Structure Calculations for Industry and Basic Sciences' (short title 'Theory meets Industry') to celebrate the start of the European Science Foundation (ESF) research program 'Electronic Structure Calculations for Elucidating the Complex Atomistic Behavior of Solids and Surfaces', known as the Ψk-network. At this workshop, researchers from academia presented recent results in the development of ab initio simulation methods and their application to key areas of condensed matter physics. Researchers from industry mainly focused on challenges arising from applied industrial research; contributions describing successful applications of DFT techniques to industrial problems were more scarce. Progress during the last decade has been very fast. The ESF research program has been renewed under the much bolder title 'Towards Computational Materials Design' and is now approaching the end of this second funding period. Due to the development of accurate, efficient and stable software packages for ab initio simulations, DFT-based techniques are now routinely used in many industrial laboratories worldwide. It was therefore considered timely to organize a second 'Theory meets Industry' workshop. The meeting took place between 12-14 June 2007 at the Erwin-Schrödinger-Institute (ESI) for Mathematical Physics in Vienna (Austria). It was sponsored by the Universität Wien through the VASP (Vienna Ab-initio Simulation Program) project, the Center for Computational Materials Science Vienna, the Erwin-Schrödinger-Institute and the ESF Program 'Towards Computational Materials Design'. The program of the workshop was decided by an international advisory board consisting of Ryoji Asahi (Toyota Central Research and Development Laboratory), Risto Nieminen (Helsinki University of Technology), Herve Toulhoat (Institut Français du Pétrole), Erich Wimmer (Materials Design Inc.), Chris Wolverton (Ford Motor Co. and Northwestern University) and Jürgen Hafner (Universität Wien). The 35 invited talks presented at the meeting were divided equally between researchers from academia and from industry. The contributions from academia concentrated on a wide range of new developments in DFT and post-DFT simulations (with contributions from the developers of leading software packages for ab initio simulations), as well as on applications in front-line materials research. In contrast to the first workshop nine years ago, all industrial speakers presented results of extensive ab initio studies in key areas of modern technology, concentrating on catalysis and chemical processing, information technologies, automotive engineering and energy. The proceedings assemble full papers summarizing 23 of the invited talks, abstracts of the remaining invited talks and abstracts of all the poster contributions. It is complemented by a conference summary written by Erich Wimmer. Erich is certainly excellently qualified for this task, because for many years he has played the role of mediator between academia and industry. I shall not anticipate his summary here, but I think that it is fair to say that tremendous progress has been made since the first workshop. Ab initio DFT simulations are now a well established tool for industrial research and, due to the availability of cheap high-performance server clusters, their use is no longer the reserve of large corporate laboratories equipped with supercomputers, but are also accessible to medium-sized enterprises. The basic methodology is still developed by the leading academic research groups. These groups urgently need support from funding agencies and/or industry not only for the basic code development, but also to bring their research codes up to industrial standards of programming, stability, user-friendliness and documentation. The fundamental challenge to theory, however, remains the same: more accurate total energies, application to larger and even more complex systems, and access to new materials properties. Responding to these challenges will require substantial effort at various levels. Achieving greatly improved accuracy of calculated total energies demands an improved description of electronic exchange and correlation. Possible routes (hybrid functionals for solids, dynamical mean field theory (DMFT), many-body perturbation theory (GW), quantum Monte-Carlo) have been presented at this meeting. Access to larger systems could be realized either by codes achieving O (N)-scaling or by adopting a strategy of multi-scale simulations. At least two different O (N)-codes have been discussed at the workshop. But even if these approaches allow ab initio calculations to be performed for ten times as many atoms as before, in terms of linear dimensions, the accessible systems size increases only by a factor of two. Therefore, multi-scale simulations strategies remain a very important issue. Access to new materials properties requires adding new routines to the basic codes. Again, this meeting has highlighted important new developments: evolutionary crystal structure predictions, transport properties of semiconductors and insulators, and calculations of free-energy reaction barriers to name only a few. The task of providing a full 'tool-box' of routines for fast and efficient calculation of many different materials properties evidently exceeds the capacity of a single group of developers. Here, collaboration is necessary between the developers of the basic DFT codes and the expert users of these codes pushing the application of the methodology to new frontiers. Again, it will be important to bring the newly developed routines into a stable, well documented form and to make them accessible to a wide range of users, both in academia and industry. Supporting these efforts is also a challenge to industry. The academic research needs industry's support in many ways. Industry has to make governmental and funding agencies aware of the vital role of our research for future technological development—and a very persuasive way to do that is to invest directly into leading academic groups. As the workshop organizer and editor of the proceedings, I would like to thank all contributors (especially those who accepted the burden of writing a full paper), the members of the Advisory Board for helping to organize such a good program, and the Institute of Physics for their help in the preparation of the proceedings.

Ab initio molecular simulations with numeric atom-centered orbitals

NASA Astrophysics Data System (ADS)

Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

2009-11-01

We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

Computational design and experimental validation of new thermal barrier systems

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

Guo, Shengmin

2015-03-31

The focus of this project is on the development of a reliable and efficient ab initio based computational high temperature material design method which can be used to assist the Thermal Barrier Coating (TBC) bond-coat and top-coat design. Experimental evaluations on the new TBCs are conducted to confirm the new TBCs’ properties. Southern University is the subcontractor on this project with a focus on the computational simulation method development. We have performed ab initio density functional theory (DFT) method and molecular dynamics simulation on screening the top coats and bond coats for gas turbine thermal barrier coating design and validationmore » applications. For experimental validations, our focus is on the hot corrosion performance of different TBC systems. For example, for one of the top coatings studied, we examined the thermal stability of TaZr 2.75O 8 and confirmed it’s hot corrosion performance.« less

Ab initio study of structural and mechanical property of solid molecular hydrogens

NASA Astrophysics Data System (ADS)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

NASA Astrophysics Data System (ADS)

Bano, Amreen; Gaur, N. K.

2018-05-01

Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

Carbon diffusion in molten uranium: an ab initio molecular dynamics study

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

Garrett, Kerry E.; Abrecht, David G.; Kessler, Sean H.

In this work we used ab initio molecular dynamics (AIMD) within the framework of density functional theory (DFT) and the projector-augmented wave (PAW) method to study carbon diffusion in liquid uranium at temperatures above 1600 K. The electronic interactions of carbon and uranium were described using the local density approximation (LDA). The self-diffusion of uranium based on this approach is compared with literature computational and experimental results for liquid uranium. The temperature dependence of carbon and uranium diffusion in the melt was evaluated by fitting the resulting diffusion coefficients to an Arrhenius relationship. We found that the LDA calculated activationmore » energy for carbon was nearly twice that of uranium: 0.55±0.03 eV for carbon compared to 0.32±0.04 eV for uranium. Structural analysis of the liquid uranium-carbon system is also discussed.« less

Acid base chemistry of luteolin and its methyl-ether derivatives: A DFT and ab initio investigation

NASA Astrophysics Data System (ADS)

Amat, Anna; De Angelis, Filippo; Sgamellotti, Antonio; Fantacci, Simona

2008-09-01

The acid-base chemistry of luteolin, a flavonoid with important pharmacological and dyeing properties, and of the related methyl ether derivatives have been investigated by DFT and MP2 methods, testing different computational setups. We calculate the pK's of all the possible deprotonation sites, for which no experimental assignment could be achieved. The calculated pK's deliver a different acidity order for the two most acidic deprotonation sites between luteolin and its methyl ether derivatives, due to intramolecular hydrogen bonding in luteolin. A lowest p Ka of 6.19 is computed for luteolin, in good agreement with available experimental data.

Maximally localized Wannier functions in LaMnO3 within PBE + U, hybrid functionals and partially self-consistent GW: an efficient route to construct ab initio tight-binding parameters for eg perovskites.

PubMed

Franchini, C; Kováčik, R; Marsman, M; Murthy, S Sathyanarayana; He, J; Ederer, C; Kresse, G

2012-06-13

Using the newly developed VASP2WANNIER90 interface we have constructed maximally localized Wannier functions (MLWFs) for the e(g) states of the prototypical Jahn-Teller magnetic perovskite LaMnO(3) at different levels of approximation for the exchange-correlation kernel. These include conventional density functional theory (DFT) with and without the additional on-site Hubbard U term, hybrid DFT and partially self-consistent GW. By suitably mapping the MLWFs onto an effective e(g) tight-binding (TB) Hamiltonian we have computed a complete set of TB parameters which should serve as guidance for more elaborate treatments of correlation effects in effective Hamiltonian-based approaches. The method-dependent changes of the calculated TB parameters and their interplay with the electron-electron (el-el) interaction term are discussed and interpreted. We discuss two alternative model parameterizations: one in which the effects of the el-el interaction are implicitly incorporated in the otherwise 'noninteracting' TB parameters and a second where we include an explicit mean-field el-el interaction term in the TB Hamiltonian. Both models yield a set of tabulated TB parameters which provide the band dispersion in excellent agreement with the underlying ab initio and MLWF bands.

On the Reliability of Pure and Hybrid DFT Methods for the Evaluation of Halogen, Chalcogen, and Pnicogen Bonds Involving Anionic and Neutral Electron Donors.

PubMed

Bauzá, Antonio; Alkorta, Ibon; Frontera, Antonio; Elguero, José

2013-11-12

In this article, we report a comprehensive theoretical study of halogen, chalcogen, and pnicogen bonding interactions using a large set of pure and hybrid functionals and some ab initio methods. We have observed that the pure and some hybrid functionals largely overestimate the interaction energies when the donor atom is anionic (Cl(-) or Br(-)), especially in the halogen bonding complexes. To evaluate the reliability of the different DFT (BP86, BP86-D3, BLYP, BLYP-D3, B3LYP, B97-D, B97-D3, PBE0, HSE06, APFD, and M06-2X) and ab initio (MP2, RI-MP2, and HF) methods, we have compared the binding energies and equilibrium distances to those obtained using the CCSD(T)/aug-cc-pVTZ level of theory, as reference. The addition of the latest available correction for dispersion (D3) to pure functionals is not recommended for the calculation of halogen, chalcogen, and pnicogen complexes with anions, since it further contributes to the overestimation of the binding energies. In addition, in chalcogen bonding interactions, we have studied how the hybridization of the chalcogen atom influences the interaction energies.

Nuclear structure and dynamics with density functional theory

NASA Astrophysics Data System (ADS)

Stetcu, Ionel

2015-10-01

Even in the absence of ab initio methods capable of tackling heavy nuclei without restrictions, one can obtain an ab initio description of ground-state properties by means of the density functional theory (DFT), and its extension to superfluid systems in its local variant, the superfluid local density approximation (SLDA). Information about the properties of excited states can be obtained in the same framework by using an extension to the time-dependent (TD) phenomena. Unlike other approaches in which the nuclear structure information is used as a separate input into reaction models, the TD approach treats on the same footing the nuclear structure and dynamics, and is well suited to provide more reliable description for a large number of processes involving heavy nuclei, from the nuclear response to electroweak probes, to nuclear reactions, such as neutron-induced reactions, or nuclear fusion and fission. Such processes, sometimes part of integrated nuclear systems, have important applications in astrophysics, energy production, global security, etc. In this talk, I will present the simulation of a simple reaction, that is the Coulomb excitation of a 238U nucleus, and discuss the application of the TD-DFT formalism to the description of induced fission. I gratefully acknowledge partial support of the U.S. Department of Energy through an Early Career Award of the LANL/LDRD Program.

Zero bias STS Kondo anomalies of Co impurities on Cu surfaces: do ab initio calculations work?

NASA Astrophysics Data System (ADS)

Baruselli, Pier Paolo; Smogunov, Alexander; Fabrizio, Michele; Requist, Ryan; Tosatti, Erio

2012-02-01

Transition metal atoms such as Co on Cu (111), (100), and (110) surfaces produce STS I-V spectra showing different zero bias Kondo anomalies [1] but these differences have been neither quantitatively predicted nor fully explained theoretically. We apply to this problem the DFT+NRG scheme of Lucignano et al [2], where one solves by NRG an Anderson model built from ab initio phase shifts provided by DFT. For Co/Cu(100) and Co/Cu(110) our calculations describe correctly the experimental trend of Kondo temperatures, and fairly the lineshapes too. By contrast, they fail to describe Co/Cu(111) where in particular the anti-lorentzian lineshape found in experiment remains unexplained. This failure underscores the role of surface states, probably relevant for Co/Cu(111) [3] but not correctly described by our thin slab calculations. Future efforts to quantitatively include Kondo screening by surface states are therefore called for. 1. N. Knorr et al PRL 88, 096804 (2002); M. Ternes et al 2009 J. Phys.: Cond. Matt. 21, 053001 (2009); A. Gumbsch et al PRB81, 165420 (2010). 2. P. Lucignano et al Nature Mat. 8, 563 (2009); P.P. Baruselli et al, Physica E, doi:10.1016/j.physe.2011.05.005. 3. C. Lin et al. PRB 71, 035417 (2005).

Combining density functional and incremental post-Hartree-Fock approaches for van der Waals dominated adsorbate-surface interactions: Ag{sub 2}/graphene

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

Lara-Castells, María Pilar de, E-mail: Pilar.deLara.Castells@csic.es; Mitrushchenkov, Alexander O.; Stoll, Hermann

2015-09-14

A combined density functional (DFT) and incremental post-Hartree-Fock (post-HF) approach, proven earlier to calculate He-surface potential energy surfaces [de Lara-Castells et al., J. Chem. Phys. 141, 151102 (2014)], is applied to describe the van der Waals dominated Ag{sub 2}/graphene interaction. It extends the dispersionless density functional theory developed by Pernal et al. [Phys. Rev. Lett. 103, 263201 (2009)] by including periodic boundary conditions while the dispersion is parametrized via the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)]. Starting with the elementary cluster unit of the target surface (benzene), continuing through the realistic cluster model (coronene), andmore » ending with the periodic model of the extended system, modern ab initio methodologies for intermolecular interactions as well as state-of-the-art van der Waals-corrected density functional-based approaches are put together both to assess the accuracy of the composite scheme and to better characterize the Ag{sub 2}/graphene interaction. The present work illustrates how the combination of DFT and post-HF perspectives may be efficient to design simple and reliable ab initio-based schemes in extended systems for surface science applications.« less

Ab-initio Density Functional Theory (DFT) Studies of Electronic, Transport, and Bulk Properties of Sodium Oxide (Na2O)

NASA Astrophysics Data System (ADS)

Polin, Daniel; Ziegler, Joshua; Malozovsky, Yuriy; Bagayoko, Diola

We present the findings of ab-initio calculations of electronic, transport, and structural properties of cubic sodium oxide (Na2O). These results were obtained using density functional theory (DFT), specifically a local density approximation (LDA) potential, and the linear combination of Gaussian orbitals (LCGO). Our implementation of LCGO followed the Bagayoko, Zhao, and Williams method as enhanced by the work of Ekuma and Franklin (BZW-EF). We describe the electronic band structure of Na2O with a direct band gap of 2.22 eV. Our results include predicted values for the electronic band structure and associated energy eigenvalues, the total and partial density of states (DOS and pDOS), the equilibrium lattice constant of Na2O, and the bulk modulus. We have also calculated the electron and holes effective masses in the Γ to L, Γ to X, and Γ to K directions. 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 No. DE- NA0002630), LaSPACE, and LONI-SUBR.

Ab-initio Calculation of Optoelectronic and Structural Properties of Cubic Lithium Oxide (Li2O)

NASA Astrophysics Data System (ADS)

Ziegler, Joshua; Polin, Daniel; Malozovsky, Yuriy; Bagayoko, Diola

Using the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), we performed ab-initio, density functional theory (DFT) calculations of optoelectronic, transport, and bulk properties of Li2S. In so doing, we avoid ``band gap'' and problems plaguing many DET calculations [AIP Advances 4, 127104 (2014)]. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). With the BZW-EF method, our results possess the full, physical content of DFT and agree with available, corresponding experimental ones. In particular, we found a room temperature indirect band gap of 6.659 eV that compares favorably with experimental values ranging from 5 to 7.99 eV. We also calculated total and partial density of states (DOS and PDOS), effective masses of charge carriers, the equilibrium lattice constant, and the bulk modulus. 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.

Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations.

PubMed

Ruggiero, Michael T; Zeitler, J Axel

2016-11-17

Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterization can be made. In this study the role of individual atomic interactions on the anharmonic properties of crystalline purine, the building block of many DNA and RNA nucleobases, is studied by experimental terahertz time-domain spectroscopy and first-principles density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD). In particular, the detailed vibrational information provided by the DFT calculations is used to interpret the atomic origins of anharmonic-related effects as determined by the AIMD calculations, which are in good agreement with the experimental data. The results highlight that anharmonicity is especially pronounced in the intermolecular interactions, particularly along the amine hydrogen bond coordinate, and yields valuable insight into what is similarly observed complex biosystems and crystalline solids.

High pressure stability of lithium metatitanate and metazirconate: Insight from experiments & ab-initio calculations

NASA Astrophysics Data System (ADS)

Chitnis, Abhishek; Chakraborty, B.; Tripathi, B. M.; Tyagi, A. K.; Garg, Nandini

2018-02-01

Lithium metatitanate (LTO) and lithium metazirconate (LZO) are lithium rich ceramics which can be used as tritium breeder materials for thermonuclear reactors. In-situ x-ray diffraction and ab-initio studies at high pressure show that LTO has a higher bulk modulus than that of LZO. In fact these studies indicate that they are the least compressible of the known lithium rich ceramics like Li2O or Li4SiO4, which are potential candidates for blanket materials. These studies show that the TiO6 octahedra are responsible for the higher bulk modulus of LTO when compared to that of LZO. It has also been shown that the compressibility and distortion of the softer LiO6 octahedra can be controlled by altering the stacking sequence of the more rigid covalently bonded octahedra. This knowledge can be used by chemists to design new lithium based ceramics with higher bulk modulus. It was observed that LTO was stable upto 34 GPa. Ab initio DFT calculations helped to understand the anisotropy in compressibility of both LZO and LTO. This study also shows, that even though the empirical potentials developed by Vijaykumar et al. successfully determine the ambient pressure structure of lithium metatitanate, they cannot be used at non ambient conditions like high pressure [1].

Electronic spectroscopy of HRe(CO) 5: a CASSCF/CASPT2 and TD-DFT study

NASA Astrophysics Data System (ADS)

Bossert, J.; Ben Amor, N.; Strich, A.; Daniel, C.

2001-07-01

The low-lying excited states of HRe(CO) 5 have been calculated at the CASSCF/CASPT2 and TD-DFT level of theory using relativistic effective core potentials (ECP) or ab initio model potentials (AIMP). The theoretical absorption spectrum is compared to the experimental one. Despite the similarity between the experimental absorption spectra of HMn(CO) 5 and HRe(CO) 5 in the UV/visible energy domain it is shown that the assignment differs significantly between the two molecules. The low-lying excited states of HRe(CO) 5 correspond to 5d→π *CO excitations whereas the spectrum of HMn(CO) 5 consists mainly of 3d→3d and 3d→ σ*Mn-H excitations. If the CASPT2 and TD-DFT results are quite comparable for the lowest excited states, the upper part assignment is more problematic with the TD-DFT method.

A theoretical study of the reaction of Ti+ with ethane

NASA Astrophysics Data System (ADS)

Moc, Jerzy; Fedorov, Dmitri G.; Gordon, Mark S.

2000-06-01

The doublet and quartet potential energy surfaces for the Ti++C2H6→TiC2H4++H2 and Ti++C2H6→TiCH2++CH4 reactions are studied using density functional theory (DFT) with the B3LYP functional and ab initio coupled cluster CCSD(T) methods with high quality basis sets. Structures have been optimized at the DFT level and the minima connected to each transition state (TS) by following the intrinsic reaction coordinate (IRC). Relative energies are calculated both at the DFT and coupled-cluster levels of theory. The relevant parts of the potential energy surface, especially key transition states, are also studied using multireference wave functions with the final energetics obtained with multireference second-order perturbation theory.

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

Rhenium Complex with Noninnocent Dioxolene Ligand: Combined Experimental and ab Initio Study of [(3,5-di-tert-Bu2C6H2O2)ReCl3(OPPh3)].

PubMed

Abramov, Pavel A; Gritsan, Nina P; Suturina, Elizaveta A; Bogomyakov, Artem S; Sokolov, Maxim N

2015-07-20

Reaction of [ReOCl3(PPh3)2] with 3,5-di-tert-butyl-1,2-benzoquinone (3,5-DTBQ) in hot toluene produces a new complex [(3,5-di-tert-Bu2C6H2O2)Re(OPPh3)Cl3] (1), which was isolated and characterized by elemental analysis, IR, UV-vis spectroscopy, and cyclic voltammetry. In order to clarify the charge state of rhenium and the coordinated dioxolene ligand, X-ray experiments at 150 and 290 K were carried out. The C-O, C-C, and Re-O bond distances at both 150 and 290 K fall between those for semiquinolate (3,5-DTBSQ) and catecholate (3,5-DTBCat) forms; an empirical "metrical oxidation state" of the dioxolene ligand was estimated to be -1.5. High-level ab initio calculations (SOC-CASSCF/NEVPT2) revealed a mixed valence nature of the triplet ground state of complex 1 corresponding to a superposition of the Re(IV)-SQ and Re(V)-cat forms. In agreement with the high-level ab initio and DFT calculations, the temperature dependence of the magnetic susceptibility (5-300 K) is well described in the assumption of the triplet ground state, with the anomalously large zero-field splitting (ZFS) arising from the spin-orbit coupling. According to the ab initio calculations, all absorption bands in the visible region of the electronic absorptions spectrum are assigned to the LMCT bands, with significant contribution of the intraligand transition in the most intense band at 555 nm.

Terahertz disorder-localized rotational modes and lattice vibrational modes in the orientationally-disordered and ordered phases of camphor.

PubMed

Nickel, Daniel V; Ruggiero, Michael T; Korter, Timothy M; Mittleman, Daniel M

2015-03-14

The temperature-dependent terahertz spectra of the partially-disordered and ordered phases of camphor (C10H16O) are measured using terahertz time-domain spectroscopy. In its partially-disordered phases, a low-intensity, extremely broad resonance is found and is characterized using both a phenomenological approach and an approach based on ab initio solid-state DFT simulations. These two descriptions are consistent and stem from the same molecular origin for the broad resonance: the disorder-localized rotational correlations of the camphor molecules. In its completely ordered phase(s), multiple lattice phonon modes are measured and are found to be consistent with those predicted using solid-state DFT simulations.

Electronic transport properties of nano-scale Si films: an ab initio study

NASA Astrophysics Data System (ADS)

Maassen, Jesse; Ke, Youqi; Zahid, Ferdows; Guo, Hong

2010-03-01

Using a recently developed first principles transport package, we study the electronic transport properties of Si films contacted to heavily doped n-type Si leads. The quantum transport analysis is carried out using density functional theory (DFT) combined with nonequilibrium Green's functions (NEGF). This particular combination of NEGF-DFT allows the investigation of Si films with thicknesses in the range of a few nanometers and lengths up to tens of nanometers. We calculate the conductance, the momentum resolved transmission, the potential profile and the screening length as a function of length, thickness, orientation and surface structure. Moreover, we compare the properties of Si films with and without a top surface passivation by hydrogen.

On the vibrational spectra and structural parameters of methyl, silyl, and germyl azide from theoretical predictions and experimental data.

PubMed

Durig, Douglas T; Durig, M S; Durig, James R

2005-05-01

The infrared and Raman spectra of methyl, silyl, and germyl azide (XN3 where X=CH3, SiH3 and GeH3) have been predicted from ab initio calculations with full electron correlation by second order perturbation theory (MP2) and hybrid density function theory (DFT) by the B3LYP method with a variety of basis sets. These predicted data are compared to previously reported experimental data and complete vibrational assignments are provided for all three molecules. It is shown that several of the assignments recently proposed [J. Mol. Struct. (Theochem.) 434 (1998) 1] for methyl azide are not correct. Structural parameters for CH3N3 and GeH3N3 have been obtained by combining the previously reported microwave rotational constants with the ab initio MP2/6-311+G(d,p) predicted values. These "adjusted r0" parameters have very small uncertainties of +/-0.003 A for the XH distances and a maximum of +/-0.005 A for the heavy atom distances and +/-0.5 degrees for the angles. The predicted distance for the terminal NN bond which is nearly a triple bond is much better predicted by the B3LYP calculations, whereas the fundamental frequencies are better predicted by the scaled ab initio calculations. The results are discussed and compared to those obtained for some similar molecules.

Ab Initio Optimized Effective Potentials for Real Molecules in Optical Cavities: Photon Contributions to the Molecular Ground State

PubMed Central

2018-01-01

We introduce a simple scheme to efficiently compute photon exchange-correlation contributions due to the coupling to transversal photons as formulated in the newly developed quantum-electrodynamical density-functional theory (QEDFT).1−5 Our construction employs the optimized-effective potential (OEP) approach by means of the Sternheimer equation to avoid the explicit calculation of unoccupied states. We demonstrate the efficiency of the scheme by applying it to an exactly solvable GaAs quantum ring model system, a single azulene molecule, and chains of sodium dimers, all located in optical cavities and described in full real space. While the first example is a two-dimensional system and allows to benchmark the employed approximations, the latter two examples demonstrate that the correlated electron-photon interaction appreciably distorts the ground-state electronic structure of a real molecule. By using this scheme, we not only construct typical electronic observables, such as the electronic ground-state density, but also illustrate how photon observables, such as the photon number, and mixed electron-photon observables, for example, electron–photon correlation functions, become accessible in a density-functional theory (DFT) framework. This work constitutes the first three-dimensional ab initio calculation within the new QEDFT formalism and thus opens up a new computational route for the ab initio study of correlated electron–photon systems in quantum cavities. PMID:29594185

Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics

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

Campetella, M.; Caminiti, R.; Bencivenni, L.

2016-07-14

In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm{supmore » −1}), where the vibrational motions involve the NH{sub 3}+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm{sup −1} where the antisymmetric stretching mode (ν{sub 3}) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D{sub 3h} symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.« less

Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces

DOE PAGES

Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos

2016-08-08

Using ab initio molecular dynamics (as implemented in periodic, self-consistent (GGA-PBE) density functional theory (DFT) we investigated the mechanism of methanol electro-oxidation on Pt(111). We investigated the role of solvation and electrode potential on the energetics of the first proton transfer step, methanol electro-oxidation to methoxy (CH 3O) or hydroxymethyl (CH 2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), while the binding energy of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrainedmore » ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Solvation reduces the barrier for both C-H and O-H bond activation steps with respect to their vapor phase values, though the effect is more pronounced for C-H bond activation due to less disruption of the hydrogen-bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased, or uncharged Pt(111). Furthermore, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.« less

Exploring the High-Pressure Behavior of PETN: A Combined Quantum Mechanical and Experimental Study

DTIC Science & Technology

2006-11-01

calculations to explore the hypothesized compression-induced polymorphic phase transition [Gruzdkov 2004]. The initial crystal in these Figure 4...Scuseria, G.E., and Chabalowski, C.F. 2004: An ab Initio Study of Solid Nitromethane, HMX , RDX , and CL20: Successes and Failures of DFT. J. Phys. Chem... RDX , HMX , HNIW, and PETN Crystals. J. Phys. Chem. B, 103, 6783. Trotter, J., 1963: Bond lengths and angles in Pentaerythritol Tetranitrate. Acta

Unscrambling micro-solvation of -COOH and -NH groups in neat dimethyl sulfoxide: insights from 1H-NMR spectroscopy and computational studies.

PubMed

Takis, Panteleimon G; Papavasileiou, Konstantinos D; Peristeras, Loukas D; Boulougouris, Georgios C; Melissas, Vasilios S; Troganis, Anastassios N

2017-05-31

Dimethyl sulfoxide (DMSO) has a significant, multi-faceted role in medicine, pharmacy, and biology as well as in biophysical chemistry and catalysis. Its physical properties and impact on biomolecular structures still attract major scientific interest, especially the interactions of DMSO with biomolecular functional groups. In the present study, we shed light on the "isolated" carboxylic (-COOH) and amide (-NH) interactions in neat DMSO via 1 H NMR studies along with extensive theoretical approaches, i.e. molecular dynamics (MD) simulations, density functional theory (DFT), and ab initio calculations, applied on model compounds (i.e. acetic and benzoic acid, ethyl acetamidocyanoacetate). Both experimental and theoretical results show excellent agreement, thereby permitting the calculation of the association constants between the studied compounds and DMSO molecules. Our coupled MD simulations, DFT and ab initio calculations, and NMR spectroscopy results indicated that complex formation is entropically driven and DMSO molecules undergo multiple strong interactions with the studied molecules, particularly with the -COOH groups. The combined experimental and theoretical techniques unraveled the interactions of DMSO with the most abundant functional groups of peptides (i.e. peptide bonds, side chain and terminal carboxyl groups) in high detail, providing significant insights on the underlying thermodynamics driving these interactions. Moreover, the developed methodology for the analysis of the simulation results could serve as a template for future thermodynamic and kinetic studies of similar systems.

Towards Highly Scalable Ab Initio Molecular Dynamics (AIMD) Simulations on the Intel Knights Landing Manycore Processor

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

Jacquelin, Mathias; De Jong, Wibe A.; Bylaska, Eric J.

2017-07-03

The Ab Initio Molecular Dynamics (AIMD) method allows scientists to treat the dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. This extremely important method has tremendous computational requirements, because the electronic Schr¨odinger equation, approximated using Kohn-Sham Density Functional Theory (DFT), is solved at every time step. With the advent of manycore architectures, application developers have a significant amount of processing power within each compute node that can only be exploited through massive parallelism. A compute intensive application such as AIMD forms a good candidate to leverage this processing power. In this paper, wemore » focus on adding thread level parallelism to the plane wave DFT methodology implemented in NWChem. Through a careful optimization of tall-skinny matrix products, which are at the heart of the Lagrange multiplier and nonlocal pseudopotential kernels, as well as 3D FFTs, our OpenMP implementation delivers excellent strong scaling on the latest Intel Knights Landing (KNL) processor. We assess the efficiency of our Lagrange multiplier kernels by building a Roofline model of the platform, and verify that our implementation is close to the roofline for various problem sizes. Finally, we present strong scaling results on the complete AIMD simulation for a 64 water molecules test case, that scales up to all 68 cores of the Knights Landing processor.« less

Theory-restricted resonant x-ray reflectometry of quantum materials

NASA Astrophysics Data System (ADS)

Fürsich, Katrin; Zabolotnyy, Volodymyr B.; Schierle, Enrico; Dudy, Lenart; Kirilmaz, Ozan; Sing, Michael; Claessen, Ralph; Green, Robert J.; Haverkort, Maurits W.; Hinkov, Vladimir

2018-04-01

The delicate interplay of competing phases in quantum materials is dominated by parameters such as the crystal field potential, the spin-orbit coupling, and, in particular, the electronic correlation strength. Whereas small quantitative variations of the parameter values can thus qualitatively change the material, these values can hitherto hardly be obtained with reasonable precision, be it theoretically or experimentally. Here we propose a solution combining resonant x-ray reflectivity (RXR) with multiplet ligand field theory (MLFT). We first perform ab initio DFT calculations within the MLFT framework to get initial parameter values, which we then use in a fit of the theoretical model to RXR. To validate our method, we apply it to NiO and SrTiO3 and obtain parameter values, which are amended by as much as 20 % compared to the ab initio results. Our approach is particularly useful to investigate topologically trivial and nontrivial correlated insulators, staggered moments in magnetically or orbitally ordered materials, and reconstructed interfaces.

Ab-initio Calculation of the XANES of Lithium Phosphates and LiFePO4

NASA Astrophysics Data System (ADS)

Yiu, Y. M.; Yang, Songlan; Wang, Dongniu; Sun, Xueliang; Sham, T. K.

2013-04-01

Lithium iron phosphate has been regarded as a promising cathode material for the next generation lithium ion batteries due to its high specific capacity, superior thermal and cyclic stability [1]. In this study, the XANES (X-ray Absorption Near Edge Structure) spectra of lithium iron phosphate and lithium phosphates of various compositions at the Li K, P L3,2, Fe M3,2 and O K-edges have been simulated self-consistently using ab-initio calculations based on multiple scattering theory (the FEFF9 code) and DFT (Density Functional Theory, the Wien2k code). The lithium phosphates under investigation include LiFePO4, γ-Li3PO4, Li4P2O7 and LiPO3. The calculated spectra are compared to the experimental XANES recorded in total electron yield (TEY) and fluorescence yield (FLY). This work was carried out to assess the XANES of possible phases presented in LiFePO4 based Li ion battery applications [2].

Ab initio random structure searching of organic molecular solids: assessment and validation against experimental data.

PubMed

Zilka, Miri; Dudenko, Dmytro V; Hughes, Colan E; Williams, P Andrew; Sturniolo, Simone; Franks, W Trent; Pickard, Chris J; Yates, Jonathan R; Harris, Kenneth D M; Brown, Steven P

2017-10-04

This paper explores the capability of using the DFT-D ab initio random structure searching (AIRSS) method to generate crystal structures of organic molecular materials, focusing on a system (m-aminobenzoic acid; m-ABA) that is known from experimental studies to exhibit abundant polymorphism. Within the structural constraints selected for the AIRSS calculations (specifically, centrosymmetric structures with Z = 4 for zwitterionic m-ABA molecules), the method is shown to successfully generate the two known polymorphs of m-ABA (form III and form IV) that have these structural features. We highlight various issues that are encountered in comparing crystal structures generated by AIRSS to experimental powder X-ray diffraction (XRD) data and solid-state magic-angle spinning (MAS) NMR data, demonstrating successful fitting for some of the lowest energy structures from the AIRSS calculations against experimental low-temperature powder XRD data for known polymorphs of m-ABA, and showing that comparison of computed and experimental solid-state NMR parameters allows different hydrogen-bonding motifs to be discriminated.

Ab initio simulations of the structure, energetics and mobility of radiation-induced point defects in bcc Nb

NASA Astrophysics Data System (ADS)

Cerdeira, M. A.; Palacios, S. L.; González, C.; Fernández-Pello, D.; Iglesias, R.

2016-09-01

The formation, binding and migration energetics of helium clusters inside a niobium crystal have been analysed via ab initio simulations. The effect of placing several He atoms within an n-vacancy previously formed or as interstitials inside the initial perfect bulk matrix has been studied. DFT-based results show that He atoms prefer to aggregate forming small clusters at n-vacancy sites rather than at interstitial positions in the perfect crystal. The minimum formation energy is found when NHe is equal to the number of vacancies, n. It follows that vacancies act as almost perfect traps for He atoms, as is well known for other metals. The migration barriers of He atoms inside vacancies increase considerably when compared to what happens for vacancies alone. A secondary consequence is that the full set of energies obtained will be highly relevant as an input for new approaches to KMC simulations of defects in Nb.

Magneto-electronic properties and spin-resolved I-V curves of a Co/GeSe heterojunction diode: an ab initio study

NASA Astrophysics Data System (ADS)

Makinistian, Leonardo; Albanesi, Eduardo A.

2013-06-01

We present ab initio calculations of magnetoelectronic and transport properties of the interface of hcp Cobalt (001) and the intrinsic narrow-gap semiconductor germanium selenide (GeSe). Using a norm-conserving pseudopotentials scheme within DFT, we first model the interface with a supercell approach and focus on the spin-resolved densities of states and the magnetic moment (spin and orbital components) at the different atomic layers that form the device. We also report a series of cuts (perpendicular to the plane of the heterojunction) of the electronic and spin densities showing a slight magnetization of the first layers of the semiconductor. Finally, we model the device with a different scheme: using semiinfinite electrodes connected to the heterojunction. These latter calculations are based upon a nonequilibrium Green's function approach that allows us to explore the spin-resolved electronic transport under a bias voltage (spin-resolved I-V curves), revealing features of potential applicability in spintronics.

Electronic structure, thermodynamic properties and hydrogenation of LaPtIn and CePtIn compounds by ab-initio methods

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

Jezierski, Andrzej, E-mail: andrzej.jezierski@ifmpan.poznan.pl; Szytuła, Andrzej

2016-02-15

The electronic structures and thermodynamic properties of LaPtIn and CePtIn are studied by means of ab-initio full-relativistic full-potential local orbital basis (FPLO) method within densities functional (DFT) methodologies. We have also examined the influence of hydrogen on the electronic structure and stability of CePtInH and LaPtInH systems. The positions of the hydrogen atoms have been found from the minimum of the total energy. Our calculations have shown that band structure and topology of the Fermi surfaces changed significantly during the hydrogenation. The thermodynamic properties (bulk modulus, Debye temperatures, constant pressure heat capacity) calculated in quasi-harmonic Debye-Grüneisen model are in amore » good agreement with the experimental data. We have applied different methods of the calculation of the equation of states (EOS) (Murnaghan, Birch-Murnaghan, Poirier–Tarantola, Vinet). The thermodynamic properties are presented for the pressure 0« less

Ab initio and density functional force field studies on the IR spectra and structure of diazonium dicyanomethylide (diazodicyanomethane)

NASA Astrophysics Data System (ADS)

Georgieva, Miglena K.

2004-03-01

The structure of diazonium dicyanomethylide (diazodicyanomethane) +N 2-C(CN) 2-↔N 2C(CN) 2 has been studied on the basis of ab initio HF, MP2 and DFT BLYP force field calculations, as well as of literature IR spectra and X-ray diffraction structural data. The results have been compared with those obtained for a series of chemical relatives of the title compound, i.e. molecules, push-pull molecules, anions and zwitterions, containing α-dicyano or diazo fragments, and especially substituted ammonium dicyanomethylides and diazomethane +N 2-CH 2-↔N 2CH 2. It has been found on the basis of spectral, bond length, bond order and electric charge analyses that the diazonium (or carbanionic, left) canonical form is much more important for the title zwitterion, than the corresponding one for diazomethane. So, the title compound can be named (and considered as) both diazonium dicyanomethylide and dicyanodiazomethane.

Two-state model based on the block-localized wave function method

NASA Astrophysics Data System (ADS)

Mo, Yirong

2007-06-01

The block-localized wave function (BLW) method is a variant of ab initio valence bond method but retains the efficiency of molecular orbital methods. It can derive the wave function for a diabatic (resonance) state self-consistently and is available at the Hartree-Fock (HF) and density functional theory (DFT) levels. In this work we present a two-state model based on the BLW method. Although numerous empirical and semiempirical two-state models, such as the Marcus-Hush two-state model, have been proposed to describe a chemical reaction process, the advantage of this BLW-based two-state model is that no empirical parameter is required. Important quantities such as the electronic coupling energy, structural weights of two diabatic states, and excitation energy can be uniquely derived from the energies of two diabatic states and the adiabatic state at the same HF or DFT level. Two simple examples of formamide and thioformamide in the gas phase and aqueous solution were presented and discussed. The solvation of formamide and thioformamide was studied with the combined ab initio quantum mechanical and molecular mechanical Monte Carlo simulations, together with the BLW-DFT calculations and analyses. Due to the favorable solute-solvent electrostatic interaction, the contribution of the ionic resonance structure to the ground state of formamide and thioformamide significantly increases, and for thioformamide the ionic form is even more stable than the covalent form. Thus, thioformamide in aqueous solution is essentially ionic rather than covalent. Although our two-state model in general underestimates the electronic excitation energies, it can predict relative solvatochromic shifts well. For instance, the intense π →π* transition for formamide upon solvation undergoes a redshift of 0.3eV, compared with the experimental data (0.40-0.5eV).

Real-Space Multiple-Scattering Theory and Its Applications at Exascale

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

Eisenbach, Markus; Wang, Yang

In recent decades, the ab initio methods based on density functional theory (DFT) (Hohenberg and Kohn 1964, Kohn and Sham 1965) have become a widely used tool in computational materials science, which allows theoretical prediction of physical properties of materials from the first principles and theoretical interpretation of new physical phenomena found in experiments. In the framework of DFT, the original problem that requires solving a quantum mechanical equation for a many-electron system is reduced to a one-electron problem that involves an electron moving in an effective field, while the effective field potential is made up of an electrostatic potential,more » also known as Hartree potential, arising from the electronic and ion charge distribution in space and an exchange–correlation potential, which is a function of the electron density and encapsulates the exchange and correlation effects of the many-electron system. Even though the exact functional form of the exchange-correlation potential is formally unknown, a local density approximation (LDA) or a generalized gradient approximation (GGA) is usually applied so that the calculation of the exchange–correlation potential, as well as the exchange–correlation energy, becomes tractable while a required accuracy is retained. Based on DFT, ab initio electronic structure calculations for a material generally involve a self-consistent process that iterates between two computational tasks: (1) solving an one-electron Schrödinger equation, also known as Kohn–Sham equation, to obtain the electron density and, if needed, the magnetic moment density, and (2) solving the Poisson equation to obtain the electrostatic potential corresponding to the electron density and constructing the effective potential by adding the exchange–correlation potential to the electrostatic potential. This self-consistent process proceeds until a convergence criteria is reached.« less

JDFTx: Software for joint density-functional theory

DOE PAGES

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.; ...

2017-11-14

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

JDFTx: Software for joint density-functional theory

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

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

ab initio MD simulations of geomaterials with ~1000 atoms

NASA Astrophysics Data System (ADS)

Martin, G. B.; Kirtman, B.; Spera, F. J.

2009-12-01

In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in SIESTA in accordance with calculations from CRYSTAL as a check on feasibility. Results are reported here that suggest SIESTA may indeed be useful to model silicate liquids at very high T and P.

An unscaled quantum mechanical harmonic force field for p-benzoquinone

NASA Astrophysics Data System (ADS)

Nonella, Marco; Tavan, Paul

1995-10-01

Structure and harmonic vibrational frequencies of p-benzoquinone have been calculated using quantum chemical ab initio and density functional methods. Our calculations show that a satisfactory description of fundamentals and normal mode compositions is achieved upon consideration of correlation effects by means of Møller-Plesset perturbation expansion (MP2) or by density functional theory (DFT). Furthermore, for correct prediction of CO bondlength and force constant, basis sets augmented by polarization functions are required. Applying such basis sets, MP2 and DFT calculations both give results which are generally in reasonable agreement with experimental data. The quantitatively better agreement, however, is achieved with the computationally less demanding DFT method. This method particularly allows very precise prediction of the experimentally important absorptions in the frequency region between 1500 and 1800 cm -1 and of the isotopic shifts of these vibrations due to 13C or 18O substitution.

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.

DFT-derived reactive potentials for the simulation of activated processes: the case of CdTe and CdTe:S.

PubMed

Hu, Xiao Liang; Ciaglia, Riccardo; Pietrucci, Fabio; Gallet, Grégoire A; Andreoni, Wanda

2014-06-19

We introduce a new ab initio derived reactive potential for the simulation of CdTe within density functional theory (DFT) and apply it to calculate both static and dynamical properties of a number of systems (bulk solid, defective structures, liquid, surfaces) at finite temperature. In particular, we also consider cases with low sulfur concentration (CdTe:S). The analysis of DFT and classical molecular dynamics (MD) simulations performed with the same protocol leads to stringent performance tests and to a detailed comparison of the two schemes. Metadynamics techniques are used to empower both Car-Parrinello and classical molecular dynamics for the simulation of activated processes. For the latter, we consider surface reconstruction and sulfur diffusion in the bulk. The same procedures are applied using previously proposed force fields for CdTe and CdTeS materials, thus allowing for a detailed comparison of the various schemes.

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

PubMed Central

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

2014-01-01

The lipophilicity of ten ruthenium(II)-arene complexes was assessed by reversed-phase thin-layer chromatography (RP-TLC) on octadecyl silica stationary phase. The binary solvent systems composed of water and acetonitrile were used as mobile phase in order to determine chromatographic descriptors for lipophilicity estimation. Octanol-water partition coefficient, logK OW, of tested complexes was experimentally determined using twenty-eight standard solutes which were analyzed under the same chromatographic conditions as target substances. In addition, ab initio density functional theory (DFT) computational approach was employed to calculate logK OW values from the differences in Gibbs' free solvation energies of the solute transfer from n-octanol to water. A good overall agreement between DFT calculated and experimentally determined logK OW values was established (R 2 = 0.8024–0.9658). PMID:24587761

Ab initio calculation of thermodynamic potentials and entropies for superionic water

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

French, Martin; Desjarlais, Michael P.; Redmer, Ronald

We construct thermodynamic potentials for two superionic phases of water [with body-centered cubic (bcc) and face-centered cubic (fcc) oxygen lattice] using a combination of density functional theory (DFT) and molecular dynamics simulations (MD). For this purpose, a generic expression for the free energy of warm dense matter is developed and parametrized with equation of state data from the DFT-MD simulations. A second central aspect is the accurate determination of the entropy, which is done using an approximate two-phase method based on the frequency spectra of the nuclear motion. The boundary between the bcc superionic phase and the ices VII andmore » X calculated with thermodynamic potentials from DFT-MD is consistent with that directly derived from the simulations. As a result, differences in the physical properties of the bcc and fcc superionic phases and their impact on interior modeling of water-rich giant planets are discussed.« less

Ab initio calculation of thermodynamic potentials and entropies for superionic water

DOE PAGES

French, Martin; Desjarlais, Michael P.; Redmer, Ronald

2016-02-25

We construct thermodynamic potentials for two superionic phases of water [with body-centered cubic (bcc) and face-centered cubic (fcc) oxygen lattice] using a combination of density functional theory (DFT) and molecular dynamics simulations (MD). For this purpose, a generic expression for the free energy of warm dense matter is developed and parametrized with equation of state data from the DFT-MD simulations. A second central aspect is the accurate determination of the entropy, which is done using an approximate two-phase method based on the frequency spectra of the nuclear motion. The boundary between the bcc superionic phase and the ices VII andmore » X calculated with thermodynamic potentials from DFT-MD is consistent with that directly derived from the simulations. As a result, differences in the physical properties of the bcc and fcc superionic phases and their impact on interior modeling of water-rich giant planets are discussed.« less

Photoinduced dynamics to photoluminescence in Ln3+ (Ln = Ce, Pr) doped β-NaYF4 nanocrystals computed in basis of non-collinear spin DFT with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Han, Yulun; Vogel, Dayton J.; Inerbaev, Talgat M.; May, P. Stanley; Berry, Mary T.; Kilin, Dmitri S.

2018-03-01

In this work, non-collinear spin DFT + U approaches with spin-orbit coupling (SOC) are applied to Ln3+ doped β-NaYF4 (Ln = Ce, Pr) nanocrystals in Vienna ab initio Simulation Package taking into account unpaired spin configurations using the Perdew-Burke-Ernzerhof functional in a plane wave basis set. The calculated absorption spectra from non-collinear spin DFT + U approaches are compared with that from spin-polarised DFT + U approaches. The spectral difference indicates the importance of spin-flip transitions of Ln3+ ions. Suite of codes for nonadiabatic dynamics has been developed for 2-component spinor orbitals. On-the-fly nonadiabatic coupling calculations provide transition probabilities facilitated by nuclear motion. Relaxation rates of electrons and holes are calculated using Redfield theory in the reduced density matrix formalism cast in the basis of non-collinear spin DFT + U with SOC. The emission spectra are calculated using the time-integrated method along the excited state trajectories based on nonadiabatic couplings.

Ab initio investigation of barium-scandium-oxygen coatings on tungsten for electron emitting cathodes

NASA Astrophysics Data System (ADS)

Vlahos, Vasilios; Booske, John H.; Morgan, Dane

2010-02-01

Microwave, x-ray, and radio-frequency radiation sources require a cathode emitting electrons into vacuum. Thermionic B-type dispenser cathodes consist of BaxOz coatings on tungsten (W), where the surface coatings lower the W work function and enhance electron emission. The new and promising class of scandate cathodes modifies the B-type surface through inclusion of Sc, and their superior emissive properties are also believed to stem from the formation of a low work function surface alloy. In order to better understand these cathode systems, density-functional theory (DFT)-based ab initio modeling is used to explore the stability and work function of BaxScyOz on W(001) monolayer-type surface structures. It is demonstrated how surface depolarization effects can be calculated easily using ab initio calculations and fitted to an analytic depolarization equation. This approach enables the rapid extraction of the complete depolarization curve (work function versus coverage relation) from relatively few DFT calculations, useful for understanding and characterizing the emitting properties of novel cathode materials. It is generally believed that the B-type cathode has some concentration of Ba-O dimers on the W surface, although their structure is not known. Calculations suggest that tilted Ba-O dimers are the stable dimer surface configuration and can explain the observed work function reduction corresponding to various dimer coverages. Tilted Ba-O dimers represent a new surface coating structure not previously proposed for the activated B-type cathode. The thermodynamically stable phase of Ba and O on the W surface was identified to be the Ba0.25O configuration, possessing a significantly lower Φ value than any of the Ba-O dimer configurations investigated. The identification of a more stable Ba0.25O phase implies that if Ba-O dimers cover the surface of emitting B-type cathodes, then a nonequilibrium steady state must dominate the emitting surface. The identification of a stable and low work function Ba0.25Sc0.25O structure suggests that addition of Sc to the B-type cathode surface could form this alloy structure under operating conditions, leading to improved cathode performance and stability. Detailed comparison to previous experimental results of BaxScyOz on W surface coatings are made to both validate the modeling and aid in interpretation of experimental data. The studies presented here demonstrate that ab initio methods are powerful for understanding the fundamental physics of electron emitting materials systems and can potentially aid in the development of improved cathodes.

Comparative studies of the spectroscopy of CuCl2: DFT versus standard ab initio approaches

NASA Astrophysics Data System (ADS)

Ramírez-Solís, A.; Poteau, R.; Vela, A.; Daudey, J. P.

2005-04-01

The XΠg2-Σg +2, XΠg2-Δg2, XΠg2-Σu +2, XΠg2-Πu2 transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the XΠg2-Σg +2 and XΠg2-Δg2 transition energies, many of them even placing the Δg2 ligand field state above the charge transfer Πu2 and Σu +2 states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the ΛSΣ density defined by the orientation of the 3d hole (σ, π, or δ) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the XΠg2 state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio values. These findings show that not only large variational ab initio calculations can produce reliable spectroscopic results for extremely complex systems where delicate electronic correlation effects have to be carefully dealt with. However, those functionals that were recently shown to perform best for a series of molecular properties [J. Chem. Phys. 121 3405 (2004)] are not the ones that produce the best transition energies for this complex case.

Enhancing the effective energy barrier of a Dy(III) SMM using a bridged diamagnetic Zn(II) ion.

PubMed

Upadhyay, Apoorva; Singh, Saurabh Kumar; Das, Chinmoy; Mondol, Ranajit; Langley, Stuart K; Murray, Keith S; Rajaraman, Gopalan; Shanmugam, Maheswaran

2014-08-18

Field induced single-molecule-magnet behaviour is observed for both a heterodinuclear [ZnDy(L(-))2](3+) complex (1) and a mononuclear [Dy(HL)2](3+) complex (2), with effective energy barriers of 83 cm(-1) and 16 cm(-1), respectively. Insights into the relaxation mechanism(s) and barrier heights are provided via ab initio and DFT calculations. Our findings reveal an interesting observation that the U(eff) of SMMs can be enhanced by incorporating diamagnetic metal ions.

Nanocarbon: Defect Architectures and Properties

NASA Astrophysics Data System (ADS)

Vuong, Amanda

The allotropes of carbon make its solid phases amongst the most diverse of any element. It can occur naturally as graphite and diamond, which have very different properties that make them suitable for a wide range of technological and commercial purposes. Recent developments in synthetic carbon include Highly Oriented Pyrolytic Graphite (HOPG) and nano-carbons, such as fullerenes, nanotubes and graphene. The main industrial application of bulk graphite is as an electrode material in steel production, but in purified nuclear graphite form, it is also used as a moderator in Advanced Gas-cooled Reactors across the United Kingdom. Both graphene and graphite are damaged over time when subjected to bombardment by electrons, neutrons or ions, and these have a wide range of effects on their physical and electrical properties, depending on the radiation flux and temperature. This research focuses on intrinsic defects in graphene and dimensional change in nuclear graphite. The method used here is computational chemistry, which complements physical experiments. Techniques used comprise of density functional theory (DFT) and molecular dynamics (MD), which are discussed in chapter 2 and chapter 3, respectively. The succeeding chapters describe the results of simulations performed to model defects in graphene and graphite. Chapter 4 presents the results of ab initio DFT calculations performed to investigate vacancy complexes that are formed in AA stacked bilayer graphene. In AB stacking, carbon atoms surrounding the lattice vacancies can form interlayer structures with sp2 bonding that are lower in energy compared to in-plane reconstructions. From the investigation of AA stacking, sp2 interlayer bonding of adjacent multivacancy defects in registry creates a type of stable sp2 bonded wormhole between the layers. Also, a new class of mezzanine structure characterised by sp3 interlayer bonding, resembling a prismatic vacancy loop has also been identified. The mezzanine, which is a V6 hexavacancy variant, where six sp3 carbon atoms sit midway between two carbon layers and bond to both, is substantially more stable than any other vacancy aggregate in AA stacked layers. Chapter 5 presents the results of ab initio DFT calculations performed to investigate the wormhole and mezzanine defect that were identified in chapter 4 and the ramp defect discovered by Trevethan et al.. DFT calculations were performed on these defects in twisted bilayer graphene. From the investigation of vacancy complexes in twisted bilayer graphene, it is found that vacancy complexes are unstable in the twisted region and are more favourable in formation energy when the stacking arrangement is close to AA or AB stacking. It has also been discovered that the ramp defect is more stable in the twisted bilayer graphene compared to the mezzanine defect. Chapter 6 presents the results of ab initio DFT calculations performed to investigate a form of extending defect, prismatic edge dislocation. Suarez-Martinez et al.'s research suggest the armchair core is disconnected from any other layer, whilst the zigzag core is connected. In the investigation here, the curvature of the mezzanine defect allows it to swing between the armchair, zigzag and Klein in the AA stacking. For the AB stacking configuration, the armchair and zigzag core are connected from any other layer. Chapter 7 present results of MD simulations using the adaptive intermolecular reactive empirical bond order (AIREBO) potential to investigate the dimensional change of graphite due to the formation of vacancies present in a single crystal. It has been identified that there is an expansion along the c-axis, whilst a contraction along the a- and b- axes due to the coalescence of vacancy forming in-plane and between the layers. The results here are in good agreement with experimental studies of low temperature irradiation. The final chapter gives conclusions to this work.

Optical properties of LiGaS2: an ab initio study and spectroscopic ellipsometry measurement

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Lin, Z. S.; Isaenko, L. I.; Kesler, V. G.; Kruchinin, V. N.; Lobanov, S. I.

2009-11-01

Electronic and optical properties of lithium thiogallate crystal, LiGaS2, have been investigated by both experimental and theoretical methods. The plane-wave pseudopotential method based on DFT theory has been used for band structure calculations. The electronic parameters of Ga 3d orbitals have been corrected by the DFT+U methods to be consistent with those measured with x-ray photoemission spectroscopy. Evolution of optical constants of LiGaS2 over a wide spectral range was determined by developed first-principles theory and dispersion curves were compared with optical parameters defined by spectroscopic ellipsometry in the photon energy range 1.2-5.0 eV. Good agreement has been achieved between theoretical and experimental results.

GW electronic Correlations in Quantum Transport : Renormalization and finite lifetime effects on real systems

NASA Astrophysics Data System (ADS)

Darancet, Pierre; Ferretti, Andrea; Mayou, Didier; Olevano, Valerio

2007-03-01

We present an ab initio approach to electronic transport in nanoscale systems which includes electronic correlations through the GW approximation. With respect to Landauer approaches based on density-functional theory (DFT), we introduce a physical quasiparticle electronic-structure into a non-equilibrium Green's function theory framework. We use an equilibrium non-selfconsistent G^0W^0 self-energy considering both full non-hermiticity and dynamical effects. The method is applied to a real system, a gold mono-atomic chain. With respect to DFT results, the conductance profile is modified and reduced by to the introduction of diffusion and loss-of-coherence effects. The linear response conductance characteristic appear to be in agreement with experimental results.

Ab Initio Design of Potent Anti-MRSA Peptides based on Database Filtering Technology

PubMed Central

Mishra, Biswajit; Wang, Guangshun

2012-01-01

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed.1 This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g. amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database2 by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 minutes. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. A combination of our ab initio design with database screening3 led to yet another peptide with enhanced potency. Because of simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well. PMID:22803960

Ab initio design of potent anti-MRSA peptides based on database filtering technology.

PubMed

Mishra, Biswajit; Wang, Guangshun

2012-08-01

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed. This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when the most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g., amino acid composition, peptide hydrophobic content, and net charge) from the antimicrobial peptide database by developing a database filtering technology (DFT). Different from classic cationic antimicrobial peptides usually with high cationicity, DFTamP1, the first anti-MRSA peptide designed using this technology, is a short peptide with high hydrophobicity but low cationicity. Such a molecular design made the peptide highly potent. Indeed, the peptide caused bacterial surface damage and killed community-associated MRSA USA300 in 60 min. Structural determination of DFTamP1 by NMR spectroscopy revealed a broad hydrophobic surface, providing a basis for its potency against MRSA known to deploy positively charged moieties on the surface as a mechanism for resistance. Our ab initio design combined with database screening led to yet another peptide with enhanced potency. Because of the simple composition, short length, stability to proteases, and membrane targeting, the designed peptides are attractive leads for developing novel anti-MRSA therapeutics. Our database-derived design concept can be applied to the design of peptide mimicries to combat MRSA as well.

Transition state theory thermal rate constants and RRKM-based branching ratios for the N((2)D) + CH(4) reaction based on multi-state and multi-reference ab initio calculations of interest for the Titan's chemistry.

PubMed

Ouk, Chanda-Malis; Zvereva-Loëte, Natalia; Scribano, Yohann; Bussery-Honvault, Béatrice

2012-10-30

Multireference single and double configuration interaction (MRCI) calculations including Davidson (+Q) or Pople (+P) corrections have been conducted in this work for the reactants, products, and extrema of the doublet ground state potential energy surface involved in the N((2)D) + CH(4) reaction. Such highly correlated ab initio calculations are then compared with previous PMP4, CCSD(T), W1, and DFT/B3LYP studies. Large relative differences are observed in particular for the transition state in the entrance channel resolving the disagreement between previous ab initio calculations. We confirm the existence of a small but positive potential barrier (3.86 ± 0.84 kJ mol(-1) (MR-AQCC) and 3.89 kJ mol(-1) (MRCI+P)) in the entrance channel of the title reaction. The correlation is seen to change significantly the energetic position of the two minima and five saddle points of this system together with the dissociation channels but not their relative order. The influence of the electronic correlation into the energetic of the system is clearly demonstrated by the thermal rate constant evaluation and it temperature dependance by means of the transition state theory. Indeed, only MRCI values are able to reproduce the experimental rate constant of the title reaction and its behavior with temperature. Similarly, product branching ratios, evaluated by means of unimolecular RRKM theory, confirm the NH production of Umemoto et al., whereas previous works based on less accurate ab initio calculations failed. We confirm the previous findings that the N((2)D) + CH(4) reaction proceeds via an insertion-dissociation mechanism and that the dominant product channels are CH(2)NH + H and CH(3) + NH. Copyright © 2012 Wiley Periodicals, Inc.

Optical absorption spectra and g factor of MgO: Mn2+explored by ab initio and semi empirical methods

NASA Astrophysics Data System (ADS)

Andreici Eftimie, E.-L.; Avram, C. N.; Brik, M. G.; Avram, N. M.

2018-02-01

In this paper we present a methodology for calculations of the optical absorption spectra, ligand field parameters and g factor for the Mn2+ (3d5) ions doped in MgO host crystal. The proposed technique combines two methods: the ab initio multireference (MR) and the semi empirical ligand field (LF) in the framework of the exchange charge model (ECM) respectively. Both methods of calculations are applied to the [MnO6]10-cluster embedded in an extended point charge field of host matrix ligands based on Gellé-Lepetit procedure. The first step of such investigations was the full optimization of the cubic structure of perfect MgO crystal, followed by the structural optimization of the doped of MgO:Mn2+ system, using periodic density functional theory (DFT). The ab initio MR wave functions approaches, such as complete active space self-consistent field (CASSCF), N-electron valence second order perturbation theory (NEVPT2) and spectroscopy oriented configuration interaction (SORCI), are used for the calculations. The scalar relativistic effects have also been taken into account through the second order Douglas-Kroll-Hess (DKH2) procedure. Ab initio ligand field theory (AILFT) allows to extract all LF parameters and spin-orbit coupling constant from such calculations. In addition, the ECM of ligand field theory (LFT) has been used for modelling theoptical absorption spectra. The perturbation theory (PT) was employed for the g factor calculation in the semi empirical LFT. The results of each of the aforementioned types of calculations are discussed and the comparisons between the results obtained and the experimental results show a reasonable agreement, which justifies this new methodology based on the simultaneous use of both methods. This study establishes fundamental principles for the further modelling of larger embedded cluster models of doped metal oxides.

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

NASA Astrophysics Data System (ADS)

Samolyuk, G. D.; Osetsky, Y. N.; Stoller, R. E.

2015-10-01

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascade production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (∼0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential. The Gao-Weber potential appears to give a more realistic description of cascade dynamics in SiC, but still has some shortcomings when the defect migration barriers are compared to the ab initio results.

The role of silicon, vacancies, and strain in carbon distribution for low temperature bainite

DOE PAGES

Sampath, S.; Rementeria, R.; Huang, X.; ...

2016-02-19

Here, we investigated the phenomenon of carbon supersaturation and carbon clustering in bainitic ferrite with atom probe tomography (APT) and ab-initio density functional theory (DFT) calculations. The experimental results show a homogeneous distribution of silicon in the microstructure, which contains both ferrite and retained austenite. This distribution is mimicked well by the computational approach. In addition, an accumulation of C in certain regions of the bainitic ferrite with C concentrations up to 13 at % is observed. Based on the DFT results, these clusters are explained as strained, tetragonal regions in the ferritic bainite, in which the solution enthalpy ofmore » C can reach large, negative values. It seems that Si itself only has a minor influence on this phenomenon.« less

Charge and Spin Currents in Open-Shell Molecules:  A Unified Description of NMR and EPR Observables.

PubMed

Soncini, Alessandro

2007-11-01

The theory of EPR hyperfine coupling tensors and NMR nuclear magnetic shielding tensors of open-shell molecules in the limit of vanishing spin-orbit coupling (e.g., for organic radicals) is analyzed in terms of spin and charge current density vector fields. The ab initio calculation of the spin and charge current density response has been implemented at the Restricted Open-Shell Hartree-Fock, Unrestricted Hartree-Fock, and unrestricted GGA-DFT level of theory. On the basis of this formalism, we introduce the definition of nuclear hyperfine coupling density, a scalar function of position providing a partition of the EPR observable over the molecular domain. Ab initio maps of spin and charge current density and hyperfine coupling density for small radicals are presented and discussed in order to illustrate the interpretative advantages of the newly introduced approach. Recent NMR experiments providing evidence for the existence of diatropic ring currents in the open-shell singlet pancake-bonded dimer of the neutral phenalenyl radical are directly assessed via the visualization of the induced current density.

Ab-Initio Molecular Dynamics Simulation of Graphene Sheet

NASA Astrophysics Data System (ADS)

Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.

2017-01-01

The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.

Electronic, magnetic properties and phase diagrams of system with Fe4N compound: An ab initio calculations and Monte Carlo study

NASA Astrophysics Data System (ADS)

Masrour, R.; Jabar, A.; Hlil, E. K.

2018-05-01

Self-consistent ab initio calculations, based on Density Functional Theory (DFT) approach and using Full potential Linear Augmented Plane Wave (FLAPW) method, are performed to investigate the electronic and magnetic properties of the Fe4N compound. Polarized spin and spin-orbit coupling are included in calculations within the framework of the ferromagnetic state between Fe(I) and Fe(II) in Fe4N compound. We have used the obtained data from abinitio calculations as an input in Monte Carlo simulation to calculate the magnetic properties of this compounds such as the ground state phase diagrams, total and partial magnetization of Fe(I) and Fe(II) as well as the transition temperatures are computed. The variation of magnetization with the crystal field are also studied. The magnetic hysteresis cycle of the same Fe4N compound are determined for different values of temperatures and crystal field values. The two-step hysteresis loop are evidenced, which is typical for Fe4N structure. The ferromagnetic and superparamagnetic phase is observed as well.

Transitioning NWChem to the Next Generation of Manycore Machines

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

Bylaska, Eric J.; Apra, E; Kowalski, Karol

The NorthWest chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers [1-3]. It contains an umbrella of modules that today includes self-consistent eld (SCF), second order Møller-Plesset perturbation theory (MP2), coupled cluster (CC), multiconguration self-consistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real-time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics (AIMD), Car-Parrinello molecular dynamics (MD), classical MD, hybrid quantum mechanicsmore » molecular mechanics (QM/MM), hybrid ab initio molecular dynamics molecular mechanics (AIMD/MM), gauge independent atomic orbital nuclear magnetic resonance (GIAO NMR), conductor like screening solvation model (COSMO), conductor-like screening solvation model based on density (COSMO-SMD), and reference interaction site model (RISM) solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities [4]. Moreover, new capabilities continue to be added with each new release.« less

Plasmons in quasi-two-dimensional metals

NASA Astrophysics Data System (ADS)

da Jornada, Felipe H.; Xian, Lede; Sen, H. Sener; Rubio, Angel; Louie, Steven G.

We employ ab initio density-functional theory (DFT) and GW calculations to understand and predict the plasmon dispersion in quasi-two-dimensional (quasi-2D) metals. We show that, unlike what is found in idealized 2D electron gases, plasmons are virtually dispersionless in real quasi-2D metals for a wide range of excitation wave vectors that are experimentally accessible. We further develop a simpler model that captures this plasmon dispersion in quasi-2D metals and which depends on a single parameter: the characteristic screening length due to interband transitions. Our ab initio calculations further predict that monolayer metallic transition metal dichalcogenides are excellent candidates to explore these dispersionless (flat) plasmons: having large excitation energy that is away from the Landau damping regions makes them ideal systems to support long-lived, spatially-localized 2D plasmons which are highly tunable with substrate. This work is supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division; the National Science Foundation; the European Research Council project (ERC-2015-AdG-694097), and the AFOSR Grant No. FA2386-15-1-0006 AOARD 144088.

Lattice dynamic properties of Rh2XAl (X=Fe and Y) alloys

NASA Astrophysics Data System (ADS)

Al, Selgin; Arikan, Nihat; Demir, Süleyman; Iyigör, Ahmet

2018-02-01

The electronic band structure, elastic and vibrational spectra of Rh2FeAl and Rh2YAl alloys were computed in detail by employing an ab-initio pseudopotential method and a linear-response technique based on the density-functional theory (DFT) scheme within a generalized gradient approximation (GGA). Computed lattice constants, bulk modulus and elastic constants were compared. Rh2YAl exhibited higher ability to resist volume change than Rh2FeAl. The elastic constants, shear modulus, Young modulus, Poisson's ratio, B/G ratio electronic band structure, total and partial density of states, and total magnetic moment of alloys were also presented. Rh2FeAl showed spin up and spin down states whereas Rh2YAl showed none due to being non-magnetic. The calculated total densities of states for both materials suggest that both alloys are metallic in nature. Full phonon spectra of Rh2FeAl and Rh2YA1 alloys in the L21 phase were collected using the ab-initio linear response method. The obtained phonon frequencies were in the positive region indicating that both alloys are dynamically stable.

The torsional energy profile of 1,2-diphenylethane: an ab initio study

NASA Astrophysics Data System (ADS)

Ivanov, Petko M.

1997-08-01

Ab initio molecular orbital calculations were carried out for the antiperiplanar (ap), the synclinal (sc), phenyl/phenyl eclipsed (syn barrier), and phenyl/H eclipsed (ap/sc barrier) conformations of 1,2-diphenylethane, and the energy ordering of conformations thus obtained was compared with the torsional energy profile estimated with the MM2 and MM3 molecular mechanics force fields. The basis set effect on the results was studied at the restricted Hartree-Fock (RHF) self-consistent field (SCF) level of theory, and the electron correlation energies were corrected by the second-order (MP2) Møller-Plesset perturbation treatment using the 6-31G * basis set. The performance of a DFT model (Becke-style three-parameter hybrid method using the correlation functional of Lee, Yang and Parr, B3LYP) was also tested to assess relative energies of the conformations using two basis sets, 6-31G * and 6-311G **. The RHF and B3LYP results are qualitatively the same, while the MP2 calculations produced significant differences in the geometries and reversed the order of preference for the antiperiplanar and the synclinal conformations.

Structure and Magnetic Properties in Ruthenium-Based Full-Heusler Alloys: AB INITIO Calculations

NASA Astrophysics Data System (ADS)

Bahlouli, S.; Aarizou, Z.; Elchikh, M.

2013-12-01

In this paper, we present ab initio calculations within density functional theory (DFT) to investigate structure, electronic and magnetic properties of Ru2CrZ (Z = Si, Ge and Sn) full-Heusler alloys. We have used the developed full-potential linearized muffin tin orbitals (FP-LMTO) based on the local spin density approximation (LSDA) with the PLane Wave expansion (PLW). In particular, we found that these Ruthenium-based Heusler alloys have the antiferromagnetic (AFM) type II as ground state. Then, we studied and discussed the magnetic properties belonging to our different magnetic structures: AFM type II, AFM type I and ferromagnetic (FM) phase. We also found that Ru2CrSi and Ru2CrGe exhibit a semiconducting behavior whereas Ru2CrSn has a semimetallic-like behavior as it is experimentally found. We made an estimation of Néel temperatures (TN) in the framework of the mean-field theory and used the energy differences approach to deduce the relevant short-range nearest-neighbor (J1) and next-nearest-neighbor (J2) interactions. The calculated TN are somewhat overestimated to the available experimental ones.

Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

PubMed

Moon, Jiwon; Kim, Joonghan

2016-09-29

Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

Vibrational spectral investigation, NBO, first hyperpolarizability and UV-Vis spectral analysis of 3,5-dichlorobenzonitrile and m-bromobenzonitrile by ab initio and density functional theory methods.

PubMed

Senthil kumar, J; Jeyavijayan, S; Arivazhagan, M

2015-02-05

The FT-IR and FT-Raman spectra of 3,5-dichlorobenzonitrile and m-bromobenzonitrile have been recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1), respectively. The optimized geometry, wave numbers and intensity of vibrational bonds of title molecules are obtained by ab initio and DFT level of theory with complete relaxation in the potential energy surface using 6-311++G(d, p) basis set. A complete vibrational assignments aided by the theoretical harmonic frequency, analysis have been proposed. The harmonic vibrational frequencies calculated have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The UV-Vis spectral analysis of the molecules has also been done which confirms the charge transfer of the molecules. Furthermore, the first hyperpolarizability and total dipole moment of the molecules have been calculated. Copyright © 2014 Elsevier B.V. All rights reserved.

First-Principles Study of the Electronic Structure and Bonding Properties of X8C46 and X8B6C40 (X: Li, Na, Mg, Ca) Carbon Clathrates

NASA Astrophysics Data System (ADS)

KoleŻyński, Andrzej; Szczypka, Wojciech

2016-03-01

Results from theoretical analysis of the crystal structure, electronic structure, and bonding properties of C46 and B6C40 carbon clathrates doped with selected alkali and alkaline earth metals cations (Li, Na, Mg, Ca) are presented. The ab initio calculations were performed by means of the WIEN2k package (full potential linearized augmented plane wave method (FP-LAPW) within density functional theory (DFT)) with PBESol and modified Becke-Johnson exchange-correlation potentials used in geometry optimization and electronic structure calculations, respectively. The bonding properties were analyzed by applying Bader's quantum theory of atoms in molecules formalism to the topological properties of total electron density obtained from ab initio calculations. Analysis of the results obtained (i.a. equilibrium geometry, equation of state, cohesive energy, band structure, density of states—both total and projected on to particular atoms, and topological properties of bond critical points and net charges of topological atoms) is presented in detail.

Copper attachment to a non-octarepeat site in prion protein

NASA Astrophysics Data System (ADS)

Hodak, Miroslav; Bernholc, Jerry

2010-03-01

Prion protein, PrP, plays a causative role in several neurodegenerative diseases, including mad cow disease in cattle and Creutzfeldt-Jakob disease in humans. The PrP is known to efficiently bind copper ions and this ability has been linked to its function. PrP contains up to six binding sites, four of which are located in the so-called octarepeat region and are now well known. The binding sites outside this region are still largely undetermined, despite evidence of their relevance to prion diseases. Using a hybrid DFT/DFT, which combines Kohn-Sham DFT with orbital-free DFT to achieve accurate and efficient description of solvent effects in ab initio calculations, we have investigated copper attachment to the sequence GGGTH, which represents the copper binding site located at His96. We have considered both NNNN and NNNO types of copper coordination, as suggested by experiments. Our calculations have determined the geometry of copper attachment site and its energetics. Comparison to the already known binding sites provides insight into the process of copper uptake in PrP.

Increasing the applicability of density functional theory. IV. Consequences of ionization-potential improved exchange-correlation potentials.

PubMed

Verma, Prakash; Bartlett, Rodney J

2014-05-14

This paper's objective is to create a "consistent" mean-field based Kohn-Sham (KS) density functional theory (DFT) meaning the functional should not only provide good total energy properties, but also the corresponding KS eigenvalues should be accurate approximations to the vertical ionization potentials (VIPs) of the molecule, as the latter condition attests to the viability of the exchange-correlation potential (VXC). None of the prominently used DFT approaches show these properties: the optimized effective potential VXC based ab initio dft does. A local, range-separated hybrid potential cam-QTP-00 is introduced as the basis for a "consistent" KS DFT approach. The computed VIPs as the negative of KS eigenvalue have a mean absolute error of 0.8 eV for an extensive set of molecule's electron ionizations, including the core. Barrier heights, equilibrium geometries, and magnetic properties obtained from the potential are in good agreement with experiment. A similar accuracy with less computational efforts can be achieved by using a non-variational global hybrid variant of the QTP-00 approach.

Ab Initio Calculation of XAFS Debye-Waller Factors for Crystalline Materials

NASA Astrophysics Data System (ADS)

Dimakis, Nicholas

2007-02-01

A direct an accurate technique for calculating the thermal X-ray absorption fine structure (XAFS) Debye-Waller factors (DWF) for materials of crystalline structure is presented. Using the Density Functional Theory (DFT) under the hybrid X3LYP functional, a library of MnO spin—optimized clusters are built and their phonon spectrum properties are calculated; these properties in the form of normal mode eigenfrequencies and eigenvectors are in turn used for calculation of the single and multiple scattering XAFS DWF. DWF obtained via this technique are temperature dependent expressions and can be used to substantially reduce the number of fitting parameters when experimental spectra are fitted with a hypothetical structure without any ad hoc assumptions. Due to the high computational demand a hybrid approach of mixing the DFT calculated DWF with the correlated Debye model for inner and outer shells respectively is presented. DFT obtained DWFs are compared with corresponding values from experimental XAFS spectra on manganosite. The cluster size effect and the spin parameter on the DFT calculated DWFs are discussed.

Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method

NASA Astrophysics Data System (ADS)

Nakata, Hiroya; Fedorov, Dmitri G.; Zahariev, Federico; Schmidt, Michael W.; Kitaura, Kazuo; Gordon, Mark S.; Nakamura, Shinichiro

2015-03-01

Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in SN2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.

Benchmarking singlet and triplet excitation energies of molecular semiconductors for singlet fission: Tuning the amount of HF exchange and adjusting local correlation to obtain accurate functionals for singlet-triplet gaps

NASA Astrophysics Data System (ADS)

Brückner, Charlotte; Engels, Bernd

2017-01-01

Vertical and adiabatic singlet and triplet excitation energies of molecular p-type semiconductors calculated with various DFT functionals and wave-function based approaches are benchmarked against MS-CASPT2/cc-pVTZ reference values. A special focus lies on the singlet-triplet gaps that are very important in the process of singlet fission. Singlet fission has the potential to boost device efficiencies of organic solar cells, but the scope of existing singlet-fission compounds is still limited. A computational prescreening of candidate molecules could enlarge it; yet it requires efficient methods accurately predicting singlet and triplet excitation energies. Different DFT formulations (Tamm-Dancoff approximation, linear response time-dependent DFT, Δ-SCF) and spin scaling schemes along with several ab initio methods (CC2, ADC(2)/MP2, CIS(D), CIS) are evaluated. While wave-function based methods yield rather reliable singlet-triplet gaps, many DFT functionals are shown to systematically underestimate triplet excitation energies. To gain insight, the impact of exact exchange and correlation is in detail addressed.

Localization and anharmonicity of the vibrational modes for GC Watson-Crick and Hoogsteen base pairs.

PubMed

Bende, Attila; Bogdan, Diana; Muntean, Cristina M; Morari, Cristian

2011-12-01

We present an ab initio study of the vibrational properties of cytosine and guanine in the Watson-Crick and Hoogsteen base pair configurations. The results are obtained by using two different implementations of the DFT method. We assign the vibrational frequencies to cytosine or to guanine using the vibrational density of states. Next, we investigate the importance of anharmonic corrections for the vibrational modes. In particular, the unusual anharmonic effect of the H(+) vibration in the case of the Hoogsteen base pair configuration is discussed.

Band structure and phonon properties of lithium fluoride at high pressure

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

Panchal, J. M., E-mail: amitjignesh@yahoo.co.in; Department of Physics, University School of Sciences, Gujarat University, Ahmedabad 380009, Gujarat; Joshi, Mitesh

2016-05-23

High pressure structural and electronic properties of Lithium Fluoride (LiF) have been studied by employing an ab-initio pseudopotential method and a linear response scheme within the density functional theory (DFT) in conjunction with quasi harmonic Debye model. The band structure and electronic density of states conforms that the LiF is stable and is having insulator behavior at ambient as well as at high pressure up to 1 Mbar. Conclusions based on Band structure, phonon dispersion and phonon density of states are outlined.

Understanding the Relativistic Generalization of Density Functional Theory (DFT) and Completing it in Practice

NASA Astrophysics Data System (ADS)

Bagayoko, Diola

In 2014, 50 years following the introduction of density functional theory (DFT), a rigorous understanding of it was published [AIP Advances, 4, 127104 (2014)]. This understanding included necessary steps ab initio electronic structure calculations have to take if their results are to possess the full physical content of DFT. These steps guarantee the fulfillment of conditions of validity of DFT; not surprisingly, they have led to accurate descriptions of several dozens of semiconductors, from first principle, without invoking derivative discontinuity or self-interaction correction. This presentation shows the mathematically and physically rigorous understanding of the relativistic extension of DFT by Rajagopal and Callaway {Phys. Rev. B 7, 1912 (1973)]. As in the non-relativistic case, the attainment of the absolute minima of the occupied energies is a necessary condition for the corresponding current density to be that of the ground state of the system and for computational results to agree with corresponding, experimental ones. Acknowledgments:This work was funded in part by the US National Science Foundation [NSF, Award Nos. EPS-1003897, NSF (2010-2015)-RII-SUBR, and HRD-1002541], the US Department of Energy, National Nuclear Security Administration (NNSA, Award No. DE-NA0002630), LaSPACE, and LONI-SUBR.

A Comparison of Density Functional Theory with Ab initio Approaches for Systems Involving First Transition Row Metals

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

Density functional theory (DFT) is found to give a better description of the geometries and vibrational frequencies of FeL and FeL(sup +) systems than second order Moller Plesset perturbation theory (MP2). Namely, the DFT correctly predicts the shift in the CO vibrational frequency between free CO and the Sigma(sup -) state of FeCO and yields a good result for the Fe-C distance in the quartet states of FeCH4(+) 4 These are properties where the MP2 results are unsatisfactory. Thus DFT appears to be an excellent approach for optimizing the geometries and computing the zero-point energies of systems containing first transition row atoms. Because the DFT approach is biased in favor of the 3d(exp 7) occupation, whereas the more traditional approaches are biased in favor of the 3d(exp 6) occupation, differences are found in the relative ordering of states. It is shown that if the dissociation is computed to the most appropriate atomic asymptote and corrected to the ground state asymptote using the experimental separations, the DFT results are in good agreement with high levels of theory. The energetics at the DFT level are much superior to the MP2 and in most cases in good agreement with high levels of theory.

Carbon dioxide capture using covalent organic frameworks (COFs) type material-a theoretical investigation.

PubMed

Dash, Bibek

2018-04-26

The present work deals with a density functional theory (DFT) study of porous organic framework materials containing - groups for CO 2 capture. In this study, first principle calculations were performed for CO 2 adsorption using N-containing covalent organic framework (COFs) models. Ab initio and DFT-based methods were used to characterize the N-containing porous model system based on their interaction energies upon complexing with CO 2 and nitrogen gas. Binding energies (BEs) of CO 2 and N 2 molecules with the polymer framework were calculated with DFT methods. Hybrid B3LYP and second order MP2 methods combined with of Pople 6-31G(d,p) and correlation consistent basis sets cc-pVDZ, cc-pVTZ and aug-ccVDZ were used to calculate BEs. The effect of linker groups in the designed covalent organic framework model system on the CO 2 and N 2 interactions was studied using quantum calculations.

Puzzle of magnetic moments of Ni clusters revisited using quantum Monte Carlo method.

PubMed

Lee, Hung-Wen; Chang, Chun-Ming; Hsing, Cheng-Rong

2017-02-28

The puzzle of the magnetic moments of small nickel clusters arises from the discrepancy between values predicted using density functional theory (DFT) and experimental measurements. Traditional DFT approaches underestimate the magnetic moments of nickel clusters. Two fundamental problems are associated with this puzzle, namely, calculating the exchange-correlation interaction accurately and determining the global minimum structures of the clusters. Theoretically, the two problems can be solved using quantum Monte Carlo (QMC) calculations and the ab initio random structure searching (AIRSS) method correspondingly. Therefore, we combined the fixed-moment AIRSS and QMC methods to investigate the magnetic properties of Ni n (n = 5-9) clusters. The spin moments of the diffusion Monte Carlo (DMC) ground states are higher than those of the Perdew-Burke-Ernzerhof ground states and, in the case of Ni 8-9 , two new ground-state structures have been discovered using the DMC calculations. The predicted results are closer to the experimental findings, unlike the results predicted in previous standard DFT studies.

Proton Affinities of Anionic Bases:  Trends Across the Periodic Table, Structural Effects, and DFT Validation.

PubMed

Swart, Marcel; Bickelhaupt, F Matthias

2006-03-01

We have carried out an extensive exploration of the gas-phase basicity of archetypal anionic bases across the periodic system using the generalized gradient approximation of density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities:  BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 1.6 kcal/mol for the proton affinity at 0 K with respect to high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the anionic conjugate bases of all main-group-element hydrides of groups 14-17 and periods 2-6. We have also studied the effect of stepwise methylation of the protophilic center of the second- and third-period bases.

Understanding and Calibrating Density-Functional-Theory Calculations Describing the Energy and Spectroscopy of Defect Sites in Hexagonal Boron Nitride.

PubMed

Reimers, Jeffrey R; Sajid, A; Kobayashi, Rika; Ford, Michael J

2018-03-13

Defect states in 2-D materials present many possible uses but both experimental and computational characterization of their spectroscopic properties is difficult. We provide and compare results from 13 DFT and ab initio computational methods for up to 25 excited states of a paradigm system, the V N C B defect in hexagonal boron nitride (h-BN). Studied include: (i) potentially catastrophic effects for computational methods arising from the multireference nature of the closed-shell and open-shell states of the defect, which intrinsically involves broken chemical bonds, (ii) differing results from DFT and time-dependent DFT (TDDFT) calculations, (iii) comparison of cluster models to periodic-slab models of the defect, (iv) the starkly differing effects of nuclear relaxation on the various electronic states that control the widths of photoabsorption and photoemission spectra as broken bonds try to heal, (v) the effect of zero-point energy and entropy on free-energy differences, (vi) defect-localized and conduction/valence-band transition natures, and (vii) strategies needed to ensure that the lowest-energy state of a defect can be computationally identified. Averaged state-energy differences of 0.3 eV are found between CCSD(T) and MRCI energies, with thermal effects on free energies sometimes also being of this order. However, DFT-based methods can perform very poorly. Simple generalized-gradient functionals like PBE fail at the most basic level and should never be applied to defect states. Hybrid functionals like HSE06 work very well for excitations within the triplet manifold of the defect, with an accuracy equivalent to or perhaps exceeding the accuracy of the ab initio methods used. However, HSE06 underestimates triplet-state energies by on average of 0.7 eV compared to closed-shell singlet states, while open-shell singlet states are predicted to be too low in energy by 1.0 eV. This leads to misassignment of the ground state of the V N C B defect. Long-range corrected functionals like CAM-B3LYP are shown to work much better and to represent the current entry level for DFT calculations on defects. As significant differences between cluster and periodic-slab models are also found, the widespread implementation of such functionals in periodic codes is in urgent need.

Preface: Introductory Remarks: Linear Scaling Methods

NASA Astrophysics Data System (ADS)

Bowler, D. R.; Fattebert, J.-L.; Gillan, M. J.; Haynes, P. D.; Skylaris, C.-K.

2008-07-01

It has been just over twenty years since the publication of the seminal paper on molecular dynamics with ab initio methods by Car and Parrinello [1], and the contribution of density functional theory (DFT) and the related techniques to physics, chemistry, materials science, earth science and biochemistry has been huge. Nevertheless, significant improvements are still being made to the performance of these standard techniques; recent work suggests that speed improvements of one or even two orders of magnitude are possible [2]. One of the areas where major progress has long been expected is in O(N), or linear scaling, DFT, in which the computer effort is proportional to the number of atoms. Linear scaling DFT methods have been in development for over ten years [3] but we are now in an exciting period where more and more research groups are working on these methods. Naturally there is a strong and continuing effort to improve the efficiency of the methods and to make them more robust. But there is also a growing ambition to apply them to challenging real-life problems. This special issue contains papers submitted following the CECAM Workshop 'Linear-scaling ab initio calculations: applications and future directions', held in Lyon from 3-6 September 2007. A noteworthy feature of the workshop is that it included a significant number of presentations involving real applications of O(N) methods, as well as work to extend O(N) methods into areas of greater accuracy (correlated wavefunction methods, quantum Monte Carlo, TDDFT) and large scale computer architectures. As well as explicitly linear scaling methods, the conference included presentations on techniques designed to accelerate and improve the efficiency of standard (that is non-linear-scaling) methods; this highlights the important question of crossover—that is, at what size of system does it become more efficient to use a linear-scaling method? As well as fundamental algorithmic questions, this brings up implementation questions relating to parallelization (particularly with multi-core processors starting to dominate the market) and inherent scaling and basis sets (in both normal and linear scaling codes). For now, the answer seems to lie between 100-1,000 atoms, though this depends on the type of simulation used among other factors. Basis sets are still a problematic question in the area of electronic structure calculations. The linear scaling community has largely split into two camps: those using relatively small basis sets based on local atomic-like functions (where systematic convergence to the full basis set limit is hard to achieve); and those that use necessarily larger basis sets which allow convergence systematically and therefore are the localised equivalent of plane waves. Related to basis sets is the study of Wannier functions, on which some linear scaling methods are based and which give a good point of contact with traditional techniques; they are particularly interesting for modelling unoccupied states with linear scaling methods. There are, of course, as many approaches to linear scaling solution for the density matrix as there are groups in the area, though there are various broad areas: McWeeny-based methods, fragment-based methods, recursion methods, and combinations of these. While many ideas have been in development for several years, there are still improvements emerging, as shown by the rich variety of the talks below. Applications using O(N) DFT methods are now starting to emerge, though they are still clearly not trivial. Once systems to be simulated cross the 10,000 atom barrier, only linear scaling methods can be applied, even with the most efficient standard techniques. One of the most challenging problems remaining, now that ab initio methods can be applied to large systems, is the long timescale problem. Although much of the work presented was concerned with improving the performance of the codes, and applying them to scientificallyimportant problems, there was another important theme: extending functionality. The search for greater accuracy has given an implementation of density functional designed to model van der Waals interactions accurately as well as local correlation, TDDFT and QMC and GW methods which, while not explicitly O(N), take advantage of localisation. All speakers at the workshop were invited to contribute to this issue, but not all were able to do this. Hence it is useful to give a complete list of the talks presented, with the names of the sessions; however, many talks fell within more than one area. This is an exciting time for linear scaling methods, which are already starting to contribute significantly to important scientific problems. Applications to nanostructures and biomolecules A DFT study on the structural stability of Ge 3D nanostructures on Si(001) using CONQUEST Tsuyoshi Miyazaki, D R Bowler, M J Gillan, T Otsuka and T Ohno Large scale electronic structure calculation theory and several applications Takeo Fujiwara and Takeo Hoshi ONETEP:Linear-scaling DFT with plane waves Chris-Kriton Skylaris, Peter D Haynes, Arash A Mostofi, Mike C Payne Maximally-localised Wannier functions as building blocks for large-scale electronic structure calculations Arash A Mostofi and Nicola Marzari A linear scaling three dimensional fragment method for ab initio calculations Lin-Wang Wang, Zhengji Zhao, Juan Meza Peta-scalable reactive Molecular dynamics simulation of mechanochemical processes Aiichiro Nakano, Rajiv K. Kalia, Ken-ichi Nomura, Fuyuki Shimojo and Priya Vashishta Recent developments and applications of the real-space multigrid (RMG) method Jerzy Bernholc, M Hodak, W Lu, and F Ribeiro Energy minimisation functionals and algorithms CONQUEST: A linear scaling DFT Code David R Bowler, Tsuyoshi Miyazaki, Antonio Torralba, Veronika Brazdova, Milica Todorovic, Takao Otsuka and Mike Gillan Kernel optimisation and the physical significance of optimised local orbitals in the ONETEP code Peter Haynes, Chris-Kriton Skylaris, Arash Mostofi and Mike Payne A miscellaneous overview of SIESTA algorithms Jose M Soler Wavelets as a basis set for electronic structure calculations and electrostatic problems Stefan Goedecker Wavelets as a basis set for linear scaling electronic structure calculationsMark Rayson O(N) Krylov subspace method for large-scale ab initio electronic structure calculations Taisuke Ozaki Linear scaling calculations with the divide-and-conquer approach and with non-orthogonal localized orbitals Weitao Yang Toward efficient wavefunction based linear scaling energy minimization Valery Weber Accurate O(N) first-principles DFT calculations using finite differences and confined orbitals Jean-Luc Fattebert Linear-scaling methods in dynamics simulations or beyond DFT and ground state properties An O(N) time-domain algorithm for TDDFT Guan Hua Chen Local correlation theory and electronic delocalization Joseph Subotnik Ab initio molecular dynamics with linear scaling: foundations and applications Eiji Tsuchida Towards a linear scaling Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics Thomas Kühne, Michele Ceriotti, Matthias Krack and Michele Parrinello Partial linear scaling for quantum Monte Carlo calculations on condensed matter Mike Gillan Exact embedding of local defects in crystals using maximally localized Wannier functions Eric Cancès Faster GW calculations in larger model structures using ultralocalized nonorthogonal Wannier functions Paolo Umari Other approaches for linear-scaling, including methods formetals Partition-of-unity finite element method for large, accurate electronic-structure calculations of metals John E Pask and Natarajan Sukumar Semiclassical approach to density functional theory Kieron Burke Ab initio transport calculations in defected carbon nanotubes using O(N) techniques Blanca Biel, F J Garcia-Vidal, A Rubio and F Flores Large-scale calculations with the tight-binding (screened) KKR method Rudolf Zeller Acknowledgments We gratefully acknowledge funding for the workshop from the UK CCP9 network, CECAM and the ESF through the PsiK network. DRB, PDH and CKS are funded by the Royal Society. References [1] Car R and Parrinello M 1985 Phys. Rev. Lett. 55 2471 [2] Kühne T D, Krack M, Mohamed F R and Parrinello M 2007 Phys. Rev. Lett. 98 066401 [3] Goedecker S 1999 Rev. Mod. Phys. 71 1085

The keto-enol equilibrium in substituted acetaldehydes: focal-point analysis and ab initio limit

NASA Astrophysics Data System (ADS)

Balabin, Roman M.

2011-10-01

High-level ab initio electronic structure calculations up to the CCSD(T) theory level, including extrapolations to the complete basis set (CBS) limit, resulted in high precision energetics of the tautomeric equilibrium in 2-substituted acetaldehydes (XH2C-CHO). The CCSD(T)/CBS relative energies of the tautomers were estimated using CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z calculations with MP2/aug-cc-pVTZ geometries. The relative enol (XHC = CHOH) stabilities (ΔE e,CCSD(T)/CBS) were found to be 5.98 ± 0.17, -1.67 ± 0.82, 7.64 ± 0.21, 8.39 ± 0.31, 2.82 ± 0.52, 10.27 ± 0.39, 9.12 ± 0.18, 5.47 ± 0.53, 7.50 ± 0.43, 10.12 ± 0.51, 8.49 ± 0.33, and 6.19 ± 0.18 kcal mol-1 for X = BeH, BH2, CH3, Cl, CN, F, H, NC, NH2, OCH3, OH, and SH, respectively. Inconsistencies between the results of complex/composite energy computations methods Gn/CBS (G2, G3, CBS-4M, and CBS-QB3) and high-level ab initio methods (CCSD(T)/CBS and MP2/CBS) were found. DFT/aug-cc-pVTZ results with B3LYP, PBE0 (PBE1PBE), TPSS, and BMK density functionals were close to the CCSD(T)/CBS levels (MAD = 1.04 kcal mol-1).

Improved assignments of the vibrational fundamental modes of ortho -, meta -, and para -xylene using gas- and liquid-phase infrared and Raman spectra combined with ab initio calculations: Quantitative gas-phase infrared spectra for detection

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

Lindenmaier, Rodica; Scharko, Nicole K.; Tonkyn, Russell G.

Xylenes contain a blend of the ortho-, meta-, and para- isomers, and all are abundant contaminants in the ground, surface waters, and air. To better characterize xylene and to better enable its detection, we report high quality quantitative vapor-phase infrared spectra of all three isomers over the 540-6500 cm -1 range. All fundamental vibrational modes are assigned based on these vapor-phase infrared spectra, liquid-phase infrared and Raman spectra, along with density functional theory (DFT), ab initio MP2 and high energy-accuracy compound theoretical model (W1BD) calculations. Both MP2 and DFT predict a single conformer with C 2v symmetry for ortho-xylene, andmore » two conformers each for meta- and para-xylene, depending on the preferred orientations of the methyl groups. For meta-xylene the two conformers have C s and C 2 symmetry, and for para-xylene these conformers have C 2v or C 2h symmetry. Since the relative population of the two conformers is approximately 50% for both isomers and predicted frequencies and intensities are very similar for each conformer, we made an arbitrary choice to discuss the C s conformer for meta-xylene and the C 2v conformer for para-xylene. We report integrated band intensities for all isomers. Using the quantitative infrared data, we determine the global warming potential values of each isomer and discuss potential bands for atmospheric monitoring.« less

Self-consistent mapping of the ab initio calculations to the multi-orbital p- d model: Magnetism in α-FeSi2 films as the effect of the local environment

NASA Astrophysics Data System (ADS)

Zhandun, V.; Zamkova, N.; Ovchinnikov, S.; Sandalov, I.

2017-11-01

To accurately translate the results obtained within density functional theory (DFT) to the language of many-body theory we suggest and test the following approach: the parameters of the formulated model are to be found from the requirement that the model self-consistent electron density and density of electron states are as close as possible to the ones found from the DFT-based calculations. The investigation of the phase diagram of the model allows us to find the critical regions in magnetic properties. Then the behavior of the real system in these regions is checked by the ab initio calculations. As an example, we studied the physics of magnetic moment (MM) formation due to substitutions of Si by Fe-atoms or vice versa in the otherwise non-magnetic alloy α-FeSi2. We find that the MM formation is essentially controlled by the interaction of Fe atoms with its next nearest atoms (NNN) and by their particular arrangement. The latter may result in different magnetic states at the same concentrations of constituents. Moreover, one of arrangements produces the counterintuitive result: a ferromagnetism arises due to an increase in Si concentration in Fe1-xSi2+ x ordered alloy. The existing phenomenological models associate the destruction of magnetic moment only with the number of Fe-Si nearest neighbors. The presented results show that the crucial role in MM formation is played by the particular local NNN environment of the metal atom in the transition metal-metalloid alloy.

Improved assignments of the vibrational fundamental modes of ortho-, meta-, and para-xylene using gas- and liquid-phase infrared and Raman spectra combined with ab initio calculations: Quantitative gas-phase infrared spectra for detection

NASA Astrophysics Data System (ADS)

Lindenmaier, Rodica; Scharko, Nicole K.; Tonkyn, Russell G.; Nguyen, Kiet T.; Williams, Stephen D.; Johnson, Timothy J.

2017-12-01

Xylenes contain a blend of the ortho-, meta-, and para- isomers, and all are abundant contaminants in the ground, surface waters, and air. To better characterize xylene and to better enable its detection, high quality quantitative vapor-phase infrared spectra of all three isomers over the 6500 - 540 cm-1 range are reported. All fundamental vibrational modes are assigned based on these vapor-phase infrared spectra, liquid-phase infrared and Raman spectra, along with density functional theory (DFT), ab initio MP2 and high energy-accuracy compound theoretical model (W1BD) calculations. Both MP2 and DFT predict a single conformer with C2v symmetry for ortho-xylene, and two conformers each for meta- and para-xylene, depending on the preferred orientations of the methyl groups. For meta-xylene the two conformers have Cs and C2 symmetry, and for para-xylene these conformers have C2v or C2h symmetry. Since the relative population of the two conformers is approximately 50% for both isomers and predicted frequencies and intensities are very similar for each conformer, an arbitrary choice to discuss the Cs conformer for meta-xylene and the C2v conformer for para-xylene is made. Integrated band intensities for all isomers are reported. Using the quantitative infrared data, the global warming potential values of each isomer are determined. Potential bands for atmospheric monitoring are also discussed.

Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

DTIC Science & Technology

2015-07-15

There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio -Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

Perspectives from ab-initio and tight-binding: Applications to transition metal compounds and superlattices

NASA Astrophysics Data System (ADS)

Venkataraman, Vijay Shankar

The experimental and theoretical study of transition metal compounds have occupied condensed matter physicists for the best part of the last century. The rich variety of physical behaviour exhibited by these compounds owes its origin to the subtle balance of the energy scales at play for the d orbitals. In this thesis, we study three different systems comprised of transition metal atoms from the third, the fourth, and the fifth group of the periodic table using a combination of ab-initio density functional theory (DFT) computations and effective tight-binding models for the electronic properties. We first consider the electronic properties of artificially fabricated perovskite superlattices of the form [(SrIrO3)m / SrTiO3] with integer m denoting the number of layers of SrIrO3. After discussing the results of experiments undertaken by our collaborators, we present the results of our DFT calculations and build tight-binding models for the m = 1 and m = 2 superlattices. The active ingredient is found to be the 5d orbitals with significant spin-orbit coupling. We then study the energies of magnetic ground states within DFT and compare and contrast our results with those obtained for the bulk Ruddlesden-Popper iridates. Together with experimental measurements, our results suggest that these superlattices are an exciting venue to probe the magnetism and metal-insulator transitions that occur from the intricate balance of the spin-orbit coupling and electron interactions, as has been reported for their bulk counterparts. Next, we consider alpha-RuCl3, a honeycomb lattice compound. We first show using DFT calculations in conjunction with experiments performed by our collaborators, how spin-orbit coupling in the 4d orbitals of Ru is essential to understand the insulating state realized in this compound. Then, in the latter half of the chapter, we study the magnetic ground states of a two-dimensional analogue of alpha-RuCl3 in weak and strong-coupling regimes obtained from a tight-binding model for the 4d orbitals. We further compare these results with energies obtained from DFT calculations. We obtain a zig-zag magnetic ground state for this compound, in all the three approaches. Within DFT, we find that correlations enhance the spin-orbit coupling in this compound and that the anisotropic Kitaev interactions between the spins are dominant in a strong-coupling model. Then, we move on to study the electronic band structures of the higher manganese silicides, which are good thermoelectric materials. Using results from DFT calculations on Mn4Si7 and structural arguments, we construct an effective tight-binding model for the first three members of this series - Mn4Si7, Mn11Si19, and Mn15Si26.

Vibrational spectroscopic study of terbutaline hemisulphate

NASA Astrophysics Data System (ADS)

Ali, H. R. H.; Edwards, H. G. M.; Kendrick, J.; Scowen, I. J.

2009-05-01

The Raman spectrum of terbutaline hemisulphate is reported for the first time, and molecular assignments are proposed on the basis of ab initio BLYP DFT calculations with a 6-31G* basis set and vibrational frequencies predicted within the quasi-harmonic approximation; these predictions compare favourably with the observed vibrational spectra. Comparison with previously published infrared data explains several spectral features. The results from this study provide data that can be used for the preparative process monitoring of terbutaline hemisulphate, an important β 2 agonist drug in various dosage forms and its interaction with excipients and other components.

Ab-initio calculation for cation vacancy formation energy in anti-fluorite structure

NASA Astrophysics Data System (ADS)

Saleel, V. P. Saleel Ahammad; Chitra, D.; Veluraja, K.; Eithiraj, R. D.

2018-04-01

Lithium oxide (Li2O) has been suggested as a suitable breeder blanket material for fusion reactors. Li+ vacancies are created by neutron irradiation, forming bulk defect complex whose extra character is experimentally unclear. We present a theoretical study of Li2O using density functional theory (DFT) with a plane-wave basis set. The generalized gradient approximation (GGA) and local-density approximation (LDA) were used for exchange and correlation. Here we address the total energy for defect free, cation defect, cation vacancy and vacancy formation energy in Li2O crystal in anti-fluorite structure.

Support vector machine regression (LS-SVM)--an alternative to artificial neural networks (ANNs) for the analysis of quantum chemistry data?

PubMed

Balabin, Roman M; Lomakina, Ekaterina I

2011-06-28

A multilayer feed-forward artificial neural network (MLP-ANN) with a single, hidden layer that contains a finite number of neurons can be regarded as a universal non-linear approximator. Today, the ANN method and linear regression (MLR) model are widely used for quantum chemistry (QC) data analysis (e.g., thermochemistry) to improve their accuracy (e.g., Gaussian G2-G4, B3LYP/B3-LYP, X1, or W1 theoretical methods). In this study, an alternative approach based on support vector machines (SVMs) is used, the least squares support vector machine (LS-SVM) regression. It has been applied to ab initio (first principle) and density functional theory (DFT) quantum chemistry data. So, QC + SVM methodology is an alternative to QC + ANN one. The task of the study was to estimate the Møller-Plesset (MPn) or DFT (B3LYP, BLYP, BMK) energies calculated with large basis sets (e.g., 6-311G(3df,3pd)) using smaller ones (6-311G, 6-311G*, 6-311G**) plus molecular descriptors. A molecular set (BRM-208) containing a total of 208 organic molecules was constructed and used for the LS-SVM training, cross-validation, and testing. MP2, MP3, MP4(DQ), MP4(SDQ), and MP4/MP4(SDTQ) ab initio methods were tested. Hartree-Fock (HF/SCF) results were also reported for comparison. Furthermore, constitutional (CD: total number of atoms and mole fractions of different atoms) and quantum-chemical (QD: HOMO-LUMO gap, dipole moment, average polarizability, and quadrupole moment) molecular descriptors were used for the building of the LS-SVM calibration model. Prediction accuracies (MADs) of 1.62 ± 0.51 and 0.85 ± 0.24 kcal mol(-1) (1 kcal mol(-1) = 4.184 kJ mol(-1)) were reached for SVM-based approximations of ab initio and DFT energies, respectively. The LS-SVM model was more accurate than the MLR model. A comparison with the artificial neural network approach shows that the accuracy of the LS-SVM method is similar to the accuracy of ANN. The extrapolation and interpolation results show that LS-SVM is superior by almost an order of magnitude over the ANN method in terms of the stability, generality, and robustness of the final model. The LS-SVM model needs a much smaller numbers of samples (a much smaller sample set) to make accurate prediction results. Potential energy surface (PES) approximations for molecular dynamics (MD) studies are discussed as a promising application for the LS-SVM calibration approach. This journal is © the Owner Societies 2011

Ab-initio Computation of the Electronic, transport, and Bulk Properties of Calcium Oxide.

NASA Astrophysics Data System (ADS)

Mbolle, Augustine; Banjara, Dipendra; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We report results from ab-initio, self-consistent, local Density approximation (LDA) calculations of electronic and related properties of calcium oxide (CaO) in the rock salt structure. We employed the Ceperley and Alder LDA potential and the linear combination of atomic orbitals (LCAO) formalism. Our calculations are non-relativistic. We implemented the LCAO formalism following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method involves a methodical search for the optimal basis set that yields the absolute minima of the occupied energies, as required by density functional theory (DFT). Our calculated, indirect band gap of 6.91eV, from towards the L point, is in excellent agreement with experimental value of 6.93-7.7eV, at room temperature (RT). We have also calculated the total (DOS) and partial (pDOS) densities of states as well as the bulk modulus. Our calculated bulk modulus is in excellent agreement with experiment. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

Ab-initio study of structural and electronic properties of WS2/h-BN van der Waals heterostructure

NASA Astrophysics Data System (ADS)

Ghasemi majd, Zahra; Amiri, Peiman; Taghizadeh, Seyed Fardin

2018-06-01

First-principle calculations with different exchange-correlation functionals, including LDA, GGA, semi-empirical and ab-initio van der Waals in the forms of vdW-DF2B86R and vdW-DF2 were performed to evaluate the performance of different functionals in describing the bonding mechanism, adsorption energy and interlayer distance of WS2 monolayer on and between h-BN layers. The finding was that the vdW-DF2B86R seems to be the approach best lending itself to this purpose. In order to include the van der Waals (vdW) interactions in our calculations, we used the DFT-D2 and vdW methods, which gave rise to a physical adsorption with no net charge transfer between the WS2 layer and the corresponding substrates. In addition, we investigated the electronic and structural properties of WS2 and h-BN heterolayers, using vdW-DF2B86R functional. Based on density functional theory calculations, WS2 on and between h-BN layers showed a direct band gap at the K-point, which was experimentally observed.

Spectroscopic (FT-IR and FT-Raman) investigation, first order hyperpolarizability, NBO, HOMO-LUMO and MEP analysis of 6-nitrochromone by ab initio and density functional theory calculations

NASA Astrophysics Data System (ADS)

Senthil kumar, J.; Jeyavijayan, S.; Arivazhagan, M.

2015-02-01

The vibrational spectral analysis is carried out using FT-Raman and FT-IR spectroscopy in the range 3500-50 cm-1 and 4000-400 cm-1, respectively, for 6-nitrochromone (6NC). The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization and normal coordinates force field calculation based on ab initio HF and DFT gradient calculations employing the HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) basis set. Stability of the molecule has been analyzed using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Thermodynamic properties like entropy, heat capacity, zero-point energy and Mulliken's charge analysis have been calculated for the 6NC. The complete assignments were performed on the basis of total energy distribution (TED) of the vibrational modes with scaled quantum mechanical (SQM) method. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms.

Insight of DFT and ab initio atomistic thermodynamics on the surface stability and morphology of In2O3

NASA Astrophysics Data System (ADS)

Zhang, Minhua; Wang, Wenyi; Chen, Yifei

2018-03-01

In2O3 catalysts show remarkable activity and selectivity in methanol synthesis from CO2 hydrogenation. In order to get insight into the surface stability of this catalyst, density functional theory and ab initio atomistic thermodynamics method were used to investigate the surface free energies of various facets as a function of oxygen chemical potential, as well as the influences of temperature, pressure and gas compositions. The results show that the (111) facet presents lowest surface free energy under oxygen-rich condition, while the indium-terminated (100) facet is the most stable one under oxygen-lean condition. Moreover, we applied Wulff construction to determine the equilibrium shape of In2O3 with different oxygen chemical potentials. The equilibrium shape under oxygen-lean condition is cubic, which only expose (100) facet, while, the equilibrium shape under oxygen-rich condition is octahedron, which only expose (111) facet. Meanwhile, the results agree well with what is observed experimentally. It is further predicted that Wulff shape of In2O3 exists in a truncated octahedron morphology in which the (100) surface becomes predominant plane under CO2 hydrogenation reaction conditions.

Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory.

PubMed

Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou

2014-01-24

Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G(*) basis set. The -311++G(**) basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of C-H bond length and the elongation of N-H bond length suggest the existence of weak C-H⋯O and N-H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P2(1) space group, with lattice parameters Z=4, a=14.9989 Å, b=4.0367 Å, c=12.9913 Å, ρ=0.998 g cm(-3). Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory

NASA Astrophysics Data System (ADS)

Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou

2014-01-01

Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G* basis set. The -311++G** basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of Csbnd H bond length and the elongation of Nsbnd H bond length suggest the existence of weak Csbnd H⋯O and Nsbnd H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P21 space group, with lattice parameters Z = 4, a = 14.9989 Å, b = 4.0367 Å, c = 12.9913 Å, ρ = 0.998 g cm-3.

Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations

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

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun

Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ionmore » diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.« less

Ab initio study of properties of BaBiO3 at high pressure

NASA Astrophysics Data System (ADS)

Martoňák, Roman; Ceresoli, Davide; Kagayama, Tomoko; Tosatti, Erio

BaBiO3 is a mixed-valence perovskite which escapes metallic state by creating a Bi-O bond disproportionation or CDW pattern, resulting in a Peierls semiconductor with gap of nearly 1 eV at zero pressure. Evolution of structural and electronic properties at high pressure is, however, largely unknown. Pressure, it might be natural to expect, could reduce the bond-disproportionation and bring the system closer to metalicity or even superconductivity. We address this question by ab initio DFT methods based on GGA and hybrid functionals in combination with crystal structure prediction techniques based on genetic algorithms. We analyze the pressure evolution of bond disproportionation as well as other order parameters related to octahedra rotation for various phases in connection with corresponding evolution of the electronic structure. Results indicate that BaBiO3 continues to resist metalization also under pressure, through structural phase transitions which sustain and in fact increase the diversity of length of Bi-O bonds for neighboring Bi ions, in agreement with preliminary high pressure resistivity data. R.M. Slovak Research and Development Agency Contract APVV-15-0496, VEGA project No. 1-0904-15; E.T. ERC MODPHYSFRICT Advanced Grant No. 320796.

Antibacterial activity, thermal stability and ab initio study of copolymer containing sulfobetaine and carboxybetaine groups

NASA Astrophysics Data System (ADS)

Tarannum, Nazia; Singh, Meenakshi; Yadav, Anil K.

2017-10-01

Here, we have explored the antibacterial activity, thermal stability and theoretical study of two copolymers that contain sulfobetaine and carboetaine moiety. Copolymers were synthesized based on Schiff base chemistry with generation of zwitterionic centres by nucleophilic addition of sultone/lactone. To predict and confirm the molecular structure of zwitterionic polyelectrolyte molecule, the theoretical study of structural features and other thermodynamic characteristics of copolymer constituents was obtained by ab initio calculations. Various parameters such as geometry optimization, energy calculations, frequency calculations and intrinsic reaction coefficient (IRC) are simulated using Hartree Fock (HF) method. The geometry optimizations are analyzed at HF/3-21 G default level of theory. The vibrational frequency is calculated via density functional theory (DFT)/B3LYP 6-31G*(d) level whose values are in accord with the experimental observed frequency. Both copolymers have been successfully assessed for antibacterial activity against Staphylococcus aureus and Pseudomonas aeuroginosa bacterial strains by disc diffusion method. The antibacterial study helped in evaluating zone of inhibition, minimum inhibitory concentration and minimum bactericidal concentration. Sulfobetaine copolymer is found to be more effective in curtailing the infection caused by bacteria as compared to carbobetaine.

Electronic and magnetic structures of Fe3O4 ferrimagnetic investigated by first principle, mean field and series expansions calculations

NASA Astrophysics Data System (ADS)

Masrour, R.; Hlil, E. K.; Hamedoun, M.; Benyoussef, A.; Mounkachi, O.; El Moussaoui, H.

2015-03-01

Self-consistent ab initio calculations, based on density functional theory (DFT) approach and using a full potential linear augmented plane wave (FLAPW) method, are performed to investigate both electronic and magnetic properties of the Fe3O4. Polarized spin and spin-orbit coupling are included in calculations within the framework of the antiferromagnetic state between two adjacent Fe plans. Magnetic moment considered to lie along (010) axes are computed. Obtained data from ab initio calculations are used as input for the high temperature series expansions (HTSEs) calculations to compute other magnetic parameters. The exchange interactions between the magnetic atoms Fe-Fe in Fe3O4 are given using the mean field theory. The high temperature series expansions (HTSEs) of the magnetic susceptibility of with the magnetic moments, mFe in Fe3O4 is given up to seventh order series in (1/kBT). The Néel temperature TN is obtained by HTSEs of the magnetic susceptibility series combined with the Padé approximant method. The critical exponent γ associated with the magnetic susceptibility is deduced as well.

Theoretical investigation of gas-phase molecular complex formation between 2-hydroxy thiophenol and a water molecule.

PubMed

Kumar Deb, Debojit; Sarkar, Biplab

2017-01-18

The torsional potential of OH and SH rotations in 2-hydroxy thiophenol is systematically studied using the MP2 ab initio method. The outcome of state-of-the-art calculations is used in the investigation of the structures and conformational preferences of 2-hydroxy thiophenol and aims at further interaction studies with a gas phase water molecule. SCS-MP2 and CCSD(T) complete basis set (CBS) limit interaction energies for these complexes are presented. The SCS-MP2/CBS limit is achieved using various two-point extrapolation methods with aug-cc-pVDZ and aug-cc-pVTZ basis sets. The CCSD(T) correction term is determined as the difference between CCSD(T) and SCS-MP2 interaction energies calculated using a smaller basis set. The effect of counterpoise correction on the extrapolation to the CBS limit is discussed. The performance of DFT based wB97XD, M06-2X and B3LYP-D3 functionals is tested against the benchmark energy from ab initio calculations. Hydrogen bond interactions are characterized by carrying out QTAIM, NCIPLOT, NBO and SAPT analyses.

Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method

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

Nakata, Hiroya, E-mail: nakata.h.ab@m.titech.ac.jp; RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198; Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083

2015-03-28

Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluatedmore » for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in S{sub N}2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.« less

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

Large hydrogen-bonded pre-nucleation (HSO4-)(H2SO4)m(H2O)k and (HSO4-)(NH3)(H2SO4)m(H2O)k clusters in the earth's atmosphere.

PubMed

Herb, Jason; Xu, Yisheng; Yu, Fangqun; Nadykto, A B

2013-01-10

The importance of pre-nucleation cluster stability as the key parameter controlling nucleation of atmospheric airborne ions is well-established. In this Article, large ternary ionic (HSO(4)(-))(H(2)SO(4))(m)(NH(3))(H(2)O)(n) clusters have been studied using Density Functional Theory (DFT) and composite ab initio methods. Twenty classes of clusters have been investigated, and thermochemical properties of common atmospheric (HSO(4)(-))(H(2)SO(4))(m)(NH(3))(0)(H(2)O)(k) and (HSO(4)(-))(H(2)SO(4))(m)(NH(3))(1)(H(2)O)(n) clusters (with m, k, and n up to 3) have been obtained. A large amount of new themochemical and structural data ready-to-use for constraining kinetic nucleation models has been reported. We have performed a comprehensive thermochemical analysis of the obtained data and have investigated the impacts of ammonia and negatively charged bisulfate ion on stability of binary clusters in some detail. The comparison of theoretical predictions and experiments shows that the PW91PW91/6-311++G(3df,3pd) results are in very good agreement with both experimental data and high level ab initio CCSD(T)/CBS values and suggest that the PW91PW91/6-311++G(3df,3pd) method is a viable alternative to higher level ab initio methods in studying large pre-nucleation clusters, for which the higher level computations are prohibitively expensive. The uncertainties in both theory and experiments have been investigated, and possible ways of their reduction have been proposed.

Theoretical study of the changes in the vibrational characteristics arising from the hydrogen bonding between Vitamin C ( L-ascorbic acid) and H 2O

NASA Astrophysics Data System (ADS)

Dimitrova, Yordanka

2006-02-01

The vibrational characteristics (vibrational frequencies, infrared intensities and Raman activities) for the hydrogen-bonded system of Vitamin C ( L-ascorbic acid) with five water molecules have been predicted using ab initio SCF/6-31G(d, p) calculations and DFT (BLYP) calculations with 6-31G(d, p) and 6-31++G(d, p) basis sets. The changes in the vibrational characteristics from free monomers to a complex have been calculated. The ab initio and BLYP calculations show that the complexation between Vitamin C and five water molecules leads to large red shifts of the stretching vibrations for the monomer bonds involved in the hydrogen bonding and very strong increase in their IR intensity. The predicted frequency shifts for the stretching vibrations from Vitamin C taking part in the hydrogen bonding are up to -508 cm -1. The magnitude of the wavenumber shifts is indicative of relatively strong OH···H hydrogen-bonded interactions. In the same time the IR intensity and Raman activity of these vibrations increase upon complexation. The IR intensity increases dramatically (up to 12 times) and Raman activity increases up to three times. The ab initio and BLYP calculations show, that the symmetric OH vibrations of water molecules are more sensitive to the complexation. The hydrogen bonding leads to very large red shifts of these vibrations and very strong increase in their IR intensity. The asymmetric OH stretching vibrations of water, free from hydrogen bonding are less sensitive to the complexation than the hydrogen-bonded symmetric O sbnd H stretching vibrations. The increases of the IR intensities for these vibrations are lower and red shifts are negligible.

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.

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

DFT study of Al doped armchair SWCNTs

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

Dhiman, Shobhna, E-mail: s-dhiman@hotmail.com; Rani, Anita; Kumar, Ranjan

2016-05-23

Electronic properties of endohedrally doped armchair single-walled carbon nanotubes (SWCNTs) with a chain of six Al atoms have been studied using ab-initio density functional theory. We investigate the binding energy/atom, ionization potential, electron Affinity and Homo-Lumo gap of doped armchair SWNTs from (4,4) to (6,6) with two ends open. BE/dopant atom and ionization potential is maximum for (6, 6) doped armchair carbon nanotube; suggest that it is more stable than (4, 4) and (5, 5) doped tubes. HOMO - LUMO gap of Al doped arm chair carbon nanotubes decreases linearly with the increase in diameter of the tube. This showsmore » that confinement induce a strong effect on electronic properties of doped tubes. These combined systems can be used for future nano electronics. The ab–initio calculations were performed with SIESTA code using generalized gradient approximation (GGA).« less

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Identifying the Role of Terahertz Vibrations in Metal-Organic Frameworks: From Gate-Opening Phenomenon to Shear-Driven Structural Destabilization

NASA Astrophysics Data System (ADS)

Ryder, Matthew R.; Civalleri, Bartolomeo; Bennett, Thomas D.; Henke, Sebastian; Rudić, Svemir; Cinque, Gianfelice; Fernandez-Alonso, Felix; Tan, Jin-Chong

2014-11-01

We present an unambiguous identification of low-frequency terahertz vibrations in the archetypal imidazole-based metal-organic framework (MOF) materials: ZIF-4, ZIF-7, and ZIF-8, all of which adopt a zeolite-like nanoporous structure. Using inelastic neutron scattering and synchrotron radiation far-infrared absorption spectroscopy, in conjunction with density functional theory (DFT), we have pinpointed all major sources of vibrational modes. Ab initio DFT calculations revealed the complex nature of the collective THz modes, which enable us to establish detailed correlations with experiments. We discover that low-energy conformational dynamics offers multiple pathways to elucidate novel physical phenomena observed in MOFs. New evidence demonstrates that THz modes are intrinsically linked, not only to anomalous elasticity underpinning gate-opening and pore-breathing mechanisms, but also to shear-induced phase transitions and the onset of structural instability.

Communication: Biological applications of coupled-cluster frozen-density embedding

NASA Astrophysics Data System (ADS)

Heuser, Johannes; Höfener, Sebastian

2018-04-01

We report the implementation of the Laplace-transform scaled opposite-spin (LT-SOS) resolution-of-the-identity second-order approximate coupled-cluster singles and doubles (RICC2) combined with frozen-density embedding for excitation energies and molecular properties. In the present work, we furthermore employ the Hartree-Fock density for the interaction energy leading to a simplified Lagrangian which is linear in the Lagrangian multipliers. This approximation has the key advantage of a decoupling of the coupled-cluster amplitude and multipliers, leading also to a significant reduction in computation time. Using the new simplified Lagrangian in combination with efficient wavefunction models such as RICC2 or LT-SOS-RICC2 and density-functional theory (DFT) for the environment molecules (CC2-in-DFT) enables the efficient study of biological applications such as the rhodopsin and visual cone pigments using ab initio methods as routine applications.

DFT-BASED AB INITIO STUDY OF THE ELECTRONIC AND OPTICAL PROPERTIES OF CESIUM BASED FLUORO-PEROVSKITE CsMF3 (M = Ca AND Sr)

NASA Astrophysics Data System (ADS)

Harmel, M.; Khachai, H.; Ameri, M.; Khenata, R.; Baki, N.; Haddou, A.; Abbar, B.; UǦUR, Ş.; Omran, S. Bin; Soyalp, F.

2012-12-01

Density functional theory (DFT) is performed to study the structural, electronic and optical properties of cubic fluoroperovskite AMF3 (A = Cs; M = Ca and Sr) compounds. The calculations are based on the total-energy calculations within the full-potential linearized augmented plane wave (FP-LAPW) method. The exchange-correlation potential is treated by local density approximation (LDA) and generalized gradient approximation (GGA). The structural properties, including lattice constants, bulk modulus and their pressure derivatives are in very good agreement with the available experimental and theoretical data. The calculations of the electronic band structure, density of states and charge density reveal that compounds are both ionic insulators. The optical properties (namely: the real and the imaginary parts of the dielectric function ɛ(ω), the refractive index n(ω) and the extinction coefficient k(ω)) were calculated for radiation up to 40.0 eV.

Ab Initio Predictions of Strong Interfaces in Transition-Metal Carbides and Nitrides for Superhard Nanocomposite Coating Applications

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

Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G.

Conceiving strong interfaces represents an effective direction in the development of superhard nanocomposite materials for practical applications in protective coatings. Additionally, in the pursuit of engineering strong nanoscale interfaces between cubic rock-salt (B1) domains, we investigate using density functional theory (DFT) coherent interface models designed based on hexagonal (HX) NiAs and WC structures, as well as experiment. The DFT screening of a collection of transition-metal (M = Zr, Hf, Nb, Ta) carbides and nitrides indicates that the interface models provided by the HX polymorphs store little coherency strain and develop an energetic advantage as the valence-electron concentration increases. Finally, ourmore » result suggests that harnessing the polymorphism encountered in transition-metal (M = Zr, Hf, Nb, Ta) carbides and nitrides for interface design represents a promising strategy for advancing superhard nanomaterials.« less

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.

Experimental and theoretical studies on the structure and spectroscopic properties of (E)-1-(2-aminophenyl)-3-(pyridine-4-yl) prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Cruz Ortiz, Andrés Felipe; Sánchez López, Alberto; García Ríos, Alejandro; Cuenú Cabezas, Fernando; Rozo Correa, Ciro Eduardo

2015-10-01

(E)-1-(2-aminophenyl)-3-(pyridine-4-yl)prop-2-en-1-one (or simply 2-aminochalcone) was synthetized and characterized by elemental analysis, FT-IR, NMR, MS and XRD. Molecular geometry optimization, vibrational harmonic frequencies, 1H and 13C NMR chemical shifts were calculated by ab initio (HF and MP2) and density functional theory (DFT) methods, with B3LYP and B3PW91 functionals, using GAUSSIAN 09 program package without any constraint on the geometry. With VEDA software vibrational frequencies were assigned in terms of the potential energy distribution. A detailed interpretation of the FT-IR, NMR and XRD, experimental and calculated, is reported. The HOMO and LUMO energy gap that reflects the chemical activity of the molecule were also studied by DFT and above basis set. All theoretical results correspond to a great extent to experimental ones.

Ab Initio Predictions of Strong Interfaces in Transition-Metal Carbides and Nitrides for Superhard Nanocomposite Coating Applications

DOE PAGES

Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G.; ...

2018-04-19

Conceiving strong interfaces represents an effective direction in the development of superhard nanocomposite materials for practical applications in protective coatings. Additionally, in the pursuit of engineering strong nanoscale interfaces between cubic rock-salt (B1) domains, we investigate using density functional theory (DFT) coherent interface models designed based on hexagonal (HX) NiAs and WC structures, as well as experiment. The DFT screening of a collection of transition-metal (M = Zr, Hf, Nb, Ta) carbides and nitrides indicates that the interface models provided by the HX polymorphs store little coherency strain and develop an energetic advantage as the valence-electron concentration increases. Finally, ourmore » result suggests that harnessing the polymorphism encountered in transition-metal (M = Zr, Hf, Nb, Ta) carbides and nitrides for interface design represents a promising strategy for advancing superhard nanomaterials.« less

Electronic structure and transport properties of zigzag MoS2 nanoribbons

NASA Astrophysics Data System (ADS)

Sharma, Uma Shankar; Shah, Rashmi; Mishra, Pankaj Kumar

2018-05-01

In present study, electronic and transport properties of the 8zigzag MoS2 nanoribbons (8ZMoS2NRs) are investigated using ab-initio density functional theory [DFT]. The calculations were performed using nonequilibrium Green's function (NEGF) formalism based on DFT as implemented in the TranSiesta code. Results show that the defect can introduces few extra states into the energy gap, which lead nanoribbons to reveal a metallic characteristic. The voltage-current (VI) graph of 8ZMoS2NRs show a threshold current increases after introducing Mo defect in the devices. when introducing a Mo vacancy under low biases, the current will be suppressed—whereas under high biases, the current through the defected 8ZMoS2NRs will increases rapidly, due to the other channel being opened, that make possibility of 8ZMoS2NRs application in electronic devices such as voltage regulation.

Metastable structure of Li13Si4

NASA Astrophysics Data System (ADS)

Gruber, Thomas; Bahmann, Silvia; Kortus, Jens

2016-04-01

The Li13Si4 phase is one out of several crystalline lithium silicide phases, which is a potential electrode material for lithium ion batteries and contains a high theoretical specific capacity. By means of ab initio methods like density functional theory (DFT) many properties such as heat capacity or heat of formation can be calculated. These properties are based on the calculation of phonon frequencies, which contain information about the thermodynamical stability. The current unit cell of "Li13Si4" given in the ICSD database is unstable with respect to DFT calculations. We propose a modified unit cell that is stable in the calculations. The evolutionary algorithm EVO found a structure very similar to the ICSD one with both of them containing metastable lithium positions. Molecular dynamic simulations show a phase transition between both structures where these metastable lithium atoms move. This phase transition is achieved by a very fast one-dimensional lithium diffusion and stabilizes this phase.

Polycyclic Aromatic Hydrocarbons Adsorption onto Graphene: A DFT and AIMD Study.

PubMed

Li, Bing; Ou, Pengfei; Wei, Yulan; Zhang, Xu; Song, Jun

2018-05-03

Density functional theory (DFT) calculations and ab-initio molecular dynamics (AIMD) simulations were performed to understand graphene and its interaction with polycyclic aromatic hydrocarbons (PAHs) molecules. The adsorption energy was predicted to increase with the number of aromatic rings in the adsorbates, and linearly correlate with the hydrophobicity of PAHs. Additionally, the analysis of the electronic properties showed that PAHs behave as mild n-dopants and introduce electrons into graphene; but do not remarkably modify the band gap of graphene, indicating that the interaction between PAHs and graphene is physisorption. We have also discovered highly sensitive strain dependence on the adsorption strength of PAHs onto graphene surface. The AIMD simulation indicated that a sensitive and fast adsorption process of PAHs can be achieved by choosing graphene as the adsorbent. These findings are anticipated to shed light on the future development of graphene-based materials with potential applications in the capture and removal of persistent aromatic pollutants.

Pair potentials for warm dense matter and their application to x-ray Thomson scattering in aluminum and beryllium.

PubMed

Harbour, L; Dharma-Wardana, M W C; Klug, D D; Lewis, L J

2016-11-01

Ultrafast laser experiments yield increasingly reliable data on warm dense matter, but their interpretation requires theoretical models. We employ an efficient density functional neutral-pseudoatom hypernetted-chain (NPA-HNC) model with accuracy comparable to ab initio simulations and which provides first-principles pseudopotentials and pair potentials for warm-dense matter. It avoids the use of (i) ad hoc core-repulsion models and (ii) "Yukawa screening" and (iii) need not assume ion-electron thermal equilibrium. Computations of the x-ray Thomson scattering (XRTS) spectra of aluminum and beryllium are compared with recent experiments and with density-functional-theory molecular-dynamics (DFT-MD) simulations. The NPA-HNC structure factors, compressibilities, phonons, and conductivities agree closely with DFT-MD results, while Yukawa screening gives misleading results. The analysis of the XRTS data for two of the experiments, using two-temperature quasi-equilibrium models, is supported by calculations of their temperature relaxation times.

FT-IR, FT-Raman, NMR studies and ab initio-HF, DFT-B3LYP vibrational analysis of 4-chloro-2-fluoroaniline

NASA Astrophysics Data System (ADS)

Arivazhagan, M.; Anitha Rexalin, D.

2012-10-01

The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 4-chloro-2-fluoroaniline (CFA) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of ab initio and density functional theory (DFT) methods. 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. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule are 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 CFA are calculated using B3LYP/6-311++G(d,p) and HF/6-311++G(d,p) methods on the finite-field approach. The calculated results also show that the CFA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The result confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. The HOMO-LUMO energies UV-vis spectral analysis and MEP are performed by B3LYP/6-311++G(d,p) approach. A detailed interpretation of the infrared and Raman spectra of CFA is also reported based on total energy distribution (TED). The difference between the observed and scaled wave number values of the most of the fundamentals is very small.

Adsorption and substitution effects of Mg on the growth of calcium sulfate hemihydrate: An ab initio DFT study

NASA Astrophysics Data System (ADS)

Xin, Yan; Hou, S. C.; Xiang, Lan; Yu, Yang-Xin

2015-12-01

Calcium sulfate hemihydrate (CaSO4·0.5H2O, CSH) whiskers with high aspect ratio are promising reinforce materials which have drawn much attention. In order to obtain high quality CSH materials, effect of Mg2+ ions on properties of the (0 0 2), (2 0 0)1 and (2 0 0)2 planes of CSH is investigated using an ab initio density functional theory (DFT) with a van der Waals (vdW) dispersion-correction. The computed results show that strong adsorption and substitution effects take place between Mg2+ ion and (2 0 0)1 plane. The adsorption energies of an Mg2+ ion on the (0 0 2), (2 0 0)1 and (2 0 0)2 planes are -0.066, -0.571 and -0.047 eV, respectively. An insight into the electrostatic potential of pristine CSH planes has demonstrated that the (2 0 0)1 plane is much more negatively charged than the (0 0 2) and (2 0 0)2 planes. The energies of the substitution of a Ca atom with an Mg atom on the CSH (0 0 2), (2 0 0)1 and (2 0 0)2 planes are 1.572, 0.063 and 1.349 eV, respectively. It is found that Ca atoms on the (2 0 0)1 plane are relatively easy to be substituted by Mg atoms. The calculation results of a Ca2+ ion adsorption on the Mg-doped (2 0 0)1 plane indicate that the adsorption energies increase apparently as the doping ratio varies from 0 to 1.0. Compared with K+, Na+ and Al3+ ions, Mg2+ ion is the most promising additive to promote the growth of CSH along c axis.

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.

FT-IR, FT-Raman, NMR studies and ab initio-HF, DFT-B3LYP vibrational analysis of 4-chloro-2-fluoroaniline.

PubMed

Arivazhagan, M; Anitha Rexalin, D

2012-10-01

The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 4-chloro-2-fluoroaniline (CFA) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of ab initio and density functional theory (DFT) methods. 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. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the Gauge including atomic orbital (GIAO) method. The first order hyperpolarizability (β(0)) of this novel molecular system and related properties (β, α(0) and Δα) of CFA are calculated using B3LYP/6-311++G(d,p) and HF/6-311++G(d,p) methods on the finite-field approach. The calculated results also show that the CFA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The result confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. The HOMO-LUMO energies UV-vis spectral analysis and MEP are performed by B3LYP/6-311++G(d,p) approach. A detailed interpretation of the infrared and Raman spectra of CFA is also reported based on total energy distribution (TED). The difference between the observed and scaled wave number values of the most of the fundamentals is very small. Copyright © 2012 Elsevier B.V. All rights reserved.

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

Proton affinities of maingroup-element hydrides and noble gases: trends across the periodic table, structural effects, and DFT validation.

PubMed

Swart, Marcel; Rösler, Ernst; Bickelhaupt, F Matthias

2006-10-01

We have carried out an extensive exploration of the gas-phase basicity of archetypal neutral bases across the periodic system using the generalized gradient approximation (GGA) of the density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities: BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 2.0 kcal/mol for the proton affinity at 298 K with respect to experiment, and 1.2 kcal/mol with high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the neutral bases constituted by all maingroup-element hydrides of groups 15-17 and the noble gases, that is, group 18, and periods 1-6. We have also studied the effect of step-wise methylation of the protophilic center of the second- and third-period bases. Copyright 2006 Wiley Periodicals, Inc.

Ammonia-water cation and ammonia dimer cation.

PubMed

Kim, Hahn; Lee, Han Myoung

2009-06-25

We have investigated the structure, interaction energy, electronic properties, and IR spectra of the ammonia-water cation (NH(3)H(2)O)(+) using density functional theory (DFT) and high-level ab initio theory. The ammonia-water cation has three minimum-energy structures of (a) H(2)NH(+)...OH(2), (b) H(3)N(+)...OH(2), and (c) H(3)NH(+)...OH. The lowest-energy structure is (a), followed by (c) and (b). The ammonia dimer cation has two minimum-energy structures [the lowest H(3)NH(+)...NH(2) structure and the second lowest (H(3)N...NH(3))(+) structure]. The minimum transition barrier for the interconversion between (a), (b), and (c) is approximately 6 kcal/mol. Most DFT calculations with various functionals, except a few cases, overstabilize the N...O and N...N binding, predicting different structures from Moller-Plesset second-order perturbation (MP2) theory and the most reliable complete basis set (CBS) limit of coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. Thus, the validity test of the DFT functionals for these ionized molecular systems would be of importance.

Importance of van der Waals interaction on structural, vibrational, and thermodynamic properties of NaCl

NASA Astrophysics Data System (ADS)

Marcondes, Michel L.; Wentzcovitch, Renata M.; Assali, Lucy V. C.

2018-05-01

Thermal equations of state (EOS) are essential in several scientific domains. However, experimental determination of EOS parameters may be limited at extreme conditions, therefore, ab initio calculations have become an important method to obtain them. Density functional theory (DFT) and its extensions with various degrees of approximations for the exchange and correlation (XC) energy is the method of choice, but large errors in the EOS parameters are still common. The alkali halides have been problematic from the onset of this field and the quest for appropriate DFT functionals for such ionic and relatively weakly bonded systems has remained an active topic of research. Here we use DFT + van der Waals functionals to calculate vibrational properties, thermal EOS, thermodynamic properties, and the B1 to B2 phase boundary of NaCl with high precision. Our results reveal a remarkable improvement over the performance of standard local density approximation and generalized gradient approximation functionals for all these properties and phase transition boundary, as well as great sensitivity of anharmonic effects on the choice of XC functional.

Influence of Van der Waals interaction on the thermodynamics properties of NaCl

NASA Astrophysics Data System (ADS)

Marcondes, M. L.; Wentzcovitch, R. M.; Assali, L. V. C.

2016-12-01

Equations of state (EoS) are extremely important in several scientific domains. However, many applications require EoS parameters at high pressures and temperatures. Experimental determination of these parameters is limited in such conditions and ab initio calculations have become important in computing them. Density Functional Theory (DFT) with its various approximations for exchange and correlation energy is the method of choice, but lack of a good description of the exchange-correlation energy results in large errors in EoS parameters. It is well known that the alkali halides have been problematic from the onset and the quest for DFT functionals appropriate for such ionic and relatively weakly bonded systems has remained an active topic of research. Here we use DFT + van der Waals functionals to calculate the thermal equation of state and thermodynamic properties of the B1 NaCl phase. Our results show a remarkable improvement over the performance of standard the LDA and GGA functionals. This is hardly surprising given that ions in this system have nearly closed shell configurations.

Cd hyperfine interactions in DNA bases and DNA of mouse strains infected with Trypanosoma cruzi investigated by perturbed angular correlation spectroscopy and ab initio calculations.

PubMed

Petersen, Philippe A D; Silva, Andreia S; Gonçalves, Marcos B; Lapolli, André L; Ferreira, Ana Maria C; Carbonari, Artur W; Petrilli, Helena M

2014-06-03

In this work, perturbed angular correlation (PAC) spectroscopy is used to study differences in the nuclear quadrupole interactions of Cd probes in DNA molecules of mice infected with the Y-strain of Trypanosoma cruzi. The possibility of investigating the local genetic alterations in DNA, which occur along generations of mice infected with T. cruzi, using hyperfine interactions obtained from PAC measurements and density functional theory (DFT) calculations in DNA bases is discussed. A comparison of DFT calculations with PAC measurements could determine the type of Cd coordination in the studied molecules. To the best of our knowledge, this is the first attempt to use DFT calculations and PAC measurements to investigate the local environment of Cd ions bound to DNA bases in mice infected with Chagas disease. The obtained results also allowed the detection of local changes occurring in the DNA molecules of different generations of mice infected with T. cruzi, opening the possibility of using this technique as a complementary tool in the characterization of complicated biological systems.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment.

PubMed

Liu, Hanchao; Wang, Yimin; Bowman, Joel M

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

NASA Astrophysics Data System (ADS)

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-01

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

PubMed

Gendron, Frédéric; Pritchard, Benjamin; Bolvin, Hélène; Autschbach, Jochen

2015-12-14

The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results. Analysis of magnetizations from ab-initio calculations may be useful in assisting research on single molecule magnets.

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

A computational study of Na behavior on graphene

NASA Astrophysics Data System (ADS)

Malyi, Oleksandr I.; Sopiha, Kostiantyn; Kulish, Vadym V.; Tan, Teck L.; Manzhos, Sergei; Persson, Clas

2015-04-01

We present the first ab initio and molecular dynamics study of Na adsorption and diffusion on ideal graphene that considers Na-Na interaction and dispersion forces. From density functional theory (DFT) calculations using the generalized gradient approximation (GGA), the binding energy (vs. the vacuum reference state) of -0.75 eV is higher than the cohesive energy of Na metal (E

Voltage clustering in redox-active ligand complexes: mitigating electronic communication through choice of metal ion

DOE PAGES

Zarkesh, Ryan A.; Ichimura, Andrew S.; Monson, Todd C.; ...

2016-02-01

We used the redox-active bis(imino)acenapthene (BIAN) ligand to synthesize homoleptic aluminum, chromium, and gallium complexes of the general formula (BIAN) 3M. The resulting compounds were characterized using X-ray crystallography, NMR, EPR, magnetic susceptibility and cyclic voltammetry measurements and modeled using both DFT and ab initio wavefunction calculations to compare the orbital contributions of main group elements and transition metals in ligand-based redox events. Ultimately, complexes of this type have the potential to improve the energy density and electrolyte stability of grid-scale energy storage technologies, such as redox flow batteries, through thermodynamically-clustered redox events.

The effective molarity (EM)--a computational approach.

PubMed

Karaman, Rafik

2010-08-01

The effective molarity (EM) for 12 intramolecular S(N)2 processes involving the formation of substituted aziridines and substituted epoxides were computed using ab initio and DFT calculation methods. Strong correlation was found between the calculated effective molarity and the experimentally determined values. This result could open a door for obtaining EM values for intramolecular processes that are difficult to be experimentally provided. Furthermore, the calculation results reveal that the driving forces for ring-closing reactions in the two different systems are proximity orientation of the nucleophile to the electrophile and the ground strain energies of the products and the reactants. Copyright 2010 Elsevier Inc. All rights reserved.

First principle study of UHTC ternary diboride, Cr2AlB2

NASA Astrophysics Data System (ADS)

Rastogi, Anugya; Rajpoot, Priyanka; Verma, U. P.

2018-04-01

In this paper ab-initio study of the structural, electronic and optical properties of ternary metal boride Cr2AlB2 using full potential linear augmented plane wave (FP-LAPW) method based on the density functional theory (DFT). The study of structural properties shows that Cr2AlB2 is metallic in nature and have orthorhombic crystal structure. The optical properties show that it possess anisotropic behavior, which have wide applications in electricity production through concentration of solar power (CSP) technology. To the best of our knowledge, theoretical study of the optical properties of Cr2AlB2 is reported for the first time.

Optimization of a hybrid exchange-correlation functional for silicon carbides

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

Oda, Takuji; Zhang, Yanwen; Weber, William J

2013-01-01

A hybrid exchange-correlation functional is optimized in order to accurately describe the nature of silicon carbides (SiC) in the framework of ab-initio calculations based on density functional theory (DFT), especially with an aim toward future applications in defect studies. It is shown that the Heyd-Scuseria-Ernzerhof (HSE) hybrid functional with the screening parameter of 0.15 -1 outperforms conventional exchange-correlation functionals and other popular hybrid functionals regarding description of band structures in SiC. High transferability is proven through assessment over various SiC polytypes, silicon and diamond. Excellent performance is also confirmed for other fundamental material properties including elastic constants and phonon frequency.

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing... the certificate was issued, and the certificate may be deemed void ab initio. (C) The manufacturer... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing...

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing... the certificate was issued, and the certificate may be deemed void ab initio. (C) The manufacturer... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing...

40 CFR 86.007-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate may be deemed void ab initio. (C) The manufacturer shall bear the burden of establishing to the... be deemed void ab initio. (C) The manufacturer shall bear the burden of establishing to the... of conformity, the Administrator may deem such certificate void ab initio. (4) In any case in which...

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing... the certificate was issued, and the certificate may be deemed void ab initio. (C) The manufacturer... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing...

Structural modeling of Ge6.25As32.5Se61.25 using a combination of reverse Monte Carlo and Ab initio molecular dynamics.

PubMed

Opletal, George; Drumm, Daniel W; Wang, Rong P; Russo, Salvy P

2014-07-03

Ternary glass structures are notoriously difficult to model accurately, and yet prevalent in several modern endeavors. Here, a novel combination of Reverse Monte Carlo (RMC) modeling and ab initio molecular dynamics (MD) is presented, rendering these complicated structures computationally tractable. A case study (Ge6.25As32.5Se61.25 glass) illustrates the effects of ab initio MD quench rates and equilibration temperatures, and the combined approach's efficacy over standard RMC or random insertion methods. Submelting point MD quenches achieve the most stable, realistic models, agreeing with both experimental and fully ab initio results. The simple approach of RMC followed by ab initio geometry optimization provides similar quality to the RMC-MD combination, for far fewer resources.

Calculated electronic, transport, and related properties of zinc blende boron arsenide (zb-BAs)

DOE PAGES

Nwigboji, Ifeanyi H.; Malozovsky, Yuriy; Franklin, Lashounda; ...

2016-10-11

Here, we present the results from ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of zinc blende boron arsenide. We utilized the local density approximation potential of Ceperley and Alder, as parameterized by Vosko and his group, the linear combination of Gaussian orbitals formalism, and the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), in carrying out our completely self-consistent calculations. With this method, the results of our calculations have the full, physical content of density functional theory (DFT). Our results include electronic energy bands, densities of states, effective masses,more » and the bulk modulus. Our calculated, indirect band gap of 1.48 eV, from C to a conduction band minimum close to X, for the room temperature lattice constant of 4.777 Å, is in an excellent agreement with the experimental value of 1.46 6 0.02 eV. We thor-oughly explain the reasons for the excellent agreement between our findings and corresponding, experimental ones. This work provides a confirmation of the capability of DFT to describe accu-rately properties of materials, provides a confirmation of the capability of DFT to describe accu-rately properties of materials, if the computations adhere strictly to the conditions of validity of DFT, as done by the BZW-EF method.« less

The electron affinity of Al13H cluster: high level ab initio study

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2014-11-01

Al13H clusters have been considered candidates for cluster assembled materials. Here we have carried out benchmark calculations for the Al13H cluster, both neutral and anionic, with the aim of verifying the nature of stationary points on the potential energy surface, studying dynamics of H atom and determining an adiabatic electron affinity. A range of correlated methods applied include second-order perturbation theory (MP2), spin-component-scaled MP2, coupled electron pair (CEPA) and coupled cluster singles and doubles with perturbative triple corrections (CCSD(T)). These methods are used in combination with the correlation consistent basis sets through aug-cc-pVTZ including extrapolation to the complete basis set (CBS) limit. Performance of several different flavours of density functional theory (DFT) such as generalised gradient approximation (GGA), hybrid GGA, meta-GGA and hybrid-meta-GGA is assessed with respect to the ab initio correlated reference data. The harmonic force constant analysis is systematically performed with the MP2 and DFT methods. The MP2 results show that for neutral Al13H only the hollow structure is a potential energy minimum, with the bridged structure being a transition state for the H shift from the hollow site to the adjacent hollow site. The CCSD(T)/aug-cc-pVTZ (CCSD(T)/CBS) estimate of the energy barrier to this H shift is 2.6 (2.9) kcal/mol, implying that the H atom movement over the Al13H cluster surface is facile. By contrast, the DFT force constant analysis results suggest additional terminal and bridged minima structures. For the anion Al13H-, exhibiting 'stiffer' potential energy surface compared to the neutral, the existence of the hollow and terminal isomers is consistent with the earlier photoelectron spectroscopy assignment. The adiabatic electron affinity of Al13H is determined to be 2.00 and 1.95 eV (the latter including the ΔZPE correction) based on the CCSD(T) energies extrapolated to the CBS limit, whereas the respective CCSD(T)/CBS thermodynamic EA values are 2.79 and 2.80 eV.

A DFT and ab initio benchmarking study of metal-alkane interactions and the activation of carbon-hydrogen bonds.

PubMed

Flener-Lovitt, Charity; Woon, David E; Dunning, Thom H; Girolami, Gregory S

2010-02-04

Density functional theory and ab initio methods have been used to calculate the structures and energies of minima and transition states for the reactions of methane coordinated to a transition metal. The reactions studied are reversible C-H bond activation of the coordinated methane ligand to form a transition metal methyl hydride complex and dissociation of the coordinated methane ligand. The reaction sequence can be summarized as L(x)M(CH(3))H <==> L(x)M(CH(4)) <==> L(x)M + CH(4), where L(x)M is the osmium-containing fragment (C(5)H(5))Os(R(2)PCH(2)PR(2))(+) and R is H or CH(3). Three-center metal-carbon-hydrogen interactions play an important role in this system. Both basis sets and functionals have been benchmarked in this work, including new correlation consistent basis sets for a third transition series element, osmium. Double zeta quality correlation consistent basis sets yield energies close to those from calculations with quadruple-zeta basis sets, with variations that are smaller than the differences between functionals. The energies of important species on the potential energy surface, calculated by using 10 DFT functionals, are compared both to experimental values and to CCSD(T) single point calculations. Kohn-Sham natural bond orbital descriptions are used to understand the differences between functionals. Older functionals favor electrostatic interactions over weak donor-acceptor interactions and, therefore, are not particularly well suited for describing systems--such as sigma-complexes--in which the latter are dominant. Newer kinetic and dispersion-corrected functionals such as MPW1K and M05-2X provide significantly better descriptions of the bonding interactions, as judged by their ability to predict energies closer to CCSD(T) values. Kohn-Sham and natural bond orbitals are used to differentiate between bonding descriptions. Our evaluations of these basis sets and DFT functionals lead us to recommend the use of dispersion corrected functionals in conjunction with double-zeta or larger basis sets with polarization functions for calculations involving weak interactions, such as those found in sigma-complexes with transition metals.

DFT benchmark study for the oxidative addition of CH 4 to Pd. Performance of various density functionals

NASA Astrophysics Data System (ADS)

de Jong, G. Theodoor; Geerke, Daan P.; Diefenbach, Axel; Matthias Bickelhaupt, F.

2005-06-01

We have evaluated the performance of 24 popular density functionals for describing the potential energy surface (PES) of the archetypal oxidative addition reaction of the methane C-H bond to the palladium atom by comparing the results with our recent ab initio [CCSD(T)] benchmark study of this reaction. The density functionals examined cover the local density approximation (LDA), the generalized gradient approximation (GGA), meta-GGAs as well as hybrid density functional theory. Relativistic effects are accounted for through the zeroth-order regular approximation (ZORA). The basis-set dependence of the density-functional-theory (DFT) results is assessed for the Becke-Lee-Yang-Parr (BLYP) functional using a hierarchical series of Slater-type orbital (STO) basis sets ranging from unpolarized double-ζ (DZ) to quadruply polarized quadruple-ζ quality (QZ4P). Stationary points on the reaction surface have been optimized using various GGA functionals, all of which yield geometries that differ only marginally. Counterpoise-corrected relative energies of stationary points are converged to within a few tenths of a kcal/mol if one uses the doubly polarized triple-ζ (TZ2P) basis set and the basis-set superposition error (BSSE) drops to 0.0 kcal/mol for our largest basis set (QZ4P). Best overall agreement with the ab initio benchmark PES is achieved by functionals of the GGA, meta-GGA, and hybrid-DFT type, with mean absolute errors of 1.3-1.4 kcal/mol and errors in activation energies ranging from +0.8 to -1.4 kcal/mol. Interestingly, the well-known BLYP functional compares very reasonably with an only slightly larger mean absolute error of 2.5 kcal/mol and an underestimation by -1.9 kcal/mol of the overall barrier (i.e., the difference in energy between the TS and the separate reactants). For comparison, with B3LYP we arrive at a mean absolute error of 3.8 kcal/mol and an overestimation of the overall barrier by 4.5 kcal/mol.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

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

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previousmore » spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.« less

Ab initio vel ex eventu

NASA Astrophysics Data System (ADS)

Thiessen, P. A.; Treder, H.-J.

Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

Towards Accurate Ab Initio Predictions of the Spectrum of Methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Kwak, Dochan (Technical Monitor)

2001-01-01

We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

Calculated electronic, transport, and related properties of zinc blende boron arsenide (zb-BAs)

NASA Astrophysics Data System (ADS)

Nwigboji, Ifeanyi H.; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

2016-10-01

We present the results from ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of zinc blende boron arsenide. We utilized the local density approximation potential of Ceperley and Alder, as parameterized by Vosko and his group, the linear combination of Gaussian orbitals formalism, and the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), in carrying out our completely self-consistent calculations. With this method, the results of our calculations have the full, physical content of density functional theory (DFT). Our results include electronic energy bands, densities of states, effective masses, and the bulk modulus. Our calculated, indirect band gap of 1.48 eV, from Γ to a conduction band minimum close to X, for the room temperature lattice constant of 4.777 Å, is in an excellent agreement with the experimental value of 1.46 ± 0.02 eV. We thoroughly explain the reasons for the excellent agreement between our findings and corresponding, experimental ones. This work provides a confirmation of the capability of DFT to describe accurately properties of materials, if the computations adhere strictly to the conditions of validity of DFT, as done by the BZW-EF method.

Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

A Simple ab initio Model for the Hydrated Electron that Matches Experiment

PubMed Central

Kumar, Anil; Walker, Jonathan A.; Bartels, David M.; Sevilla, Michael D.

2015-01-01

Since its discovery over 50 years ago, the “structure” and properties of the hydrated electron has been a subject for wonderment and also fierce debate. In the present work we seriously explore a minimal model for the aqueous electron, consisting of a small water anion cluster embedded in a polarized continuum, using several levels of ab initio calculation and basis set. The minimum energy zero “Kelvin” structure found for any 4-water (or larger) anion cluster, at any post-Hartree-Fock theory level, is very similar to a recently reported embedded-DFT-in-classical-water-MD simulation (UMJ: Uhlig, Marsalek, and Jungwirth, Journal of Physical Chemistry Letters 2012, 3, 3071-5), with four OH bonds oriented toward the maximum charge density in a small central “void”. The minimum calculation with just four water molecules does a remarkably good job of reproducing the resonance Raman properties, the radius of gyration derived from the optical spectrum, the vertical detachment energy, and the hydration free energy. For the first time we also successfully calculate the EPR g-factor and (low temperature ice) hyperfine couplings. The simple tetrahedral anion cluster model conforms very well to experiment, suggesting it does in fact represent the dominant structural motif of the hydrated electron. PMID:26275103

On the transport coefficients of hydrogen in the inertial confinement fusion regime

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

Lambert, Flavien; Recoules, Vanina; Decoster, Alain

2011-05-15

Ab initio molecular dynamics is used to compute the thermal and electrical conductivities of hydrogen from 10 to 160 g cm{sup -3} and temperatures up to 800 eV, i.e., thermodynamical conditions relevant to inertial confinement fusion (ICF). The ionic structure is obtained using molecular dynamics simulations based on an orbital-free treatment for the electrons. The transport properties were computed using ab initio simulations in the DFT/LDA approximation. The thermal and electrical conductivities are evaluated using Kubo-Greenwood formulation. Particular attention is paid to the convergence of electronic transport properties with respect to the number of bands and atoms. These calculations aremore » then used to check various analytical models (Hubbard's, Lee-More's and Ichimaru's) widely used in hydrodynamics simulations of ICF capsule implosions. The Lorenz number, which is the ratio between thermal and electrical conductivities, is also computed and compared to the well-known Wiedemann-Franz law in different regimes ranging from the highly degenerate to the kinetic one. This allows us to deduce electrical conductivity from thermal conductivity for analytical model. We find that the coupling of Hubbard and Spitzer models gives a correct description of the behavior of electrical and thermal conductivities in the whole thermodynamic regime.« less

Ab initio theory of point defects in oxide materials: structure, properties, chemical reactivity

NASA Astrophysics Data System (ADS)

Pacchioni, Gianfranco

2000-05-01

Point defects play a fundamental role in determining the physical and chemical properties of inorganic materials. This holds not only for the bulk properties but also for the surface of oxides where several kinds of point defects exist and exhibit a rich and complex chemistry. A particularly important defect in oxides is the oxygen vacancy. Depending on the electronic structure of the material the nature of oxygen vacancies changes dramatically. In this article we provide a rationalization of the very different electronic structure of neutral and charged oxygen vacancies in SiO 2 and MgO, two oxide materials with completely different electronic structure (from very ionic, MgO, to largely covalent, SiO 2). We used methods of ab initio quantum chemistry, from density functional theory (DFT) to configuration interaction (CI), to determine the ground and excited state properties of these defects. The theoretical results are combined with recent spectroscopic measurements. A series of observable properties has been determined in this way: defect formation energies, hyperfine interactions in electron paramagnetic resonance (EPR) spectra of paramagnetic centers, optical spectra, surface chemical reactivity. The interplay between experimental and theoretical information allows one to unambiguously identify the structure of oxygen vacancies in these binary oxides and on their surfaces.

Ab Initio Molecular Dynamics Study on the Interactions between Carboxylate Ions and Metal Ions in Water.

PubMed

Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Trinh, Thuat T; Grimes, Brian A

2015-08-20

The interaction between a carboxylate anion (deprotonated propanoic acid) and the divalent Mg(2+), Ca(2+), Sr(2+), Ba(2+) metal ions is studied via ab initio molecular dynamics. The main focus of the study is the selectivity of the carboxylate-metal ion interaction in aqueous solution. The interaction is modeled by explicitly accounting for the solvent molecules on a DFT level. The hydration energies of the metal ions along with their diffusion and mobility coefficients are determined and a trend correlated with their ionic radius is found. Subsequently, a series of 16 constrained molecular dynamics simulations for every ion is performed, and the interaction free energy is obtained from thermodynamic integration of the forces between the metal ion and the carboxylate ion. The results indicate that the magnesium ion interacts most strongly with the carboxylate, followed by calcium, strontium, and barium. Because the interaction free energy is not enough to explain the selectivity of the reaction observed experimentally, more detailed analysis is performed on the simulation trajectories to understand the steric changes in the reaction complex during dissociation. The solvent dynamics appear to play an important role during the dissociation of the complex and also in the observed selectivity behavior of the divalent ions.

Perpendicular magnetic anisotropy in Mn2VIn (001) films: An ab initio study

NASA Astrophysics Data System (ADS)

Zipporah, Muthui; Robinson, Musembi; Julius, Mwabora; Arti, Kashyap

2018-05-01

First principles study of the magnetic anisotropy of Mn2VIn (001) films show perpendicular magnetic anisotropy (PMA), which increases as a function of the thickness of the film. Density functional theory (DFT) as implemented in the Vienna Ab initio simulation package (VASP) is employed here to perform a comprehensive theoretical investigation of the structural, electronic and magnetic properties of the Mn2VIn(001) films of varying thickness. Our calculations were performed on fully relaxed structures, with five to seventeen mono layers (ML). The degree of spin polarization is higher in the (001) Mn2VIn thin films as compared to the bulk in contrast to what is usually the case and as in Mn2VAl, which is isoelectronic to Mn2VIn as well as inCo2VIn (001) films studied for comparison. Tetragonal distortions are found in all the systems after relaxation. The distortion in the Mn2VIn system persists even for the 17ML thin film, resulting in PMA in the Mn2VIn system. This significant finding has potential to contribute to spin transfer torque (STT) and magnetic random access memory MRAM applications, as materials with PMA derived from volume magnetocrystalline anisotropy are being proposed as ideal magnetic electrodes.

The modular approach enables a fully ab initio simulation of the contacts between 3D and 2D materials.

PubMed

Fediai, Artem; Ryndyk, Dmitry A; Cuniberti, Gianaurelio

2016-10-05

Up to now, the electrical properties of the contacts between 3D metals and 2D materials have never been computed at a fully ab initio level due to the huge number of atomic orbitals involved in a current path from an electrode to a pristine 2D material. As a result, there are still numerous open questions and controversial theories on the electrical properties of systems with 3D/2D interfaces-for example, the current path and the contact length scalability. Our work provides a first-principles solution to this long-standing problem with the use of the modular approach, a method which rigorously combines a Green function formalism with the density functional theory (DFT) for this particular contact type. The modular approach is a general approach valid for any 3D/2D contact. As an example, we apply it to the most investigated among 3D/2D contacts-metal/graphene contacts-and show its abilities and consistency by comparison with existing experimental data. As it is applicable to any 3D/2D interface, the modular approach allows the engineering of 3D/2D contacts with the pre-defined electrical properties.

Ab Initio Modeling of Structure and Properties of Single and Mixed Alkali Silicate Glasses.

PubMed

Baral, Khagendra; Li, Aize; Ching, Wai-Yim

2017-10-12

A density functional theory (DFT)-based ab initio molecular dynamics (AIMD) has been applied to simulate models of single and mixed alkali silicate glasses with two different molar concentrations of alkali oxides. The structural environments and spatial distributions of alkali ions in the 10 simulated models with 20% and 30% of Li, Na, K and equal proportions of Li-Na and Na-K are studied in detail for subtle variations among the models. Quantum mechanical calculations of electronic structures, interatomic bonding, and mechanical and optical properties are carried out for each of the models, and the results are compared with available experimental observation and other simulations. The calculated results are in good agreement with the experimental data. We have used the novel concept of using the total bond order density (TBOD), a quantum mechanical metric, to characterize internal cohesion in these glass models. The mixed alkali effect (MAE) is visible in the bulk mechanical properties but not obvious in other physical properties studied in this paper. We show that Li doping deviates from expected trend due to the much stronger Li-O bonding than those of Na and K doping. The approach used in this study is in contrast with current studies in alkali-doped silicate glasses based only on geometric characterizations.

Ab initio Hartree-Fock and density functional theory investigations on the conformational stability, molecular structure and vibrational spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one drug molecule.

PubMed

Taşal, Erol; Kumalar, Mustafa

2012-09-01

In this work, the experimental and theoretical spectra of 5-chloro-3-(2-(4-methylpiperazin-1-yl)-2-oxoethyl)benzo[d]thiazol-2(3H)-one molecule (abbreviated as 5CMOT) are studied. The molecular geometry and vibrational frequencies are calculated in the ground state of molecule using ab initio Hartree-Fock (HF) and Density Function Theory (DFT) methods with 6-311++G(d,p), 6-31G++(d,p), 6-31G(d,p), 6-31G(d) and 6-31G basis sets. Three staggered stable conformers were observed on the torsional potential energy surfaces. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes calculated. The comparison of the theoretical and experimental geometries of the title compound indicated that the X-ray parameters fairly well agree with the theoretically obtained values for the most stable conformer. The theoretical results showed an excellent agreement with the experimental values. The calculated HOMO and LUMO energies show that the charge transfer occurs within the molecule. Copyright © 2012 Elsevier B.V. All rights reserved.

Thermal transport properties of bulk and monolayer MoS2: an ab-initio approach

NASA Astrophysics Data System (ADS)

Bano, Amreen; Khare, Preeti; Gaur, N. K.

2017-05-01

The transport properties of semiconductors are key to the performance of many solid-state devices (transistors, data storage, thermoelectric cooling and power generation devices, etc). In recent years simulation tools based on first-principles calculations have been greatly improved, being able to obtain the fundamental ground-state properties of materials accurately. The quasi harmonic thermal properties of bulk and monolayer of MoS2 has been computed with ab initio periodic simulations based of density functional theory (DFT). The temperature dependence of bulk modulus, specific heat, thermal expansion and gruneisen parameter have been calculated in our work within the temperature range of 0K to 900K with projected augmented wave (PAW) method using generalized gradient approximation (GGA). Our results show that the optimized lattice parameters are in good agreement with the earlier reported works and also for thermoelastic parameter, i.e. isothermal bulk modulus (B) at 0K indicates that monolayer MoS2 (48.5 GPa)is more compressible than the bulk structure (159.23 GPa). The thermal expansion of monolayer structure is slightly less than the bulk. Similarly, other parameters like heat capacity and gruneisen parameter shows different nature which is due to the confinement of 3 dimensional structure to 2 dimension (2D) for improving its transport characteristics.

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions.

PubMed

Paton, Robert S; Goodman, Jonathan M

2009-04-01

We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol(-1) for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol(-1). For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.

Ab-initio study of liquid systems: Concentration dependence of electrical resistivity of binary liquid alloy Rb1-xCsx

NASA Astrophysics Data System (ADS)

Thakur, Anil; Sharma, Nalini; Chandel, Surjeet; Ahluwalia, P. K.

2013-02-01

The electrical resistivity (ρL) of Rb1-XCsX binary alloys has been made calculated using Troullier Martins ab-initio pseudopotentials. The present results of the electrical resistivity (ρL) of Rb1-XCsX binary alloys have been found in good agreement with the experimental results. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys. Hence ab-initio pseudopotentials can be used instead of model pseudopotentials having problem of transferability.

Topological Semimetals Studied by Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

2018-04-01

In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.

Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

PubMed

Exner, Kai S; Over, Herbert

2017-05-16

Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a simple ab initio thermodynamics treatment. We show that ab initio thermodynamics leads to erroneous conclusions about kinetic and mechanistic aspects for the CER over RuO 2 (110), while the kinetics of the OER over RuO 2 (110) and ORR over Pt(111) are reasonably well described. Microkinetics of an electrocatalyzed reaction is largely simplified by the quasi-equilibria of the RI preceding the rate-determining step (rds) with the reactants. Therefore, in ab initio kinetics the rate of an electrocatalyzed reaction is governed by the transition state (TS) with the highest free energy G rds # , defining also the rate-determining step (rds). Ab initio thermodynamics may be even more powerful, when using the highest free energy of an reaction intermediate G max (RI) rather than the highest free energy difference between consecutive reaction intermediates, ΔG loss , as a descriptor for the kinetics.

Towards accurate ab initio predictions of the vibrational spectrum of methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.

2002-01-01

We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born-Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

PubMed

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

NASA Astrophysics Data System (ADS)

Miller, Thomas F., III; Clary, David C.

We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of the adrenaline molecule.

HPAM: Hirshfeld Partitioned Atomic Multipoles

PubMed Central

Elking, Dennis M.; Perera, Lalith; Pedersen, Lee G.

2011-01-01

An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank lmax on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from lmax = 0 (atomic charges) to lmax = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank lmax are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ lmax. In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (lmax = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used. PMID:22140274

On the incorporation of the geometric phase in general single potential energy surface dynamics: A removable approximation to ab initio data.

PubMed

Malbon, Christopher L; Zhu, Xiaolei; Guo, Hua; Yarkony, David R

2016-12-21

For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian H d (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the H d by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding H d determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.

Investigation of the Fe{sup 3+} centers in perovskite KMgF{sub 3} through a combination of ab initio (density functional theory) and semi-empirical (superposition model) calculations

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

Emül, Y.; Department of Software Engineering, Cumhuriyet University, 58140 Sivas; Erbahar, D.

2015-08-14

Analyses of the local crystal and electronic structure in the vicinity of Fe{sup 3+} centers in perovskite KMgF{sub 3} crystal have been carried out in a comprehensive manner. A combination of density functional theory (DFT) and a semi-empirical superposition model (SPM) is used for a complete analysis of all Fe{sup 3+} centers in this study for the first time. Some quantitative information has been derived from the DFT calculations on both the electronic structure and the local geometry around Fe{sup 3+} centers. All of the trigonal (K-vacancy case, K-Li substitution case, and normal trigonal Fe{sup 3+} center case), FeF{sub 5}Omore » cluster, and tetragonal (Mg-vacancy and Mg-Li substitution cases) centers have been taken into account based on the previously suggested experimental and theoretical inferences. The collaboration between the experimental data and the results of both DFT and SPM calculations provides us to understand most probable structural model for Fe{sup 3+} centers in KMgF{sub 3}.« less

Modeling of a Tröger’s tweezer and its complexation properties

NASA Astrophysics Data System (ADS)

Parchaňský, Václav; Matějka, Pavel; Dolenský, Bohumil; Havlík, Martin; Bouř, Petr

2009-09-01

Molecular tweezers attracted attention because of their potential to selectively bind important chemicals, which can be utilized in medicine or in pollution treatment. In this study, the aromatic binding properties of a recently synthesized tweezer based on the Tröger's base and its complex with nitrobenzene are investigated ab initio, using the DFT and MP2 computations. The predicted geometries and energies of the complex with nitrobenzene are well comparable with the experimental data. The B3LYP and BPW91 functionals did not provide a stable binding, in contrast to the observation. Only addition of the empirical Grimme correction for the van der Waals forces, not present in conventional DFT, yielded results consistent with the experiment, MP2 computations, and similar benchmark models. The correction also caused minor improvements of the Raman and infrared spectra, but not in the entire region of vibrational frequencies. The results suggest that the role of the electrostatic interaction in the investigated complex is minor and the interaction stabilization is driven by the contact area between the polarizable aromatic systems. The vdW-DFT method thus provides an efficient tool for the rational synthesis of the complexes.

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.

Band-edge engineering of Silicon by Surface Functionalization: a Combined Ab-initio and Photoemission Study

NASA Astrophysics Data System (ADS)

Li, Yan; O'Leary, Leslie; Lewis, Nathan; Galli, Giulia

2012-02-01

The electrode material choice is limited in solar to fuel formation devices because of the requirement of band-edge matching to the fixed fuel formation potential. This limitation can be relieved via band-edge engineering. The changes of band-edge positions of Si electrodes induced by the adsorption of H-, Cl-, Br- and short-chain alkyl groups were investigated by combining density functional (DFT), many-body perturbation theory (MBPT), and ultraviolet photoelectron spectroscopy. The band edge shifts are related to the formation of surface dipole moments, and determine the barrier height of electrons and holes in doped silicon surfaces. We find that the trends of the sign and magnitude of the computed surface dipoles as a function of the adsorbate may be explained by simple electronegative rules. We show that quasi-particle energies obtained within MBPT are in good agreement with experiment, while DFT values may exhibit substantial errors. However computed band edge differences are in good agreement with spectroscopic and electrical measurements even at the DFT level of theory. [1] Y. Li and G. Galli, Phys. Rev. B 82, 045321 (2010). [2] Y. Li, L. O'Leary, N. Lewis and G. Galli, to be submitted.

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.

Ab Initio High Pressure and Temperature Investigation on Cubic PbMoO3 Perovskite

NASA Astrophysics Data System (ADS)

Dar, Sajad Ahmad; Srivastava, Vipul; Sakalle, Umesh Kumar

2017-12-01

A combined high pressure and temperature investigation on recently reported cubic perovskite PbMoO3 have been performed within the most accurate density functional theory (DFT). The structure was found stable in cubic paramagnetic phase. The DFT calculated analytical and experimental lattice constant were found in good agreement. The analytical tolerance factor as well as the elastic properties further verifies the cubic stability for PbMoO3. The spin polarized electronic band structure and density of states presented metallic nature with symmetry in up and down states. The insignificant magnetic moment also confirms the paramagnetic nature for the compound. The high pressure elastic and mechanical study up to 35 GPa reveal the structural stability of the material in this pressure range. The compound was found to establish a ductile nature. The electrical conductivity obtained from the band structure results show a decreasing trend with increasing temperature. The temperature dependence of thermodynamic parameters such as specific heat ( C v), thermal expansion ( α) has also been evaluated.

Phonon properties and slow organic-to-inorganic sub-lattice thermalization in hybrid perovskites

NASA Astrophysics Data System (ADS)

Chan, Maria; Chang, Angela; Xia, Yi; Sadasivam, Sridhar; Guo, Peijun; Kinaci, Alper; Lin, Hao-Wu; Darancet, Pierre; Schaller, Richard

Organic-inorganic hybrid perovskite halide compounds have been investigated extensively for photovoltaics (PVs) and related applications. The thermal transport properties of hybrid perovskites, including phonon-carrier and phonon-phonon interactions, are of significance for their PV and solar thermoelectric applications. The interlocking organic and inorganic sublattices can be thought of as an extreme form of nanostructuring. A result of this nanostructuring is the large gap in phonon frequencies between the organic and inorganic sublattices, which is expected to create bottlenecks in phonon equilibration. In this work, we use a combination of ultrafast spectroscopy including photoluminescence and transient absorption, as well as first principles density functional theory (DFT), ab initio molecular dynamics calculations, phonon lifetimes derived from DFT force constants, and non-equilibrium phonon dynamics accounting for phonon lifetimes, to determine the phonon and charge interaction processes. We find evidence that thermalization of carriers occur at an atypically slow 50-100 ps time scale owing to the complex interplay between electronic and phonon excitations.

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.

Spin polarized electronic states and spin textures at the surface of oxygen-deficient SrTiO3

NASA Astrophysics Data System (ADS)

Jeschke, Harald O.; Altmeyer, Michaela; Rozenberg, Marcelo; Gabay, Marc; Valenti, Roser

We investigate the electronic structure and spin texture at the (001) surface of SrTiO3 in the presence of oxygen vacancies by means of ab initio density functional theory (DFT) calculations of slabs. Relativistic non-magnetic DFT calculations exhibit Rashba-like spin winding with a characteristic energy scale ~ 10 meV. However, when surface magnetism on the Ti ions is included, bands become spin-split with an energy difference ~ 100 meV at the Γ point. This energy scale is comparable to the observations in SARPES experiments performed on the two-dimensional electronic states confined near the (001) surface of SrTiO3. We find the spin polarized state to be the ground state of the system, and while magnetism tends to suppress the effects of the relativistic Rashba interaction, signatures of it are still clearly visible in terms of complex spin textures. We gratefully acknowledge financial support from the Deutsche Forschungsgemeinschaft through grants SFB/TR 49 and FOR 1346.

Silicon Framework Allotropes for Li-ion and Na-ion Batteries: New Insight for a Reversible Capacity.

NASA Astrophysics Data System (ADS)

Marzouk, Asma; Soto, Fernando; Burgos, Juan; Balbuena, Perla; El-Mellouhi, Fadwa

Silicon has the capacity to host a large amount of Li which makes it an attractive anode material despite suffering from swelling problem leading to irreversible capacity loss. The possibility of an easy extraction of Na atoms from Si24Na4 inspired us to adopt the Si24 as an anode material for Lithium-ion and sodium-ion Batteries. Using DFT, we evaluate the specific capacity and the intercalation potential of Si24 allotrope. Enhanced capacities are sought by designing a new silicon allotrope. We demonstrated that these Si24 allotropes show a negligible volume expansion and conserve their periodic structures after the maximum insertion/disinsertion of the ions which is crucial to prevent the capacity loss during cycling. DFT and ab-initio molecular dynamics (AIMD) studies give insights on the most probable surface adsorption and reaction sites, lithiation and sodiation, as well as initial stages of SEI formation and ionic diffusion. Qatar National Research Fund (QNRF) (NPRP 7-162-2-077).

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

PubMed

Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

2018-01-18

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

Stability of Hydrocarbons of the Polyhedrane Family: Convergence of ab Initio Calculations and Corresponding Assessment of DFT Main Approximations.

PubMed

Sancho-García, J C

2011-09-13

Highly accurate coupled-cluster (CC) calculations with large basis sets have been performed to study the binding energy of the (CH)12, (CH)16, (CH)20, and (CH)24 polyhedral hydrocarbons in two, cage-like and planar, forms. We also considered the effect of other minor contributions: core-correlation, relativistic corrections, and extrapolations to the limit of the full CC expansion. Thus, chemically accurate values could be obtained for these complicated systems. These nearly exact results are used to evaluate next the performance of main approximations (i.e., pure, hybrid, and double-hybrid methods) within density functional theory (DFT) in a systematic fashion. Some commonly used functionals, including the B3LYP model, are affected by large errors, and only those having reduced self-interaction error (SIE), which includes the last family of conjectured expressions (double hybrids), are able to achieve reasonable low deviations of 1-2 kcal/mol especially when an estimate for dispersion interactions is also added.

Methods and Strategies for the Ab Initio Design of Novel Manganese Oxide- Based Water Splitting Photocatalyst Materials

NASA Astrophysics Data System (ADS)

Kanan, Dalal K.

Photoelectrochemical cells (PECs) use sunlight to drive endoergic reactions such as carbon dioxide reduction to fuels or water-splitting for renewable hydrogen production. However, materials that combine both the efficiency and low cost needed to make solar-powered catalysis a practical reality have yet to be discovered. This thesis presents methods and new design strategies for developing novel, efficient, robust, and inexpensive photocatalysts based on transition metal oxides (TMOs). Quantum mechanics methodologies are developed and tested for their ability to predict the properties of known materials and then used to predict how altering the composition by alloying and doping with abundant elements affects optical, electronic, transport, and catalytic properties. The first material considered for photocatalysis is MnO, the bio-inspired solid state analogue of the photosystem II active site. GW theory with input from hybrid DFT and ab initio DFT+U capably predicts the photoemission/inverse photoemission (PE/IPE) band gap and dielectric properties. An ab initio value of U-J = 3.5 eV for Mn2+ was determined using unrestricted Hartree-Fock theory on cluster-size-converged electrostatically embedded clusters. The lowest-lying excitations in MnO, studied using ECW theory, are found to be single Mn d → d ligand field excitations (~2.5 eV, ~108 s lifetime), followed by double d → d excitations (~5.2 eV, ~106 s lifetime), Mn 3d-4s excitations (~6.3 eV, ~10-3 s lifetime), and higher-lying O 2p → Mn 3d ligand-to-metal charge-transfer (LMCT) excitations (~10.1 eV, ~10-4 s lifetime). The longer-lived transitions should exhibit better electron-hole pair separation and enhance photoconductivity depending on ease of carrier transport. While MnO possesses suitable band edge energies, its band gap is too large for efficient sunlight absorption. We predict alloying MnO with ZnO in varying amounts reduces the PE/IPE band gap (to 2.6 eV for the 1:1 alloy) while preserving potential redox reactivity. Optical excitation studies show alloying lowers the LMCT transition to ~8.3 eV leaving all other absorption properties relatively unchanged. We find near degeneracies among spin-allowed and spin-forbidden LMCT states that could facilitate intersystem crossing (ISC) resulting in longer lifetimes. We suggest seeking other materials that exhibit similar LMCT excitations but that are visible-light activated as a design strategy for further enhancing photon conversion efficiencies. Additionally, several dopants (Al, Ga, In, Sc, Y, Ti, Sb, Gd, F (n-type dopants) and Li (a p-type dopant)) were assessed for their ability to enhance conductivity in MnO:ZnO. We find Ga, Sc, Ti, F, and Sb dopants create deep traps whereas In forms shallower traps that merit further investigation. In contrast, Y, Al, Gd, and Li dopants should increase the carrier concentration while maintaining favorable electron and hole transport pathways. The adsorption and oxidation of water on MnO:ZnO(001) surface was studied with ab initio DFT+U calculations. The computed phase diagram for the water/MnO:ZnO(001) interface reveals the surface is quite hydrophilic with the half-dissociated 1 ML (2 ML) structure being most stable under water-poor (water-rich) conditions. For the gas phase water oxidation reaction, we compute a thermodynamic overpotential of 0.82 V without yet modeling reaction kinetics or solvation. The overpotential mainly results from the *OOH intermediate being too weakly bound to the surface because of a loss of resonance stabilization in the adsorbate. We suggest judicious doping as a way to stabilize *OOH and potentially reduce the overpotential to just 0.05 V (for 0.5 ML reaction coverage). (Abstract shortened by UMI.)

libvdwxc: a library for exchange-correlation functionals in the vdW-DF family

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Kuisma, Mikael; Löfgren, Joakim; Pouillon, Yann; Erhart, Paul; Hyldgaard, Per

2017-09-01

We present libvdwxc, a general library for evaluating the energy and potential for the family of vdW-DF exchange-correlation functionals. libvdwxc is written in C and provides an efficient implementation of the vdW-DF method and can be interfaced with various general-purpose DFT codes. Currently, the Gpaw and Octopus codes implement interfaces to libvdwxc. The present implementation emphasizes scalability and parallel performance, and thereby enables ab initio calculations of nanometer-scale complexes. The numerical accuracy is benchmarked on the S22 test set whereas parallel performance is benchmarked on ligand-protected gold nanoparticles ({{Au}}144{({{SC}}11{{NH}}25)}60) up to 9696 atoms.

Molecules for organic electronics studied one by one.

PubMed

Meyer, Jörg; Wadewitz, Anja; Lokamani; Toher, Cormac; Gresser, Roland; Leo, Karl; Riede, Moritz; Moresco, Francesca; Cuniberti, Gianaurelio

2011-08-28

The electronic and geometrical structure of single difluoro-bora-1,3,5,7-tetraphenyl-aza-dipyrromethene (aza-BODIPY) molecules adsorbed on the Au(111) surface is investigated by low temperature scanning tunneling microscopy and spectroscopy in conjunction with ab initio density functional theory simulations of the density of states and of the interaction with the substrate. Our DFT calculations indicate that the aza-bodipy molecule forms a chemical bond with the Au(111) substrate, with distortion of the molecular geometry and significant charge transfer between the molecule and the substrate. Nevertheless, most likely due to the low corrugation of the Au(111) surface, diffusion of the molecule is observed for applied bias in excess of 1 V.

Ab-initio thermodynamic and elastic properties of AlNi and AlNi3 intermetallic compounds

NASA Astrophysics Data System (ADS)

Yalameha, Shahram; Vaez, Aminollah

2018-04-01

In this paper, thermodynamic and elastic properties of the AlNi and AlNi3 were investigated using density functional theory (DFT). The full-potential linearized augmented plane-wave (APW) in the framework of the generalized gradient approximation as used as implemented in the Wien2k package. The temperature dependence of thermal expansion coefficient, bulk modulus and heat capacity in a wide range of temperature (0-1600 K) were investigated. The calculated elastic properties of the compounds show that both intermetallic compounds of AlNi and AlNi3 have surprisingly negative Poisson’s ratio (NPR). The results were compared with other experimental and computational data.

Metallic → Semiconducting transitions in HX(X=F, Br, Cl) adsorbed (5,5) and (7,7) carbon nanotubes: DFT study

NASA Astrophysics Data System (ADS)

Srivastava, Reena; Shrivastava, Sadhana; Srivastava, Anurag

2018-05-01

The edge sensitivity of two different chirality (5,5) and (7,7) armchair carbon nanotubes towards toxic hydrogen halides (HF, HBr and HCl) has been analyzed by using density functional theory based ab-initio approach. The edge sensitivity has been discussed in terms of the variations in the electronic band structure of (5,5) and (7,7) carbon nanotube. The observation shows metallic to semiconducting phase transition in HF and HBr adsorbed (5,5) CNT, whereas for HCl adsorbed, it is more metallic. Whereas HBr and HCl adsorbed (7,7) CNT confirms metallic→semiconducting transition and shows diameter dependence of properties of CNTs.

On real-space Density Functional Theory for non-orthogonal crystal systems: Kronecker product formulation of the kinetic energy operator

NASA Astrophysics Data System (ADS)

Sharma, Abhiraj; Suryanarayana, Phanish

2018-05-01

We present an accurate and efficient real-space Density Functional Theory (DFT) framework for the ab initio study of non-orthogonal crystal systems. Specifically, employing a local reformulation of the electrostatics, we develop a novel Kronecker product formulation of the real-space kinetic energy operator that significantly reduces the number of operations associated with the Laplacian-vector multiplication, the dominant cost in practical computations. In particular, we reduce the scaling with respect to finite-difference order from quadratic to linear, thereby significantly bridging the gap in computational cost between non-orthogonal and orthogonal systems. We verify the accuracy and efficiency of the proposed methodology through selected examples.

Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2004-01-01

We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Structural predictions for Correlated Electron Materials Using the Functional Dynamical Mean Field Theory Approach

NASA Astrophysics Data System (ADS)

Haule, Kristjan

2018-04-01

The Dynamical Mean Field Theory (DMFT) in combination with the band structure methods has been able to address reach physics of correlated materials, such as the fluctuating local moments, spin and orbital fluctuations, atomic multiplet physics and band formation on equal footing. Recently it is getting increasingly recognized that more predictive ab-initio theory of correlated systems needs to also address the feedback effect of the correlated electronic structure on the ionic positions, as the metal-insulator transition is almost always accompanied with considerable structural distortions. We will review recently developed extension of merger between the Density Functional Theory (DFT) and DMFT method, dubbed DFT+ embedded DMFT (DFT+eDMFT), whichsuccessfully addresses this challenge. It is based on the stationary Luttinger-Ward functional to minimize the numerical error, it subtracts the exact double-counting of DFT and DMFT, and implements self-consistent forces on all atoms in the unit cell. In a few examples, we will also show how the method elucidated the important feedback effect of correlations on crystal structure in rare earth nickelates to explain the mechanism of the metal-insulator transition. The method showed that such feedback effect is also essential to understand the dynamic stability of the high-temperature body-centered cubic phase of elemental iron, and in particular it predicted strong enhancement of the electron-phonon coupling over DFT values in FeSe, which was very recently verified by pioneering time-domain experiment.

Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

On the Interaction between Carbon Dioxide and Nanomaterials with High Accuracy ab initio and DFT Calculations

NASA Astrophysics Data System (ADS)

Vogiatzis, Konstantinos D.; Mavrandonakis, Antreas; Klopper, Wim; Froudakis, George

2009-08-01

The separation, capture and storage of carbon dioxide from the flue gas is an environmental and economical problem of significant importance. Zeolites and activated carbons have been used from the industries in order to reduce the emissions of CO2. A new family of materials, the metal-organic frameworks (MOFs), has been recently proposed as an efficient substitute of the abovementioned materials. In particular, materials based on zinc complexes with imidazo-like aromatic compounds which builds frameworks similar with those of Zeolites (Zeolite-Imidazolium Frameworks, ZIFs), have the potential for efficient separation of CO2 from CO and CH4. [1]. Weak interactions between carbon dioxide and heterocyclic aromatic compounds are being examined with high accuracy ab initio methods. CO2 has zero dipole moment but a significant quadrupole moment enables it to operate as a weak acid or weak base, according to his environment. Nitrogen-containing aromatic compounds act as electron donors, while CO2 acts as an electron acceptor. Electrostatic interactions induce a non-permanent dipole moment on CO2 and the complex is stabilized by in-plane hydrogen bonds between the charged oxygens of CO2 and nearby hydrogen of the aromatic molecule. In addition, dispersion forces from the electron correlation contribute to the interaction energy. By using explicitly correlated methods (MP2-F12/aug-cc-pVTZ) [2] and by adding the contribution from the triples excitations, calculated with a smaller basis (6-311++G**), we reach to an approximate CCSD(T) complete basis set result. [3] Extrapolation schemes were used in order to reach the MP2 basis set limit and compare it with the CCSD(T)/CBS result. Those results are in excellent agreement with the explicitly correlated MP2-F12. In addition, our complexes are being investigated with DFT methods that calculate separately the dispersion energy (DFT-D) [4] and modified MP2 which scaling of spin pair correlation [5]. DFT-D results are in good agreement with CCSD(T)/CBS results, providing us a computational cheap method with high accuracy. The quantization of the interaction is examined by changing the aromaticity of the heterocyclic molecules and by talking into account the electron correlation. [6] The electron density of the nitrogen that binds CO2 is gradually decreasing by substituting carbons with nitrogens in pyridine (pyrimidine, pyrazine, triazine), leading to lower binding energy.

Ab initio MD simulations of Mg2SiO4 liquid at high pressures and temperatures relevant to the Earth's mantle

NASA Astrophysics Data System (ADS)

Martin, G. B.; Kirtman, B.; Spera, F. J.

2010-12-01

Computational studies implementing Density Functional Theory (DFT) methods have become very popular in the Materials Sciences in recent years. DFT codes are now used routinely to simulate properties of geomaterials—mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only 100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it would be useful to be able to compute larger systems especially for extracting transport properties and coordination statistics. Previous studies have used codes such as VASP where CPU time increases as N2, making calculations on systems of more than 100 atoms computationally very taxing. SIESTA (Soler, et al. 2002) is a an order-N (linear-scaling) DFT code that enables electronic structure and MD computations on larger systems (N 1000) by making approximations such as localized numerical orbitals. Here we test the applicability of SIESTA to simulate geosilicates in the liquid and glass state. We have used SIESTA for MD simulations of liquid Mg2SiO4 at various state points pertinent to the Earth’s mantle and congruous with those calculated in a previous DFT study using the VASP code (DeKoker, et al. 2008). The core electronic wave functions of Mg, Si, and O were approximated using pseudopotentials with a core cutoff radius of 1.38, 1.0, and 0.61 Angstroms respectively. The Ceperly-Alder parameterization of the Local Density Approximation (LDA) was used as the exchange-correlation functional. Known systematic overbinding of LDA was corrected with the addition of a pressure term, P 1.6 GPa, which is the pressure calculated by SIESTA at the experimental zero-pressure volume of forsterite under static conditions (Stixrude and Lithgow-Bertollini 2005). Results are reported here that show SIESTA calculations of T and P on densities in the range of 2.7 - 5.0 g/cc of liquid Mg2SiO4 are similar to the VASP calculations of DeKoker et al. (2008), which used the same functional. This opens the possibility of conducting fast /emph{ab initio} MD simulations of geomaterials with a hundreds of atoms.

Search for effective spin injection heterostructures based on half-metal Heusler alloys/gallium arsenide semiconductors: A theoretical investigation

NASA Astrophysics Data System (ADS)

Sivakumar, Chockalingam

Efficient electrical spin injection from half-metal (HM) electrodes into semiconducting (SC) channel material is a desirable aspect in spintronics, but a challenging one. Half-metals based on the Heusler alloy family are promising candidates as spin sources due to their compatibility with compound SCs, and very high Curie temperatures. Numerous efforts were made in the past two decades to grow atomically abrupt interfaces between HM_Heusler and SC heterostructures. However, diffusion of magnetic impurities into the semiconductor, defects and disorder near the interface, and formation of reacted phases were great challenges. A number of theoretical efforts were undertaken to understand the role of such material defects in destroying the half-metallicity and also to propose promising half-metal/SC heterostructures based on first principles. This dissertation summarizes the investigations undertaken to decode the complexity of, and to understand the various physical properties of, a number of real-world Heusler/SC heterostructure samples, based on the ab initio density functional theory (DFT) approach. In addition, it summarizes various results from the first principles-based search for promising half-metal/SC heterostructures. First, I present results from DFT-based predictive models of actual Co 2MnSi (CMS)/GaAs heterostructures grown in (001) texture. I investigate the physical, chemical, electronic, and magnetic properties to understand the complexity of these structures and to pinpoint the origin of interfacial effects, when present. Based on the investigations of such models, I discuss the utility of those actual samples in spintronic applications. Next, I summarise the results from an ab initio DFT-based survey of 6 half-Heusler half-metal/GaAs heterostructure models in (110) texture, since compound semiconductors such as GaAs have very long spin lifetime in (110) layering. I show 3 half-Heusler alloys (CoVAs, NiMnAs, and RhFeGe), that when interfaced with GaAs(110), fully preserve the half-metallicity at the interface. Finally, I show the advantages of inserting half-Heusler SCs, particularly CoTiAs and CoTiSb, as spacers in between CMS/GaAs systems in (110) layering. Based on DFT calculations, I show that CoTiAs is a promising spacer that could enhance the perpendicular magnetic anisotropy in CMS, while preserving the important half-metallic character at the heterojunctions between CMS/CoTiAs/GaAs(110). This spacer could also serve to prevent in-diffusion of magnetic impurities into the channel material.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction.

PubMed

Brasil, Christiane Regina Soares; Delbem, Alexandre Claudio Botazzo; da Silva, Fernando Luís Barroso

2013-07-30

This article focuses on the development of an approach for ab initio protein structure prediction (PSP) without using any earlier knowledge from similar protein structures, as fragment-based statistics or inference of secondary structures. Such an approach is called purely ab initio prediction. The article shows that well-designed multiobjective evolutionary algorithms can predict relevant protein structures in a purely ab initio way. One challenge for purely ab initio PSP is the prediction of structures with β-sheets. To work with such proteins, this research has also developed procedures to efficiently estimate hydrogen bond and solvation contribution energies. Considering van der Waals, electrostatic, hydrogen bond, and solvation contribution energies, the PSP is a problem with four energetic terms to be minimized. Each interaction energy term can be considered an objective of an optimization method. Combinatorial problems with four objectives have been considered too complex for the available multiobjective optimization (MOO) methods. The proposed approach, called "Multiobjective evolutionary algorithms with many tables" (MEAMT), can efficiently deal with four objectives through the combination thereof, performing a more adequate sampling of the objective space. Therefore, this method can better map the promising regions in this space, predicting structures in a purely ab initio way. In other words, MEAMT is an efficient optimization method for MOO, which explores simultaneously the search space as well as the objective space. MEAMT can predict structures with one or two domains with RMSDs comparable to values obtained by recently developed ab initio methods (GAPFCG , I-PAES, and Quark) that use different levels of earlier knowledge. Copyright © 2013 Wiley Periodicals, Inc.

Electronic absorption, vibrational spectra, nonlinear optical properties, NBO analysis and thermodynamic properties of N-(4-nitro-2-phenoxyphenyl) methanesulfonamide molecule by ab initio HF and density functional methods.

PubMed

Rajamani, T; Muthu, S; Karabacak, M

2013-05-01

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 4000-100 cm(-1) and 4000-400 cm(-1), respectively, for N-(4-nitro-2-phenoxyphenyl) methanesulfonamide molecule. Theoretical calculations were performed by ab initio RHF and density functional theory (DFT) method using 6-31G(d,p) and 6-311G(d,p) basis sets. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The frontier orbital energy gap and dipole moment illustrates the high reactivity of the title molecule. The first order hyperpolarizability (β0) and related properties (μ, α and Δα) of the molecule were also calculated. Stability of the molecule arising from hyperconjugative interactions and charge delocalization were analyzed using natural bond orbital (NBO) analysis. The results show that electron density (ED) in the σ(*) and π(*) anti-bonding orbitals and second order delocalization energies (E2) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. UV-vis spectrum of the compound was recorded in the region 200-500 nm in ethanol and electronic properties such as excitation energies, oscillator strength and wavelength were calculated by TD-DFT/B3LYP, CIS and TD-HF methods using 6-31G(d,p) basis set. Molecular electrostatic potential (MEP) and HOMO-LUMO energy levels are also constructed. The thermodynamic properties of the title compound were calculated at different temperatures and the results reveals the heat capacity (C), and entropy (S) increases with rise in temperature. Copyright © 2013 Elsevier B.V. All rights reserved.

Ab initio Quantum Chemical and Experimental Reaction Kinetics Studies in the Combustion of Bipropellants

DTIC Science & Technology

2017-03-24

NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for

An ab initio study of the conformational energy map of acetylcholine

NASA Astrophysics Data System (ADS)

Segall, M. D.; Payne, M. C.; Boyes, R. N.

An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans , gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.

A computational ab initio study of surface diffusion of sulfur on the CdTe (111) surface

NASA Astrophysics Data System (ADS)

Naderi, Ebadollah; Ghaisas, S. V.

2016-08-01

In order to discern the formation of epitaxial growth of CdS shell over CdTe nanocrystals, kinetics related to the initial stages of the growth of CdS on CdTe is investigated using ab-initio methods. We report diffusion of sulfur adatom on the CdTe (111) A-type (Cd-terminated) and B-type (Te-terminated) surfaces within the density functional theory (DFT). The barriers are computed by applying the climbing Nudge Elastic Band (c-NEB) method. From the results surface hopping emerges as the major mode of diffusion. In addition, there is a distinct contribution from kick-out type diffusion in which a CdTe surface atom is kicked out from its position and is replaced by the diffusing sulfur atom. Also, surface vacancy substitution contributes to the concomitant dynamics. There are sites on the B- type surface that are competitively close in terms of the binding energy to the lowest energy site of epitaxy on the surface. The kick-out process is more likely for B-type surface where a Te atom of the surface is displaced by a sulfur adatom. Further, on the B-type surface, subsurface migration of sulfur is indicated. Furthermore, the binding energies of S on CdTe reveal that on the A-type surface, epitaxial sites provide relatively higher binding energies and barriers than on B-type.

A computational ab initio study of surface diffusion of sulfur on the CdTe (111) surface

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

Naderi, Ebadollah, E-mail: enaderi42@gmail.com; Ghaisas, S. V.

2016-08-15

In order to discern the formation of epitaxial growth of CdS shell over CdTe nanocrystals, kinetics related to the initial stages of the growth of CdS on CdTe is investigated using ab-initio methods. We report diffusion of sulfur adatom on the CdTe (111) A-type (Cd-terminated) and B-type (Te-terminated) surfaces within the density functional theory (DFT). The barriers are computed by applying the climbing Nudge Elastic Band (c-NEB) method. From the results surface hopping emerges as the major mode of diffusion. In addition, there is a distinct contribution from kick-out type diffusion in which a CdTe surface atom is kicked outmore » from its position and is replaced by the diffusing sulfur atom. Also, surface vacancy substitution contributes to the concomitant dynamics. There are sites on the B- type surface that are competitively close in terms of the binding energy to the lowest energy site of epitaxy on the surface. The kick-out process is more likely for B-type surface where a Te atom of the surface is displaced by a sulfur adatom. Further, on the B-type surface, subsurface migration of sulfur is indicated. Furthermore, the binding energies of S on CdTe reveal that on the A-type surface, epitaxial sites provide relatively higher binding energies and barriers than on B-type.« less

Large scale Full QM-MD investigation of small peptides and insulin adsorption on ideal and defective TiO2 (1 0 0) surfaces. Influence of peptide size on interfacial bonds

NASA Astrophysics Data System (ADS)

Dubot, Pierre; Boisseau, Nicolas; Cenedese, Pierre

2018-05-01

Large biomolecule interaction with oxide surface has attracted a lot of attention because it drives behavior of implanted devices in the living body. To investigate the role of TiO2 surface structure on a large polypeptide (insulin) adsorption, we use a homemade mixed Molecular Dynamics-Full large scale Quantum Mechanics code. A specific re-parameterized (Ti) and globally convergent NDDO method fitted on high level ab initio method (coupled cluster CCSD(T) and DFT) allows us to safely describe the electronic structure of the whole insulin-TiO2 surface system (up to 4000 atoms). Looking specifically at carboxylate residues, we demonstrate in this work that specific interfacial bonds are obtained from the insulin/TiO2 system that are not observed in the case of smaller peptides (tripeptides, insulin segment chains with different configurations). We also demonstrate that a large part of the adsorption energy is compensated by insulin conformational energy changes and surface defects enhanced this trend. Large slab dimensions allow us to take into account surface defects that are actually beyond ab initio capabilities owing to size effect. These results highlight the influence of the surface structure on the conformation and therefore of the possible inactivity of an adsorbed polypeptides.

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.

PubMed

Dobes, Petr; Otyepka, Michal; Strnad, Miroslav; Hobza, Pavel

2006-05-24

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.

Infrared signature of micro-hydration in the organophosphate sarin: An ab initio study

DOE PAGES

Alam, Todd M.; Pearce, Charles Joseph

2015-06-28

The infrared (IR) spectra of micro-hydrated Sarin•(H 2O) n clusters containing between one and four explicit waters have been studied using ab initio density functional theory (DFT) methods. The phosphate group P=O bond vibration region (~1270 to 1290 cm –1) revealed the largest frequency variation with hydration, with a frequency red shift reflecting the direct hydrogen bond formation between the P=O of Sarin and water. Small variations to the P-F stretch (~810 to 815 cm –1) and the C-O-P vibrational modes (~995 to 1004 cm –1) showed that the water interactions with these functional groups were minor, and that themore » structures of Sarin were not extensively perturbed in the hydrated complexes. Increasing the number of explicit hydration waters produced only small vibrational changes in the lowest free energy complexes. These minor changes were consistent with a single water-phosphate hydrogen bond being the dominant structure, though a second water-phosphate hydrogen bond was observed in some complexes and was identified by an additional red shift of the P=O bond vibration. As a result, the H 2O•H 2O vibrational modes (~3450 to 3660 cm –1) increased in complexity with higher hydration levels and reflect the extended hydrogen bonding networks formed between the explicit waters in the hydrated Sarin clusters.« less

Etude de l'electrocatalyse de la reduction de l'oxygene sur des alliages de palladium cuivre

NASA Astrophysics Data System (ADS)

Fouda-Onana, Frederic

This thesis is on the development of the ORR on Pd-Cu alloys in acid medium. Density Functional Theory (DFT) was used to determine the intrinsic properties of the alloys. The alloys were fabricated by RF sputtering on glassy carbon support and chemical salt reduction on carbon support. They characterised by electrochemical methods and correlations were made between the intrinsic properties and the experimental electrochemical parameters. These correlations were used to explain the electrocatalytic performance of the ORR on these aklooys and to determine the mechanism of this reaction on these electrocatalysts. Accordingly the following aspects were studied in details. In the first step, ab initio investigations of the effect of the intermediate adsorption on the variation of the reversible potential of the ORR on Pt(100) was shown. Density Functional Theory (DFT) was used to determine the energies and the geometry parameters of the intermediates which can be adsorbed on Pt(100) during the oxygen reduction reaction (ORR) and their effect on the . The Comparison of these energies and parameters using the Bridge or the Griffiths sites adsorption mechanism suggests that the two paths are feasible. In both mechanisms, the total adsorption energies of the intermediates species continuously decrease. Moreover, according to the geometry analysis, the O-O bond distance in H2O2 is higher in both (Bridge and Griffiths) processes compared to the gas phase. Such a result suggests a dissociative H2O2 adsorption whatever the type of the involved mechanism involved. In the second step, the Oxygen reduction reaction (ORR) on palladium-copper alloys was studied through two approaches. The first one is based on the correlations between the surface chemical composition and the kinetics parameters of the ORR. The second approach is focused on the correlations between the adsorption energies of O2 and OH of Pd-Cu(111) surfaces and the electronic properties of the alloys. The adsorbtion energy calculations are based on on ab initio calculation using the program VASP (Vienna ab initio program) in a MeDeA environnement (software purchased from Materials Design, Inc. The studies of the oxygen reduction reaction were performed in an acidic media on Palladium-Copper alloys as catalyst. The variation of the intrinsic metal surface properties (lattice parameter, binding energy, work function (Wf), d-band filling and d-band center epsilond) and O2 and OH adsorption energies of on (111) Pd-Cu surface alloys were determined using ab initio program. Calculations of these parameters were based on plane waves approach on slab system with density functional theory (DFT) using the Vienna ab initio simulation program (VASP). It was shown that insertion of Cu atoms in Pd lattice affects geometric and electronic properties of Pd. These changes influence significantly O2 and OH adsorption. In the third step, the oxygen reduction reaction (ORR) on Pd-Cu catalyst has been studied in acidic media. The palladium alloys were prepared by RF magnetron using a palladium and a copper wafer as targets on the glassy carbon substrate. The dual sputtering we used allowed the deposition of about 1micrometer thin film of Pd-Cu on glassy carbon (GC). The ORR kinetics was studied on these catalysts in 0,1M HClO4. Cyclic voltammetry (CV) was used to determine the electrochemical active surface area (Sa). An increase in Sa with the Cu content in the alloy was observed for the alloys containing more than 50% in Cu. The Pd-Cu alloys containing more than 50% in Cu exhibits a constant value of 23 cm2 for Sa. It was further shown that the ORR on the Pd-Cu alloys proceeds through the 4 electrons transfer mechanism and a Tafel slope of 60 mV/dec. The Pd 50Cu50 exhibits the highest activity for this reaction. The enhancement of the electro catalytic activity is attributed to an optimal d band property that makes easier the OOH dissociative adsorption which is considered as chemical rate determining step (RDS) for the ORR. It was also found that all the Pd-Cu alloys exhibited better electrocatalystic performances for the ORR than Pd or Cu alone. From the polarisation of the ORR in 0,1 M HClO4 it was shown that the curve of the Pd electrode was shifted to the lower potentials than those of the Pd-Cu alooys. In addition, the variation of the kinetic current of the ORR at 0,6 V vs. SCE (0,841 V vs. RHE) on the Pd-Cu alloys with the composition of in Cu content exhibited a volcano-shape. (Abstract shortened by UMI.)

Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet.

PubMed

Rana, Malay Kumar; Chandra, Amalendu

2013-05-28

The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.

Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

PubMed

Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

2017-09-05

Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

Identification and Characterization of Molecular Bonding Structures by ab initio Quasi-Atomic Orbital Analyses.

PubMed

West, Aaron C; Duchimaza-Heredia, Juan J; Gordon, Mark S; Ruedenberg, Klaus

2017-11-22

The quasi-atomic analysis of ab initio electronic wave functions in full valence spaces, which was developed in preceding papers, yields oriented quasi-atomic orbitals in terms of which the ab initio molecular wave function and energy can be expressed. These oriented quasi-atomic orbitals are the rigorous ab initio counterparts to the conceptual bond forming atomic hybrid orbitals of qualitative chemical reasoning. In the present work, the quasi-atomic orbitals are identified as bonding orbitals, lone pair orbitals, radical orbitals, vacant orbitals and orbitals with intermediate character. A program determines the bonding characteristics of all quasi-atomic orbitals in a molecule on the basis of their occupations, bond orders, kinetic bond orders, hybridizations and local symmetries. These data are collected in a record and provide the information for a comprehensive understanding of the synergism that generates the bonding structure that holds the molecule together. Applications to a series of molecules exhibit the complete bonding structures that are embedded in their ab initio wave functions. For the strong bonds in a molecule, the quasi-atomic orbitals provide quantitative ab initio amplifications of the Lewis dot symbols. Beyond characterizing strong bonds, the quasi-atomic analysis also yields an understanding of the weak interactions, such as vicinal, hyperconjugative and radical stabilizations, which can make substantial contributions to the molecular bonding structure.

Ab initio interatomic potentials and the thermodynamic properties of fluids

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-07-01

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

NASA Astrophysics Data System (ADS)

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

2016-07-01

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-06-01

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Bicanonical ab Initio Molecular Dynamics for Open Systems.

PubMed

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Ab initio interatomic potentials and the thermodynamic properties of fluids.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-07-14

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-06-28

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

PubMed

Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

2016-07-07

Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

PubMed Central

Füsti-Molnár, László; Merz, Kenneth M.

2008-01-01

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

Ab Initio Surface Phase Diagrams for Coadsorption of Aromatics and Hydrogen on the Pt(111) Surface

DOE PAGES

Ferguson, Glen Allen; Vorotnikov, Vassili; Wunder, Nicholas; ...

2016-11-02

Supported metal catalysts are commonly used for the hydrogenation and deoxygenation of biomass-derived aromatic compounds in catalytic fast pyrolysis. To date, the substrate-adsorbate interactions under reaction conditions crucial to these processes remain poorly understood, yet understanding this is critical to constructing detailed mechanistic models of the reactions important to catalytic fast pyrolysis. Density functional theory (DFT) has been used in identifying mechanistic details, but many of these works assume surface models that are not representative of realistic conditions, for example, under which the surface is covered with some concentration of hydrogen and aromatic compounds. In this study, we investigate hydrogen-guaiacolmore » coadsorption on Pt(111) using van der Waals-corrected DFT and ab initio thermodynamics over a range of temperatures and pressures relevant to bio-oil upgrading. We find that relative coverage of hydrogen and guaiacol is strongly dependent on the temperature and pressure of the system. Under conditions relevant to ex situ catalytic fast pyrolysis (CFP; 620-730 K, 1-10 bar), guaiacol and hydrogen chemisorb to the surface with a submonolayer hydrogen (~0.44 ML H), while under conditions relevant to hydrotreating (470-580 K, 10-200 bar), the surface exhibits a full-monolayer hydrogen coverage with guaiacol physisorbed to the surface. These results correlate with experimentally observed selectivities, which show ring saturation to methoxycyclohexanol at hydrotreating conditions and deoxygenation to phenol at CFP-relevant conditions. Additionally, the vibrational energy of the adsorbates on the surface significantly contributes to surface energy at higher coverage. Ignoring this contribution results in not only quantitatively, but also qualitatively incorrect interpretation of coadsorption, shifting the phase boundaries by more than 200 K and ~10-20 bar and predicting no guaiacol adsorption under CFP and hydrotreating conditions. We discuss the implications of this work in the context of modeling hydrogenation and deoxygenation reactions on Pt(111), and we find that only the models representative of equilibrium surface coverage can capture the hydrogenation kinetics correctly. Lastly, as a major outcome of this work, we introduce a freely available web-based tool, dubbed the Surface Phase Explorer (SPE), which allows researchers to conveniently determine surface composition for any one- or two-component system at thermodynamic equilibrium over a wide range of temperatures and pressures on any crystalline surface using standard DFT output.« less

Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

NASA Astrophysics Data System (ADS)

Mishra, S. B.; Nanda, B. R. K.

2017-05-01

Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

Ab initio theory and modeling of water.

PubMed

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C; Calegari Andrade, Marcos F; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L; Perdew, John P; Wu, Xifan

2017-10-10

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice I h at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner.

Ab initio theory and modeling of water

PubMed Central

Chen, Mohan; Ko, Hsin-Yu; Remsing, Richard C.; Calegari Andrade, Marcos F.; Santra, Biswajit; Sun, Zhaoru; Selloni, Annabella; Car, Roberto; Klein, Michael L.; Perdew, John P.; Wu, Xifan

2017-01-01

Water is of the utmost importance for life and technology. However, a genuinely predictive ab initio model of water has eluded scientists. We demonstrate that a fully ab initio approach, relying on the strongly constrained and appropriately normed (SCAN) density functional, provides such a description of water. SCAN accurately describes the balance among covalent bonds, hydrogen bonds, and van der Waals interactions that dictates the structure and dynamics of liquid water. Notably, SCAN captures the density difference between water and ice Ih at ambient conditions, as well as many important structural, electronic, and dynamic properties of liquid water. These successful predictions of the versatile SCAN functional open the gates to study complex processes in aqueous phase chemistry and the interactions of water with other materials in an efficient, accurate, and predictive, ab initio manner. PMID:28973868

A quantum chemistry study of Qinghaosu

NASA Astrophysics Data System (ADS)

Gu, Jian-De; Chen, Kai-Xian; Jiang, Hua-Liang; Zhu, Wei-Liang; Chen, Jian-Zhong; Ji, Ru-Yun

1997-10-01

The powerful anti-malarial drug, Qinghaosu (Artemisinin), has been studied using ab initio methods. The DFT B3LYP method with the 6-31G ∗ basis set gives an excellent geometry compared to experiments, especially for the OO bond length and the 1,2,4-Trioxane ring subsystem. The R(OO) bond length predicted at this level is 1.460 Å, only 0.018 Å shorter than the experimental measurement. The vibrational analysis shows that the OO stretching mode is combined with the OC vibration mode, having the character of an OOC entity. The OO vibrational band at 722 cm -1 suggested in the experimental studies has been assigned as 1,2,4-trioxane ring breathing.

Carrier mobility and scattering lifetime in electric double-layer gated few-layer graphene

NASA Astrophysics Data System (ADS)

Piatti, E.; Galasso, S.; Tortello, M.; Nair, J. R.; Gerbaldi, C.; Bruna, M.; Borini, S.; Daghero, D.; Gonnelli, R. S.

2017-02-01

We fabricate electric double-layer field-effect transistor (EDL-FET) devices on mechanically exfoliated few-layer graphene. We exploit the large capacitance of a polymeric electrolyte to study the transport properties of three, four and five-layer samples under a large induced surface charge density both above and below the glass transition temperature of the polymer. We find that the carrier mobility shows a strong asymmetry between the hole and electron doping regime. We then employ ab initio density functional theory (DFT) calculations to determine the average scattering lifetime from the experimental data. We explain its peculiar dependence on the carrier density in terms of the specific properties of the electrolyte we used in our experiments.

Atomic picture of elastic deformation in a metallic glass

NASA Astrophysics Data System (ADS)

Wang, X. D.; Aryal, S.; Zhong, C.; Ching, W. Y.; Sheng, H. W.; Zhang, H.; Zhang, D. X.; Cao, Q. P.; Jiang, J. Z.

2015-03-01

The tensile behavior of a Ni60Nb40 metallic glass (MG) has been studied by using ab initio density functional theory (DFT) calculation with a large cell containing 1024 atoms (614 Ni and 410 Nb). We provide insight into how a super elastic limit can be achieved in a MG. Spatially inhomogeneous responses of single atoms and also major polyhedra are found to change greatly with increasing external stress when the strain is over 2%, causing the intrinsically viscoelastic behavior. We uncover the origin of the observed super elastic strain limit under tension (including linear and viscoelastic strains) in small-sized MG samples, mainly caused by inhomogeneous distribution of excess volumes in the form of newly formed subatomic cavities.

Atomic picture of elastic deformation in a metallic glass.

PubMed

Wang, X D; Aryal, S; Zhong, C; Ching, W Y; Sheng, H W; Zhang, H; Zhang, D X; Cao, Q P; Jiang, J Z

2015-03-17

The tensile behavior of a Ni60Nb40 metallic glass (MG) has been studied by using ab initio density functional theory (DFT) calculation with a large cell containing 1024 atoms (614 Ni and 410 Nb). We provide insight into how a super elastic limit can be achieved in a MG. Spatially inhomogeneous responses of single atoms and also major polyhedra are found to change greatly with increasing external stress when the strain is over 2%, causing the intrinsically viscoelastic behavior. We uncover the origin of the observed super elastic strain limit under tension (including linear and viscoelastic strains) in small-sized MG samples, mainly caused by inhomogeneous distribution of excess volumes in the form of newly formed subatomic cavities.

Atomic picture of elastic deformation in a metallic glass

DOE PAGES

Wang, X. D.; Aryal, S.; Zhong, C.; ...

2015-03-17

The tensile behavior of a Ni₆₀Nb₄₀ metallic glass (MG) has been studied by using ab initio density functional theory (DFT) calculation with a large cell containing 1024 atoms (614 Ni and 410 Nb). We provide insight into how a super elastic limit can be achieved in a MG. Spatially inhomogeneous responses of single atoms and also major polyhedra are found to change greatly with increasing external stress when the strain is over 2%, causing the intrinsically viscoelastic behavior. We uncover the origin of the observed super elastic strain limit under tension (including linear and viscoelastic strains) in small-sized MG samples,more » mainly caused by inhomogeneous distribution of excess volumes in the form of newly formed subatomic cavities.« less

Pressure Induced Phase Transition and Electronic Properties of 1d ZnO Nanocrystal: AN AB INITIO Study

NASA Astrophysics Data System (ADS)

Srivastava, Anurag; Tyagi, Neha

2012-10-01

We have analyzed the one-dimensional (1D) ZnO nanocrystals in its wurtzite (B4); zinc-blende (B3) and rocksalt (B1) type phases, by means of density functional theory (DFT) calculations. The energetic stability of nanocrystal has been analyzed using Revised Perdew-Burke-Ernzerhof (revPBE) type parameterized GGA potential. The B3 type phase is most stable amongst other phases of nanocrystals. The computation of ground state properties for all the phases of ZnO nanocrystals finds that the bulk modulus are smaller than their bulk counterpart, in turn softening the material at reduced dimensions. The electronic band structure analysis confirms the semiconducting nature of B4 type phase whereas other two are metallic.

Structural, Electronic and Elastic Properties of Half-Heusler Alloys CrNiZ (Z = Al, Si, Ge and As)

NASA Astrophysics Data System (ADS)

Zitouni, A.; Benstaali, W.; Abbad, A.; Lantri, T.; Bouadjemi, B.; Aziz, Z.

2018-06-01

In the present work, a self-consistent ab-initio calculation using the full- potential linearized augmented plane wave (FP-LAPW) method within the framework of the spin-polarized density functional theory (DFT) was used to study the structural, electronic, magnetic and elastic properties of the half Heusler alloys CrNiZ (Z = Al, Si, Ge and As) in three phases ( α, β and γ phases). The generalized gradient approximation (GGA) described by Perdew-Burke-Ernzerhof (PBE) was used. The results obtained for the spin-polarized band structure and the density of states show a halfmetallic behavior for the four compounds. The elastic constants ( C ij ) show that our compounds are ductile, stiff and anisotropic.

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations.

PubMed

Alexandrova, Anastassia N; Boldyrev, Alexander I; Li, Xiang; Sarkas, Harry W; Hendricks, Jay H; Arnold, Susan T; Bowen, Kit H

2011-01-28

Structural and energetic properties of small, deceptively simple anionic clusters of lithium, Li(n)(-), n = 3-7, were determined using a combination of anion photoelectron spectroscopy and ab initio calculations. The most stable isomers of each of these anions, the ones most likely to contribute to the photoelectron spectra, were found using the gradient embedded genetic algorithm program. Subsequently, state-of-the-art ab initio techniques, including time-dependent density functional theory, coupled cluster, and multireference configurational interactions methods, were employed to interpret the experimental spectra.

The appropriateness of density-functional theory for the calculation of molecular electronics properties.

PubMed

Reimers, Jeffrey R; Cai, Zheng-Li; Bilić, Ante; Hush, Noel S

2003-12-01

As molecular electronics advances, efficient and reliable computation procedures are required for the simulation of the atomic structures of actual devices, as well as for the prediction of their electronic properties. Density-functional theory (DFT) has had widespread success throughout chemistry and solid-state physics, and it offers the possibility of fulfilling these roles. In its modern form it is an empirically parameterized approach that cannot be extended toward exact solutions in a prescribed way, ab initio. Thus, it is essential that the weaknesses of the method be identified and likely shortcomings anticipated in advance. We consider four known systematic failures of modern DFT: dispersion, charge transfer, extended pi conjugation, and bond cleavage. Their ramifications for molecular electronics applications are outlined and we suggest that great care is required when using modern DFT to partition charge flow across electrode-molecule junctions, screen applied electric fields, position molecular orbitals with respect to electrode Fermi energies, and in evaluating the distance dependence of through-molecule conductivity. The causes of these difficulties are traced to errors inherent in the types of density functionals in common use, associated with their inability to treat very long-range electron correlation effects. Heuristic enhancements of modern DFT designed to eliminate individual problems are outlined, as are three new schemes that each represent significant departures from modern DFT implementations designed to provide a priori improvements in at least one and possible all problem areas. Finally, fully semiempirical schemes based on both Hartree-Fock and Kohn-Sham theory are described that, in the short term, offer the means to avoid the inherent problems of modern DFT and, in the long term, offer competitive accuracy at dramatically reduced computational costs.

Spectral Analysis of 3-(Adamantan-1-yl)-4-Ethyl-1-[(4-Phenylpiperazin-1-yl) Methyl]-1 H-1,2,4-Triazole-5(4 H)-Thione

NASA Astrophysics Data System (ADS)

Mindarava, Y. L.; Shundalau, M. B.; Al-Wahaibi, L. H.; El-Emam, A. A.; Matsukovich, A. S.; Gaponenko, S. V.

2018-05-01

Vibrational IR (3200-650 cm-1) and Raman spectra (3200-150 cm-1) of adamantane-containing 3-(adamantan-1-yl)-4-ethyl-1-[(4-phenylpiperazin-1-yl)methyl]-1H-1,2,4-triazole-5(4H)-thione, which is promising for drug design, were examined. The UV/Vis spectrum (450-200 nm) of the compound in EtOH was measured. Full geometry optimization using density functional theory (DFT) in the B3LYP/cc-pVDZ approximation allowed the equilibrium configuration of the molecule to be determined and IR and Raman spectra to be calculated. Based on these, the experimental vibrational IR and Raman spectra were interpreted and the biological activity indices were predicted. The UV/Vis spectrum of the title compound was simulated at the time-dependent DFT/CAM-B3LYP/cc-pVDZ level with and without solvent effects and at the ab initio multi-reference perturbation theory XMCQDPT2 level. The UV/Vis spectrum that was simulated using the multi-reference XMCQDPT2 approximation agreed very successfully with the experimental data, in contrast to the single-reference DFT method. This was probably a consequence of intramolecular charge transfer.

DFT Predictions of Electronic, Transport, and Bulk Properties of Cubic Antifluorite A2B Compounds (A = Li, Na, B = O,S,Se)

NASA Astrophysics Data System (ADS)

Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We present results from ab-initio,self-consistent calculations of electronic, transport, and bulk properties of cubic antifluorite (anti-CaF2) compounds A2B (A = Li, Na, B = O, S, Se). Our computations employed the local density approximation (LDA) potential of Ceperley and Alder and the linear combination of atomic orbital (LCAO) formalism. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams method, as enhanced by Ekuma and Franklin (BZW-EF). Consequently, our calculations search for and attained the ground states of the systems under study, as required by DFT; our results therefore possess the full, physical content of DFT. We discuss band structures, band gaps, and related properties of these materials, including calculated, total and partial densities of states (DOS and PDOS), effective masses of charge carriers, equilibrium lattice constants, and the bulk moduli of cubic antifluorite compounds A2B (A = Li, Na, B = O, S, Se). Our results are predictions in some cases, due to the lack of experimental data. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

FTIR, FT-Raman, FT-NMR, UV-visible and quantum chemical investigations of 2-amino-4-methylbenzothiazole.

PubMed

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

2012-03-01

The FT-IR (4000-400 cm(-1)) and FT-Raman (4000-100 cm(-1)) spectral measurements and complete assignments of the observed spectra of 2-amino-4-methylbenzothiazole (2A4MBT) have been proposed. Ab initio and DFT calculations have been performed and the structural parameters of the compound were determined from the optimised geometry with 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets and giving energies, harmonic vibrational frequencies, depolarisation ratios, IR intensities and Raman activities. (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO, LUMO and band gap energies were measured by time-dependent DFT (TD-DFT) approach. The geometric parameters, energies, harmonic vibrational frequencies, IR intensities, Raman activities chemical shifts and absorption wavelengths were compared with the available experimental data of the molecule. The influences of methyl and amino groups on the skeletal modes and on the proton chemical shifts have been investigated. Copyright © 2011 Elsevier B.V. All rights reserved.

Spectral Analysis of 3-(Adamantan-1-yl)-4-Ethyl-1-[(4-Phenylpiperazin-1-yl) Methyl]-1H-1,2,4-Triazole-5(4H)-Thione

NASA Astrophysics Data System (ADS)

Mindarava, Y. L.; Shundalau, M. B.; Al-Wahaibi, L. H.; El-Emam, A. A.; Matsukovich, A. S.; Gaponenko, S. V.

2018-05-01

Vibrational IR (3200-650 cm-1) and Raman spectra (3200-150 cm-1) of adamantane-containing 3-(adamantan-1-yl)-4-ethyl-1-[(4-phenylpiperazin-1-yl)methyl]-1H-1,2,4-triazole-5(4H)-thione, which is promising for drug design, were examined. The UV/Vis spectrum (450-200 nm) of the compound in EtOH was measured. Full geometry optimization using density functional theory (DFT) in the B3LYP/cc-pVDZ approximation allowed the equilibrium configuration of the molecule to be determined and IR and Raman spectra to be calculated. Based on these, the experimental vibrational IR and Raman spectra were interpreted and the biological activity indices were predicted. The UV/Vis spectrum of the title compound was simulated at the time-dependent DFT/CAM-B3LYP/cc-pVDZ level with and without solvent effects and at the ab initio multi-reference perturbation theory XMCQDPT2 level. The UV/Vis spectrum that was simulated using the multi-reference XMCQDPT2 approximation agreed very successfully with the experimental data, in contrast to the single-reference DFT method. This was probably a consequence of intramolecular charge transfer.

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.

Mechanical properties of non-centrosymmetric CePt3Si and CePt3B

NASA Astrophysics Data System (ADS)

Rogl, G.; Legut, D.; Sýkora, R.; Müller, P.; Müller, H.; Bauer, E.; Puchegger, S.; Zehetbauer, M.; Rogl, P.

2017-05-01

Elastic moduli, hardness (both at room temperature) and thermal expansion (4.2-670 K) have been experimentally determined for polycrystalline CePt3Si and its prototype compound CePt3B as well as for single-crystalline CePt3Si. Resonant ultrasound spectroscopy was used to determine elastic properties (Young’s modulus E and Poisson’s ratio ν) via the eigenfrequencies of the sample and the knowledge of sample mass and dimensions. Bulk and shear moduli were calculated from E and ν, and the respective Debye temperatures were derived. In addition, ab initio DFT calculations were carried out for both compounds. A comparison of parameters evaluated from DFT with those of experiments revealed, in general, satisfactory agreement. Positive and negative thermal expansion values obtained from CePt3Si single crystal data are fairly well explained in terms of the crystalline electric field model, using CEF parameters derived recently from inelastic neutron scattering. DFT calculations, in addition, demonstrate that the atomic vibrations keep almost unaffected by the antisymmetric spin-orbit coupling present in systems with crystal structures having no inversion symmetry. This is opposite to electronic properties, where the antisymmetric spin-orbit interaction has shown to distinctly influence features like the superconducting condensate of CePt3Si.

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.

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

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2010 CFR

2010-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2013 CFR

2013-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

40 CFR 86.094-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., the Administrator may deem such certificate void ab initio. (4) In any case in which certification of... fraud or other misconduct as makes the certification invalid ab initio. (6) The manufacturer may request...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2012 CFR

2012-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2011 CFR

2011-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2014 CFR

2014-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

Evaluating High-Throughput Ab Initio Gene Finders to Discover Proteins Encoded in Eukaryotic Pathogen Genomes Missed by Laboratory Techniques

PubMed Central

Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T.

2012-01-01

Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. PMID:23226328

77 FR 21154 - BNSF Railway Company-Abandonment Exemption-in Oklahoma County, OK

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-09

... proceeding and reject BNSF's notice of exemption as void ab initio on the grounds that BNSF had provided... misleading information, the exemption is void ab initio. BNSF has filed a combined environmental and historic... DEPARTMENT OF TRANSPORTATION Surface Transportation Board [Docket No. AB 6 (Sub-No. 480X)] BNSF...

Ab initio calculations of the electronic structure and specific optical features of β-LiNH4SO4 single crystals

NASA Astrophysics Data System (ADS)

Rudysh, M. Ya.; Brik, M. G.; Stadnyk, V. Yo.; Brezvin, R. S.; Shchepanskyi, P. A.; Fedorchuk, A.; Khyzhun, O. Y.; Kityk, I. V.; Piasecki, M.

2018-01-01

In the present work complex experimental and theoretical studies of electronic and optical properties for β-lithium-ammonium sulfate crystals of good optical quality are performed using the X-ray photoelectron spectroscopy (XPS) and X-ray emission spectroscopy (XES). Standard immersion and spectroscopic techniques accompanied by the theoretical quantum-chemical calculations in the density functional theory (DFT) framework were applied. Calculations of band structure and related properties were carried out within a framework of local density and generalized gradient approximations as well as hybrid B3LYP functionals. The energy levels features and their origin are established from the DFT calculations and they were ferified by XPS and XES measurements. Theoretical and experimental refractive indices dispersions along the principal crystallographic directions (nx, ny and nz) as well as birefringence dispersion (Δnx, Δny and Δnz) in the visible spectral range are obtained. It was found a closeness of nx and ny curves for the titled crystals. More precise birefringence examining predicts their intersection at λ ≈ 190 nm.

Ground-State Electronic Structure of RC-LH1 and LH2 Pigment Assemblies of Purple Bacteria via the EBF-MO Method.

PubMed

Shrestha, Kushal; Jakubikova, Elena

2015-08-20

Light-harvesting antennas are protein-pigment complexes that play a crucial role in natural photosynthesis. The antenna complexes absorb light and transfer energy to photosynthetic reaction centers where charge separation occurs. This work focuses on computational studies of the electronic structure of the pigment networks of light-harvesting complex I (LH1), LH1 with the reaction center (RC-LH1), and light-harvesting complex II (LH2) found in purple bacteria. As the pigment networks of LH1, RC-LH1, and LH2 contain thousands of atoms, conventional density functional theory (DFT) and ab initio calculations of these systems are not computationally feasible. Therefore, we utilize DFT in conjunction with the energy-based fragmentation with molecular orbitals method and a semiempirical approach employing the extended Hückel model Hamiltonian to determine the electronic properties of these pigment assemblies. Our calculations provide a deeper understanding of the electronic structure of natural light-harvesting complexes, especially their pigment networks, which could assist in rational design of artificial photosynthetic devices.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

A DFT study for the structural and electronic properties of Zn m Se n nanoclusters

NASA Astrophysics Data System (ADS)

Yadav, Phool Singh; Pandey, Dheeraj Kumar

2012-09-01

An ab initio study has been performed for the stability, structural and electronic properties of 19 small zinc selenide Zn m Se n ( m + n = 2-4) nanoclusters. Out of these nanoclusters, one nanocluster is found to be unstable due to its imaginary vibrational frequency. A B3LYP-DFT/6-311G(3df) method is used in the optimization of the geometries of the nanoclusters. We have calculated the zero point energy (ZPE), which is ignored by the other workers. The binding energies (BE), HOMO-LUMO gaps and bond lengths have been obtained for all the optimized nanoclusters. For the same value of ` m' and ` n', we designate the most stable structure the one, which has maximum final binding energy (FBE) per atom. The adiabatic and vertical ionization potentials (IP) and electron affinities (EA), dipole moments and charge on atoms have been investigated for the most stable nanoclusters. For the same value of ` m' and ` n', the nanocluster containing maximum number of Se atoms is found to be most stable.

Atomic structure of a metal-supported two-dimensional germania film

NASA Astrophysics Data System (ADS)

Lewandowski, Adrián Leandro; Schlexer, Philomena; Büchner, Christin; Davis, Earl M.; Burrall, Hannah; Burson, Kristen M.; Schneider, Wolf-Dieter; Heyde, Markus; Pacchioni, Gianfranco; Freund, Hans-Joachim

2018-03-01

The growth and microscopic characterization of two-dimensional germania films is presented. Germanium oxide monolayer films were grown on Ru(0001) by physical vapor deposition and subsequent annealing in oxygen. We obtain a comprehensive image of the germania film structure by combining intensity-voltage low-energy electron diffraction (I/V-LEED) and ab initio density functional theory (DFT) analysis with atomic-resolution scanning tunneling microscopy (STM) imaging. For benchmarking purposes, the bare Ru(0001) substrate and the (2 ×2 )3 O covered Ru(0001) were analyzed with I/V-LEED with respect to previous reports. STM topographic images of the germania film reveal a hexagonal network where the oxygen and germanium atom positions appear in different imaging contrasts. For quantitative LEED, the best agreement has been achieved with DFT structures where the germanium atoms are located preferentially on the top and fcc hollow sites of the Ru(0001) substrate. Moreover, in these atomically flat germania films, local site geometries, i.e., tetrahedral building blocks, ring structures, and domain boundaries, have been identified, indicating possible pathways towards two-dimensional amorphous networks.

Effects of Transition-Metal Mixing on Na Ordering and Kinetics in Layered P 2 Oxides

NASA Astrophysics Data System (ADS)

Zheng, Chen; Radhakrishnan, Balachandran; Chu, Iek-Heng; Wang, Zhenbin; Ong, Shyue Ping

2017-06-01

Layered P 2 oxides are promising cathode materials for rechargeable sodium-ion batteries. In this work, we systematically investigate the effects of transition-metal (TM) mixing on Na ordering and kinetics in the NaxCo1 -yMnyO2 model system using density-functional-theory (DFT) calculations. The DFT-predicted 0-K stability diagrams indicate that Co-Mn mixing reduces the energetic differences between Na orderings, which may account for the reduction of the number of phase transformations observed during the cycling of mixed-TM P 2 layered oxides compared to a single TM. Using ab initio molecular-dynamics simulations and nudged elastic-band calculations, we show that the TM composition at the Na(1) (face-sharing) site has a strong influence on the Na site energies, which in turn impacts the kinetics of Na diffusion towards the end of the charge. By employing a site-percolation model, we establish theoretical upper and lower bounds for TM concentrations based on their effect on Na(1) site energies, providing a framework to rationally tune mixed-TM compositions for optimal Na diffusion.

Methane dissociation on Ni(111): A fifteen-dimensional potential energy surface using neural network method

NASA Astrophysics Data System (ADS)

Shen, Xiangjian; Chen, Jun; Zhang, Zhaojun; Shao, Kejie; Zhang, Dong H.

2015-10-01

In the present work, we develop a highly accurate, fifteen-dimensional potential energy surface (PES) of CH4 interacting on a rigid flat Ni(111) surface with the methodology of neural network (NN) fit to a database consisted of about 194 208 ab initio density functional theory (DFT) energy points. Some careful tests of the accuracy of the fitting PES are given through the descriptions of the fitting quality, vibrational spectrum of CH4 in vacuum, transition state (TS) geometries as well as the activation barriers. Using a 25-60-60-1 NN structure, we obtain one of the best PESs with the least root mean square errors: 10.11 meV for the entrance region and 17.00 meV for the interaction and product regions. Our PES can reproduce the DFT results very well in particular for the important TS structures. Furthermore, we present the sticking probability S0 of ground state CH4 at the experimental surface temperature using some sudden approximations by Jackson's group. An in-depth explanation is given for the underestimated sticking probability.

Highly Accurate Calculations of the Phase Diagram of Cold Lithium

NASA Astrophysics Data System (ADS)

Shulenburger, Luke; Baczewski, Andrew

The phase diagram of lithium is particularly complicated, exhibiting many different solid phases under the modest application of pressure. Experimental efforts to identify these phases using diamond anvil cells have been complemented by ab initio theory, primarily using density functional theory (DFT). Due to the multiplicity of crystal structures whose enthalpy is nearly degenerate and the uncertainty introduced by density functional approximations, we apply the highly accurate many-body diffusion Monte Carlo (DMC) method to the study of the solid phases at low temperature. These calculations span many different phases, including several with low symmetry, demonstrating the viability of DMC as a method for calculating phase diagrams for complex solids. Our results can be used as a benchmark to test the accuracy of various density functionals. This can strengthen confidence in DFT based predictions of more complex phenomena such as the anomalous melting behavior predicted for lithium at high pressures. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.

DSMC study of oxygen shockwaves based on high-fidelity vibrational relaxation and dissociation models

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Kulakhmetov, Marat; Alexeenko, Alina

2017-01-01

This work evaluates high-fidelity vibrational-translational (VT) energy relaxation and dissociation models for pure O2 normal shockwave simulations with the direct simulation Monte Carlo (DSMC) method. The O2-O collisions are described using ab initio state-specific relaxation and dissociation models. The Macheret-Fridman (MF) dissociation model is adapted to the DSMC framework by modifying the standard implementation of the total collision energy (TCE) model. The O2-O2 dissociation is modeled with this TCE+MF approach, which is calibrated with O2-O ab initio data and experimental equilibrium dissociation rates. The O2-O2 vibrational relaxation is modeled via the Larsen-Borgnakke model, calibrated to experimental VT rates. All the present results are compared to experimental data and previous calculations available in the literature. It is found that, in general, the ab initio dissociation model is better than the TCE model at matching the shock experiments. Therefore, when available, efficient ab initio models are preferred over phenomenological models. We also show that the proposed TCE + MF formulation can be used to improve the standard TCE model results when ab initio data are not available or limited.

Multiple time step integrators in ab initio molecular dynamics.

PubMed

Luehr, Nathan; Markland, Thomas E; Martínez, Todd J

2014-02-28

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

21 CFR 701.9 - Exemptions from labeling requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., become void ab initio if the cosmetic comprising such shipment, delivery, or part is adulterated or... a cosmetic under paragraph (a)(2) of this section shall become void ab initio with respect to the...

Block-localized wavefunction (BLW) method at the density functional theory (DFT) level.

PubMed

Mo, Yirong; Song, Lingchun; Lin, Yuchun

2007-08-30

The block-localized wavefunction (BLW) approach is an ab initio valence bond (VB) method incorporating the efficiency of molecular orbital (MO) theory. It can generate the wavefunction for a resonance structure or diabatic state self-consistently by partitioning the overall electrons and primitive orbitals into several subgroups and expanding each block-localized molecular orbital in only one subspace. Although block-localized molecular orbitals in the same subspace are constrained to be orthogonal (a feature of MO theory), orbitals between different subspaces are generally nonorthogonal (a feature of VB theory). The BLW method is particularly useful in the quantification of the electron delocalization (resonance) effect within a molecule and the charge-transfer effect between molecules. In this paper, we extend the BLW method to the density functional theory (DFT) level and implement the BLW-DFT method to the quantum mechanical software GAMESS. Test applications to the pi conjugation in the planar allyl radical and ions with the basis sets of 6-31G(d), 6-31+G(d), 6-311+G(d,p), and cc-pVTZ show that the basis set dependency is insignificant. In addition, the BLW-DFT method can also be used to elucidate the nature of intermolecular interactions. Examples of pi-cation interactions and solute-solvent interactions will be presented and discussed. By expressing each diabatic state with one BLW, the BLW method can be further used to study chemical reactions and electron-transfer processes whose potential energy surfaces are typically described by two or more diabatic states.

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.

Molecular structure and vibrational assignments of 2,4-dichlorophenoxyacetic acid herbicide

NASA Astrophysics Data System (ADS)

Badawi, Hassan M.

2010-09-01

The structural stability of 2,4-dichlorophenoxyacetic acid was investigated by the DFT-B3LYP and the ab initio MP2 calculations with the 6-311G** basis set. From the calculations at both levels of theory the Cgcpp structure was predicted to be the lowest energy minimum for the acid. The DFT and the MP2 levels disagreed about the nature of the second stable structure of 2,4-dichlorophenoxyacetic acid. At the DFT-B3LYP level of calculation the planar Tttp ( transoid O dbnd C sbnd O sbnd H) and the non-planar Tgcpp ( cisoid O dbnd C sbnd O sbnd H) forms were predicted to be 0.7 and 1.5 kcal/mol, respectively higher in energy than the Cgcpp conformation. At the MP2 level the two high energy Tttp and Tgcpp forms were predicted to be 2.7 and 1.4 kcal/mol, respectively higher in energy than the ground state Cgcpp structure. The Tgcpp form was adopted as the second possible structure of 2,4-dichlorophenoxyacetic acid on the basis of the fact that the Møller-Plesset calculations account better than the DFT ones for the non-bonding O⋯H interactions. The vibrational frequencies of the lowest energy Cgcpp conformer were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of normal coordinate analysis and experimental infrared and Raman data.

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2010 CFR

2010-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

21 CFR 501.100 - Animal food; exemptions from labeling.

Code of Federal Regulations, 2014 CFR

2014-04-01

... become void ab initio if the food comprising such shipment, delivery, or part is adulterated or... a food under paragraph (d)(2) of this section shall become void ab initio with respect to the person...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2014 CFR

2014-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2011 CFR

2011-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2012 CFR

2012-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2013 CFR

2013-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

Many-body optimization using an ab initio monte carlo method.

PubMed

Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

2003-01-01

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

Ab initio investigation of the thermal decomposition of n-butylcyclohexane.

PubMed

Ali, Mohamad Akbar; Dillstrom, V Tyler; Lai, Jason Y W; Violi, Angela

2014-02-13

Environmental and energy security concerns have motivated an increased focus on developing clean, efficient combustors, which increasingly relies on insight into the combustion chemistry of fuels. In particular, naphthenes (cycloalkanes and alkylcycloalkanes) are important chemical components of distillate fuels, such as diesel and jet fuels. As such, there is a growing interest in describing napthene reactivity with kinetic mechanisms. Use of these mechanisms in predictive combustion models aids in the development of combustors. This study focuses on the pyrolysis of n-butylcyclohexane (n-BCH), an important representative of naphthenes in jet fuels. Seven different unimolecular decomposition pathways of C-C bond fission were explored utilizing ab initio/DFT methods. Accurate reaction energies were computed using the high-level quantum composite G3B3 method. Variational transition state theory, Rice-Ramsperger-Kassel-Marcus/master equation simulations provided temperature- and pressure-dependent rate constants. Implementation of these pathways into an existing chemical kinetic mechanism improved the prediction of experimental OH radical and H2O speciation in shock tube oxidation. Simulations of this combustion showed a change in the expected decomposition chemistry of n-BCH, predicting increased production of cyclic alkyl radicals instead of straight-chain alkenes. The most prominent reaction pathway for the decomposition of n-BCH is n-BCH = C3H7 + C7H13. The results of this study provide insight into the combustion of n-BCH and will aid in the future development of naphthene kinetic mechanisms.

Accurate bond energies of hydrocarbons from complete basis set extrapolated multi-reference singles and doubles configuration interaction.

PubMed

Oyeyemi, Victor B; Pavone, Michele; Carter, Emily A

2011-12-09

Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: 1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; 2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and 3) DFT-B3LYP calculations of minimum-energy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of CC and CH bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

PubMed

Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

2015-12-01

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Ab initio theory of spin-orbit coupling for quantum bits in diamond exhibiting dynamic Jahn-Teller effect

NASA Astrophysics Data System (ADS)

Gali, Adam; Thiering, Gergő

Dopants in solids are promising candidates for implementations of quantum bits for quantum computing. In particular, the high-spin negatively charged nitrogen-vacancy defect (NV) in diamond has become a leading contender in solid-state quantum information processing. The initialization and readout of the spin is based on the spin-selective decay of the photo-excited electron to the ground state which is mediated by spin-orbit coupling between excited states states and phonons. Generally, the spin-orbit coupling plays a crucial role in the optical spinpolarization and readout of NV quantum bit (qubit) and alike. Strong electron-phonon coupling in dynamic Jahn-Teller (DJT) systems can substantially influence the effective strength of spin-orbit coupling. Here we show by ab initio supercell density functional theory (DFT) calculations that the intrinsic spin-orbit coupling is strongly damped by DJT effect in the triplet excited state that has a consequence on the rate of non-radiative decay. This theory is applied to the ground state of silicon-vacancy (SiV) and germanium-vacancy (GeV) centers in their negatively charged state that can also act like qubits. We show that the intrinsic spin-orbit coupling in SiV and GeV centers is in the 100 GHz region, in contrast to the NV center of 10 GHz region. Our results provide deep insight in the nature of SiV and GeV qubits in diamond. EU FP7 DIADEMS project (Contract No. 611143).

Ab-initio study of electronic, magnetic and thermoelectric behaviors of LiV2O4 and LiCr2O4 using modified Becke-Johson (mBJ) potential

NASA Astrophysics Data System (ADS)

Ali, Saima; Rashid, Muhammad; Hassan, M.; Noor, N. A.; Mahmood, Q.; Laref, A.; Haq, Bakhtiar Ul

2018-05-01

Owing to the large energy storage capacity and higher working voltage, the spinel oxides LiV2O4 and LiCr2O4, have remained under intense research attention for utilization as electrode materials in lithium-ion batteries. In this study, we explore the half-metallic nature and thermoelectric response in both LiV2O4 and LiCr2O4 spinel oxides using ab-initio density functional theory (DFT) based computations. The ground-state energies of these compounds have been studied at the optimized structural parameters in the ferromagnetic phase. In order to obtain a correct picture of the electronic structure and magnetic properties, the modified Becke-Johnson (mBJ) potential is applied to compute the electronic structures. The half-metallic behavior is confirmed by the spin-polarized electronic band structures and density of state plots. The magnetic nature is elucidated by computing the John-Teller energy, direct and indirect exchange and crystal field splitting energies. Our computations indicate strong hybridization decreasing the V/Cr site magnetic moments and increasing magnetic momenta at the nonmagnetic atomic sites. We also present the computed parameters significant for expressing the thermoelectric response, which are electrical conductivity, thermal conductivity, See-beck coefficient and power factor. The computed properties are of immense interest owing to the potential spintronics and Li-ion battery applications of the studied spinel materials.

The disclosure of mesoscale behaviour of a 3d-SMM monolayer on Au(111) through a multilevel approach.

PubMed

Fernandez Garcia, Guglielmo; Lunghi, Alessandro; Totti, Federico; Sessoli, Roberta

2018-02-22

Here we present a computational study of a full- and a half-monolayer of a Fe 4 single molecule magnet ([Fe 4 (L) 2 (dpm) 6 ], where H 3 L = 2-hydroxymethyl-2-phenylpropane-1,3-diol and Hdpm = dipivaloylmethane, Fe 4 Ph) on an unreconstructed surface of Au(111). This has been possible through the application of an integrated approach, which allows the explicit inclusion of the packing effects in the classical dynamics to be used in a second step in periodic and non-periodic high level DFT calculations. In this way we can obtain access to mesoscale geometrical data and verify how they can influence the magnetic properties of interest of the single Fe 4 molecule. The proposed approach allows to overcome the ab initio state-of-the-art approaches used to study Single Molecule Magnets (SMMs), which are based on the study of one single adsorbed molecule and cannot represent effects on the scale of a monolayer. Indeed, we show here that it is possible to go beyond the computational limitations inherent to the use, for such complex systems, of accurate calculation techniques (e.g. ab initio molecular dynamics) without losing the level of accuracy necessary to gain new detailed insights, hardly reachable at the experimental level. Indeed, long-range and edge effects on the Fe 4 structures and their easy axis of magnetization orientations have been evidenced as their different contributions to the overall macroscopic behavior.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

Ab Initio Reaction Kinetics of CH 3 O$$\\dot{C}$$(=O) and $$\\dot{C}$$H 2 OC(=O)H Radicals

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

Tan, Ting; Yang, Xueliang; Ju, Yiguang

The dissociation and isomerization kinetics of the methyl ester combustion intermediates methoxycarbonyl radical (CH3Omore » $$\\dot{C}$$(=O)) and (formyloxy)methyl radical ($$\\dot{C}$$H2OC(=O)H) are investigated theoretically using high-level ab initio methods and Rice–Ramsperger–Kassel–Marcus (RRKM)/master equation (ME) theory. Geometries obtained at the hybrid density functional theory (DFT) and coupled cluster singles and doubles with perturbative triples correction (CCSD(T)) levels of theory are found to be similar. We employ high-level ab initio wave function methods to refine the potential energy surface: CCSD(T), multireference singles and doubles configuration interaction (MRSDCI) with the Davidson–Silver (DS) correction, and multireference averaged coupled-pair functional (MRACPF2) theory. MRSDCI+DS and MRACPF2 capture the multiconfigurational character of transition states (TSs) and predict lower barrier heights than CCSD(T). The temperature- and pressure-dependent rate coefficients are computed using RRKM/ME theory in the temperature range 300–2500 K and a pressure range of 0.01 atm to the high-pressure limit, which are then fitted to modified Arrhenius expressions. Dissociation of CH3O$$\\dot{C}$$(=O) to $$\\dot{C}$$H3 and CO2 is predicted to be much faster than dissociating to CH3$$\\dot{O}$$ and CO, consistent with its greater exothermicity. Isomerization between CH3O$$\\dot{C}$$(=O) and $$\\dot{C}$$H2OC(=O)H is predicted to be the slowest among the studied reactions and rarely happens even at high temperature and high pressure, suggesting the decomposition pathways of the two radicals are not strongly coupled. The predicted rate coefficients and branching fractions at finite pressures differ significantly from the corresponding high-pressure-limit results, especially at relatively high temperatures. Finally, because it is one of the most important CH3$$\\dot{O}$$ removal mechanisms under atmospheric conditions, the reaction kinetics of CH3$$\\dot{O}$$ + CO was also studied along the PES of CH3O$$\\dot{C}$$(=O); the resulting kinetics predictions are in remarkable agreement with experiments.« less

Electronic couplings for molecular charge transfer: Benchmarking CDFT, FODFT, and FODFTB against high-level ab initio calculations

NASA Astrophysics Data System (ADS)

Kubas, Adam; Hoffmann, Felix; Heck, Alexander; Oberhofer, Harald; Elstner, Marcus; Blumberger, Jochen

2014-03-01

We introduce a database (HAB11) of electronic coupling matrix elements (Hab) for electron transfer in 11 π-conjugated organic homo-dimer cations. High-level ab inito calculations at the multireference configuration interaction MRCI+Q level of theory, n-electron valence state perturbation theory NEVPT2, and (spin-component scaled) approximate coupled cluster model (SCS)-CC2 are reported for this database to assess the performance of three DFT methods of decreasing computational cost, including constrained density functional theory (CDFT), fragment-orbital DFT (FODFT), and self-consistent charge density functional tight-binding (FODFTB). We find that the CDFT approach in combination with a modified PBE functional containing 50% Hartree-Fock exchange gives best results for absolute Hab values (mean relative unsigned error = 5.3%) and exponential distance decay constants β (4.3%). CDFT in combination with pure PBE overestimates couplings by 38.7% due to a too diffuse excess charge distribution, whereas the economic FODFT and highly cost-effective FODFTB methods underestimate couplings by 37.6% and 42.4%, respectively, due to neglect of interaction between donor and acceptor. The errors are systematic, however, and can be significantly reduced by applying a uniform scaling factor for each method. Applications to dimers outside the database, specifically rotated thiophene dimers and larger acenes up to pentacene, suggests that the same scaling procedure significantly improves the FODFT and FODFTB results for larger π-conjugated systems relevant to organic semiconductors and DNA.

Ab-initio calculation of EuO doped with 5% of (Ti, V, Cr and Fe): GGA and SIC approximation

NASA Astrophysics Data System (ADS)

Rouchdi, M.; Salmani, E.; Bekkioui, N.; Ez-Zahraouy, H.; Hassanain, N.; Benyoussef, A.; Mzerd, A.

2017-12-01

In this research, a simple theoretical method is proposed to investigate the electronic, magnetic and optical properties of Europium oxide (EuO) doped with 5% of (Ti, V, Cr and Fe). For a basic understanding of these properties, we employed Density-Functional Theory (DFT) based calculations with the Korringa-Kohn-Rostoker code (KKR) combined with the Coherent Potential Approximation (CPA). Also we investigated the half-metallic ferromagnetic behavior of EuO doped with 5% of (Ti, V, Cr and Fe) within the self-interaction-corrected Generalized Gradient Approximation (GGA-SIC). Our calculated results revealed that the Eu0.95TM0.05O is ferromagnetic with a high transition temperature. Moreover, the optical absorption spectra revealed that the half metallicity has been also predicted.

Proximity vs. strain in intramolecular ring-closing reactions

NASA Astrophysics Data System (ADS)

Karaman, Rafik

2010-07-01

The DFT and ab initio calculation results for ring-closing reactions of eight different ω-bromoalkanecarboxylate anions (1-8) reveal that the activation energy (ΔG ‡) for the intramolecular cyclization process is strongly correlated with both (i) the experimental intramolecular cyclization rate (log k intra) and (ii) the distance between the two reactive centres, whereas the slope values of the change in enthalpy (ΔH) vs. the attack angle (α) and the distance between the two reacting centres (r) were found to correlate strongly with the experimental strain energy of the cycle being formed (E s Exp). These results assist in designing pro-prodrug systems that can be utilized to improve the overall biopharmaceutical profile of current medications in order to enhance their effectiveness and ease their utility.

Ab-initio study of (Ga,Cr)N and (Ga,Mn)N DMSs: under hydrostatic pressure

NASA Astrophysics Data System (ADS)

Rani, Anita; Kumar, Ranjan

2018-03-01

The influence of hydrostatic pressure between 0-100 GPa on structural, electronic and magnetic properties of CrxGa1-xN and MnxGa1-xN (x = 0.25) diluted magnetic semiconductors has been studied. The calculations have been performed using DFT as implemented in code SIESTA. LDA + U as exchange-correlation (XC) potential have been used to study the parameters. Under external pressure, shifting in both valence band and conduction band energy levels from their actual positions has been observed, which lead to modification of electronic properties. Also, N0 α, s-d exchange constant and p-d exchange constants, N0 β have been calculated at different pressures. Both the compounds show half metallic nature at studied pressure range.

Growth of carbon structured over Pd, Pt and Ni: A comparative DFT study

NASA Astrophysics Data System (ADS)

Quiroga, Matías Abel

2013-03-01

To elucidate the graphene-like structures mechanisms growth over the M(1 1 1) surface (M = Pd, Pt and Ni) we performed ab initio calculus in the frame of density functional theory with the exchange-correlation functional treated according to the Generalized Gradient Approximation (GGA). In order to avoid the problem that represent the complex interaction between the well formed graphene layer and the metallic surface, we recreate the carbon rings formation initial steps, by adding one by one carbon atoms over M(1 1 1) surface. With this strategy, the chemical bonding is always present until the graphene layer is well formed, in which case the GGA neglects van der Waals dispersive forces. We investigate the electronic properties by studying the band structure and the density of states.

Phenylalanine ab initio models for the simulation of skin natural moisturizing factor

NASA Astrophysics Data System (ADS)

Carvalho, B. G.; Raniero, L. J.; Martin, A. A.; Favero, P. P.

2013-04-01

In this study, we evaluated models that can be used to simulate amino acids in biological environments via density functional theory (DFT). The goal was to obtain realistic representations that combine computational economy and result quality when compared to experimental data. We increased the complexity of the models by using a model of an amino acid in a vacuum, followed by a water-solvated amino acid model. To consider pH variation, we simulated zwitterionic and nonionic amino acid configurations. The amino acid chosen for testing was phenylalanine, an aromatic amino acid present in high concentrations in the natural moisturizing factor of skin that plays a fundamental role in ultraviolet protection and vitiligo disease. To validate the models, vibrational modes and electronic properties were calculated and compared to experimental results.

Ab Initio: And a New Era of Airline Pilot Training.

ERIC Educational Resources Information Center

Gesell, Laurence E.

1995-01-01

Expansion of air transportation and decreasing numbers seeking pilot training point to a shortage of qualified pilots. Ab initio training, in which candidates with no flight time are trained to air transport proficiency, could resolve the problem. (SK)

Concentration dependence of electrical resistivity of binary liquid alloy HgZn: Ab-initio study

NASA Astrophysics Data System (ADS)

Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

2013-06-01

The electrical resistivity of HgZn liquid alloy has been made calculated using Troullier and Martins ab-initio pseudopotential as a function of concentration. Hard sphere diameters of Hg and Zn are obtained through the inter-ionic pair potential have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys.

Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1992-01-01

The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

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.

Analysis of fcc metals fracture behaviour: Fracture behaviour of fcc metals: brittle/ductile behaviour criteria : with ab-initio, embedded atom and pseudopotential parameterization for Au, Ir and Al. analysis for Au, Ir and Al.

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.; Katsnelson, M. I.; Mryasov, Oleg N.; Freeman, A. J.; Trefilov, M. V.

1998-03-01

Theoretical analysis of the fracture behaviour of fcc Au, Ir and Al have been performed within various brittle/ductile criteria (BDC) with ab-initio, embedded atom (EAM), and pseudopotential parameterizations. We systematically examined several important aspects of the fracture behaviour: (i) dislocation structure, (ii) energetics of the cleavage decohesion and (iii) character of the interatomic interactions. Unit dislocation structures were analyzed within a two dimensional generalization of the Peierls-Nabarro model with restoring forces determined from ab-initio total energy calculations and found to be split with well defined highly mobile partials for all considered metals. We find from ab-initio and pseudopotential that in contrast with most of fcc metals, cleavage decohesion curve for Al appreciably differs from UBER relation. Finally, using ab-initio, EAM and pseudopotential parameterizations, we demonstrate that (i) Au (as a typical example of a ductile metal) is well described within existing BDC's, (ii) anomalous cleavage-like crack propagation of Ir is driven predominantly by it's high elastic modulus and (iii) Al is not described within BDC due to it's long-range interatomic interactions (and hence requires adjustments of the brittle/ductile criteria).

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

PubMed Central

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian

2017-01-01

Abstract Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Results: We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28453681

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

PubMed Central

Zhang, Yang

2014-01-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. PMID:23760925

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

PubMed

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

2017-05-01

Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

PubMed

Zhang, Yang

2014-02-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials

NASA Astrophysics Data System (ADS)

Prahl, Ulrich; Bleck, Wolfgang; Saeed-Akbari, Alireza

This contribution reports the results of the collaborative research unit SFB 761 "Steel — ab initio", a cooperative project between RWTH Aachen University and the Max-Planck-Institute for Iron Research in Düsseldorf (MPIE) financed by the German Research Foundation (DFG). For the first time, it is exploited how ab initio approaches may lead to a detailed understanding and thus to a specific improvement of material development. The challenge lies in the combination of abstract natural science theories with rather engineering-like established concepts. Aiming at the technological target of the development of a new type of structural materials based on Fe-Mn-C alloys, the combination of ab initio and engineering methods is new, but could be followed quite successfully. Three major topics are treated in this research unit: a) development of a new method for material- and process-development based on ab initio calculations; b) design of a new class of structural materials with extraordinary property combinations; c) acceleration of development time and reduction of experimental efforts and complexity for material- and process-development. In the present work, an overview of the results of the first five years as well as an outlook for the upcoming three-year period is given.

Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI.

PubMed

Antipova, Valeriya N; Zheleznaya, Lyudmila A; Zyrina, Nadezhda V

2014-08-01

In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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

DOE PAGES

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

2016-09-09

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

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

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

Gillet, Natacha; Berstis, Laura; Wu, Xiaojing

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

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.

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

PubMed

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

2016-10-11

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

Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.

PubMed

Kramer, Christian; Gedeck, Peter; Meuwly, Markus

2013-03-12

Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol).

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

PubMed

Timko, Jeff; Kuyucak, Serdar

2012-11-28

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

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

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

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

Turi, László, E-mail: turi@chem.elte.hu

2016-04-21

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions withmore » n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.« less

On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

NASA Astrophysics Data System (ADS)

Turi, László

2016-04-01

We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

Effect of BrU on the transition between wobble Gua-Thy and tautomeric Gua-Thy base-pairs: ab initio molecular orbital calculations

NASA Astrophysics Data System (ADS)

Nomura, Kazuya; Hoshino, Ryota; Hoshiba, Yasuhiro; Danilov, Victor I.; Kurita, Noriyuki

2013-04-01

We investigated transition states (TS) between wobble Guanine-Thymine (wG-T) and tautomeric G-T base-pair as well as Br-containing base-pairs by MP2 and density functional theory (DFT) calculations. The obtained TS between wG-T and G*-T (asterisk is an enol-form of base) is different from TS got by the previous DFT calculation. The activation energy (17.9 kcal/mol) evaluated by our calculation is significantly smaller than that (39.21 kcal/mol) obtained by the previous calculation, indicating that our TS is more preferable. In contrast, the obtained TS and activation energy between wG-T and G-T* are similar to those obtained by the previous DFT calculation. We furthermore found that the activation energy between wG-BrU and tautomeric G-BrU is smaller than that between wG-T and tautomeric G-T. This result elucidates that the replacement of CH3 group of T by Br increases the probability of the transition reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G base is accelerated by the introduction of wG-BrU base-pair.

Controlling Magnetic and Ferroelectric Order Through Geometry: Synthesis, Ab Initio Theory, Characterization of New Multi-Ferric Fluoride Materials

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

Halasyamani, Shiv; Fennie, Craig

2016-11-03

We have focused on the synthesis, characterization, and ab initio theory on multi-functional mixed-metal fluorides. With funding from the DOE, we have successfully synthesized and characterized a variety of mixed metal fluoride materials.

7Be(p,gamma)8B S-factor from Ab Initio Wave Functions

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

Navratil, P; Bertulani, C A; Caurier, E

2006-10-12

There has been a significant progress in ab initio approaches to the structure of light nuclei. Starting from realistic two- and three-nucleon interactions the ab initio no-core shell model (NCSM) predicts low-lying levels in p-shell nuclei. It is a challenging task to extend ab initio methods to describe nuclear reactions. We present here a brief overview of the first steps taken toward nuclear reaction applications. In particular, we discuss our calculation of the {sup 7}Be(p,{gamma}){sup 8}B S-factor. We also present our first results of the {sup 3}He({alpha},{gamma}){sup 7}Be S-factor and of the S-factor of the mirror reaction {sup 3}H({alpha},{gamma}){sup 7}Li.more » The {sup 7}Be(p,{gamma}){sup 8}B and {sup 3}He({alpha},{gamma}){sup 7}Be reactions correspond to the most important uncertainties in solar model predictions of neutrino fluxes.« less

An ab initio-based Er–He interatomic potential in hcp Er

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

Yang, Li; ye, Yeting; Fan, K. M.

2014-09-01

We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations.more » The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.« less

Ab initio Studies of Magnetism in the Iron Chalcogenides FeTe and FeSe

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Misawa, Takahiro; Miyake, Takashi; Imada, Masatoshi

2015-09-01

The iron chalcogenides FeTe and FeSe belong to the family of iron-based superconductors. We study the magnetism in these compounds in the normal state using the ab initio downfolding scheme developed for strongly correlated electron systems. In deriving ab initio low-energy effective models, we employ the constrained GW method to eliminate the double counting of electron correlations originating from the exchange correlations already taken into account in the density functional theory. By solving the derived ab initio effective models, we reveal that the elimination of the double counting is important in reproducing the bicollinear antiferromagnetic order in FeTe, as is observed in experiments. We also show that the elimination of the double counting induces a unique degeneracy of several magnetic orders in FeSe, which may explain the absence of the magnetic ordering. We discuss the relationship between the degeneracy and the recently found puzzling phenomena in FeSe as well as the magnetic ordering found under pressure.

Materials Screening for the Discovery of New Half-Heuslers: Machine Learning versus ab Initio Methods.

PubMed

Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio

2018-01-18

Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

Resolution of ab initio shapes determined from small-angle scattering.

PubMed

Tuukkanen, Anne T; Kleywegt, Gerard J; Svergun, Dmitri I

2016-11-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.

Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction.

PubMed

Huang, Ying; Chen, Shi-Yi; Deng, Feilong

2016-01-01

In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools.

Resolution of ab initio shapes determined from small-angle scattering

PubMed Central

Tuukkanen, Anne T.; Kleywegt, Gerard J.; Svergun, Dmitri I.

2016-01-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models. PMID:27840683

A coupled channel study of HN2 unimolecular decay based on a global ab initio potential surface

NASA Technical Reports Server (NTRS)

Koizumi, Hiroyasu; Schatz, George C.; Walch, Stephen P.

1991-01-01

The unimolecular decay lifetimes of several vibrational states of HN2 are determined on the basis of an accurate coupled channel dynamics study using a global analytical potential surface. The surface reproduces the ab initio points with an rms error of 0.08 kcal/mol for energies below 20 kcal/mol. Modifications to the potential that describe the effect of improving the basis set in the ab initio calculations are provided. Converged coupled channel calculations are performed for the ground rotational state of HN2 to determine the lifetimes of the lowest ten vibrational states. Only the ground vibrational state (000) and first excited bend (001) are found to have lifetimes longer than 1 ps. The lifetimes of these states are estimated at 3 x 10 to the -9th and 2 x 10 to the -10th s, respectively. Variation of these results with quality of the ab initio calculations is not more than a factor of 5.

A highly accurate ab initio potential energy surface for methane.

PubMed

Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

2016-09-14

A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of (12)CH4 reproduced with a root-mean-square error of 0.70 cm(-1). The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

Ab-initio study of the energetics and thermodynamics of the reaction CH3H + O( 3P) → CF3H … O → CF3 + OH

NASA Astrophysics Data System (ADS)

Kreye, W. C.

1996-07-01

Ab-initio computations at 298.15 K were made of the activation quantities ΔH ‡, ΔS ‡, and ΔG ‡ and of the reaction quantities ΔHr and ΔSr for CF3H + O( 3P) → CF3H … O → .CF3.OH. CF 3H … O is the transition state (TS). GAUSSIAN92 was used and energies computed at a slightly modified Gaussian-2 level. Two potential surfaces for the TS had symmetries 3A' and 3A″. The two rate constants included a semi-classical, quantum-mechanical-tunneling transmission coefficient. The ab-initio ΔH ‡and ΔH r values were in excellent agreement (± 1 kcal/mol) with experiment; but the ΔS ‡, ΔG ‡, and ΔS r values yielded somewhat poorer agreement. Experimental and ab-initio structures were in excellent agreement.

Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions

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

Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.

2015-09-14

We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t tomore » be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.« less

Conventional and Explicitly Correlated ab Initio Benchmark Study on Water Clusters: Revision of the BEGDB and WATER27 Data Sets.

PubMed

Manna, Debashree; Kesharwani, Manoj K; Sylvetsky, Nitai; Martin, Jan M L

2017-07-11

Benchmark ab initio energies for BEGDB and WATER27 data sets have been re-examined at the MP2 and CCSD(T) levels with both conventional and explicitly correlated (F12) approaches. The basis set convergence of both conventional and explicitly correlated methods has been investigated in detail, both with and without counterpoise corrections. For the MP2 and CCSD-MP2 contributions, rapid basis set convergence observed with explicitly correlated methods is compared to conventional methods. However, conventional, orbital-based calculations are preferred for the calculation of the (T) term, since it does not benefit from F12. CCSD(F12*) converges somewhat faster with the basis set than CCSD-F12b for the CCSD-MP2 term. The performance of various DFT methods is also evaluated for the BEGDB data set, and results show that Head-Gordon's ωB97X-V and ωB97M-V functionals outperform all other DFT functionals. Counterpoise-corrected DSD-PBEP86 and raw DSD-PBEPBE-NL also perform well and are close to MP2 results. In the WATER27 data set, the anionic (deprotonated) water clusters exhibit unacceptably slow basis set convergence with the regular cc-pVnZ-F12 basis sets, which have only diffuse s and p functions. To overcome this, we have constructed modified basis sets, denoted aug-cc-pVnZ-F12 or aVnZ-F12, which have been augmented with diffuse functions on the higher angular momenta. The calculated final dissociation energies of BEGDB and WATER27 data sets are available in the Supporting Information. Our best calculated dissociation energies can be reproduced through n-body expansion, provided one pushes to the basis set and electron correlation limit for the two-body term; for the three-body term, post-MP2 contributions (particularly CCSD-MP2) are important for capturing the three-body dispersion effects. Terms beyond four-body can be adequately captured at the MP2-F12 level.

First-principles calculations of novel materials

NASA Astrophysics Data System (ADS)

Sun, Jifeng

Computational material simulation is becoming more and more important as a branch of material science. Depending on the scale of the systems, there are many simulation methods, i.e. first-principles calculation (or ab-initio), molecular dynamics, mesoscale methods and continuum methods. Among them, first-principles calculation, which involves density functional theory (DFT) and based on quantum mechanics, has become to be a reliable tool in condensed matter physics. DFT is a single-electron approximation in solving the many-body problems. Intrinsically speaking, both DFT and ab-initio belong to the first-principles calculation since the theoretical background of ab-initio is Hartree-Fock (HF) approximation and both are aimed at solving the Schrodinger equation of the many-body system using the self-consistent field (SCF) method and calculating the ground state properties. The difference is that DFT introduces parameters either from experiments or from other molecular dynamic (MD) calculations to approximate the expressions of the exchange-correlation terms. The exchange term is accurately calculated but the correlation term is neglected in HF. In this dissertation, DFT based first-principles calculations were performed for all the novel materials and interesting materials introduced. Specifically, the DFT theory together with the rationale behind related properties (e.g. electronic, optical, defect, thermoelectric, magnetic) are introduced in Chapter 2. Starting from Chapter 3 to Chapter 5, several representative materials were studied. In particular, a new semiconducting oxytelluride, Ba2TeO is studied in Chapter 3. Our calculations indicate a direct semiconducting character with a band gap value of 2.43 eV, which agrees well with the optical experiment (˜ 2.93 eV). Moreover, the optical and defects properties of Ba2TeO are also systematically investigated with a view to understanding its potential as an optoelectronic or transparent conducting material. We find relatively modest band masses for both electrons and holes suggesting applications. Optical properties show a infrared-red absorption when doped. This could potentially be useful for combining wavelength filtering and transparent conducting functions. Furthermore, our defect calculations show that Ba 2TeO is intrinsically p-type conducting under Ba-poor condition. However, the spontaneous formation of the donor defects may constrain the p-type transport properties and would need to be addressed to enable applications. Chapter 4 mainly devotes to the thermoelectric properties of the famous phase change material, Ge2Sb2Te5 (GST). GST has been used in data storage for more than a decade because of their fast phase switching between metastable crystalline (cubic) and amorphous phases. It also exhibits interesting thermoelectric properties, and we did a systematic study on the two crystalline phases (hexagonal and cubic) and the amorphous phase. We found a high Seebeck coefficient with a broad doping concentrations for both n-type and p-type, at and below room temperatures (300 K) for both the cubic and amorphous phases. This finding will be of crucial interests in further understand the thermoelectric properties experimentally and find device applications in the ultimate goal. Several magnetic materials that involve lanthanide elements are reported in Chapter 5. First of all, the electronic and magnetic properties of the BaLn2O4 (Ln = La-Lu, Y) family compound are studied. The series has been synthesized for the first time in single crystalline form, using a molten metal flux. They crystallize in the CaV 2O4 structure type with primitive orthorhombic symmetry (space group Pnma, #62). Our calculations show an insulating character with band gaps ranging from 3 eV to 4.5 eV for the three representative compounds, BaLa2O4, BaGd2O4 and BaLu 2O4. Moreover, the superexchange magnetism is also studied. Secondly, a strong correlated system with cerium is investigated. As expected, we find a value of 15 states eV-1 that stems from the Ce 4f orbitals at the Fermi energy which indicates intermetallic heavy fermion behavior. The Fermi surface calculation shows nesting feature which might be useful to further understand the antiferromagnetic magnetism. Thirdly, the DFT calculations of another lanthanide oxide involving transition element, LaMo16O44, are also presented. This material crystallizes with a complicated crystal structure consists of MoO6 magnetic clusters. The band structure calculations indicate a spin-polarized half metal feature that comes from different crystallographic sites of Mo since La occurs as trivalent with empty f shell thus no contribution to the magnetic moment. Last but not least, we studied the electronic properties of another newly found oxytellride that having lanthanide, Ba3Yb 2O5Te. We find a insulating behavior with a direct band-gap value of 1.9 eV using the DFT+U methodology.

Density functional theory: Foundations reviewed

NASA Astrophysics Data System (ADS)

Kryachko, Eugene S.; Ludeña, Eduardo V.

2014-11-01

Guided by the above motto (quotation), we review a broad range of issues lying at the foundations of Density Functional Theory, DFT, a theory which is currently omnipresent in our everyday computational study of atoms and molecules, solids and nano-materials, and which lies at the heart of modern many-body computational technologies. The key goal is to demonstrate that there are definitely the ways to improve DFT. We start by considering DFT in the larger context provided by reduced density matrix theory (RDMT) and natural orbital functional theory (NOFT), and examine the implications that N-representability conditions on the second-order reduced density matrix (2-RDM) have not only on RDMT and NOFT but, also, by extension, on the functionals of DFT. This examination is timely in view of the fact that necessary and sufficient N-representability conditions on the 2-RDM have recently been attained. In the second place, we review some problems appearing in the original formulation of the first Hohenberg-Kohn theorem which is still a subject of some controversy. In this vein we recall Lieb's comment on this proof and the extension to this proof given by Pino et al. (2009), and in this context examine the conditions that must be met in order that the one-to-one correspondence between ground-state densities and external potentials remains valid for finite subspaces (namely, the subspaces where all Kohn-Sham solutions are obtained in practical applications). We also consider the issue of whether the Kohn-Sham equations can be derived from basic principles or whether they are postulated. We examine this problem in relation to ab initio DFT. The possibility of postulating arbitrary Kohn-Sham-type equations, where the effective potential is by definition some arbitrary mixture of local and non-local terms, is discussed. We also deal with the issue of whether there exists a universal functional, or whether one should advocate instead the construction of problem-geared functionals. These problems are discussed by making reference to ab initio DFT as well as to the local-scaling-transformation version of DFT, LS-DFT. In addition, we examine the question of the accuracy of approximate exchange-correlation functionals in the light of their non-observance of the variational principle. Why do approximate functionals yield reasonable (and accurate) descriptions of many molecular and condensed matter properties? Are the conditions imposed on exchange and correlation functionals sufficiently adequate to produce accurate semi-empirical functionals? In this respect, we consider the question of whether the results reflect a true approach to chemical accuracy or are just the outcome of a virtuoso-like performance which cannot be systematically improved. We discuss the issue of the accuracy of the contemporary DFT results by contrasting them to those obtained by the alternative RDMT and NOFT. We discuss the possibility of improving DFT functionals by applying in a systematic way the N-representability conditions on the 2-RDM. In this respect, we emphasize the possibility of constructing 2-matrices in the context of the local scaling transformation version of DFT to which the N-representability condition of RDM theory may be applied. We end up our revision of HKS-DFT by considering some of the problems related to spin symmetry and discuss some current issues dealing with a proper treatment of open-shell systems. We are particularly concerned, as in the rest of this paper, mostly with foundational issues arising in the construction of functionals. We dedicate the whole Section 4 to the local-scaling transformation version of density functional theory, LS-DFT. The reason is that in this theory some of the fundamental problems that appear in HKS-DFT, have been solved. For example, in LS-DFT the functionals are, in principle, designed to fulfill v- and N-representability conditions from the outset. This is possible because LS-DFT is based on density transformation (local-scaling of coordinates proceeds through density transformation) and so, because these functionals are constructed from prototype N-particle wavefunctions, the ensuing density functionals already have built-in N-representability conditions. This theory is presented in great detail with the purpose of illustrating an alternative way to HKS-DFT which could be used to improve the construction of HKS-DFT functionals. Let us clearly indicate, however, that although appealing from a theoretical point of view, the actual application of LS-DFT to large systems has not taken place mostly because of technical difficulties. Thus, our aim in introducing this theory is to foster a better understanding of its foundations with the hope that it may promote a cross-hybridization with the already existing approaches. Also, to complete our previous discussion on symmetry, in particular, spin-symmetry, we discuss this issue from the perspective of LS-DFT. Finally, in Section 6, we discuss dispersion molecular forces emphasizing their relevance to DFT approaches.

Hydrogen bonding interactions in PN...HX complexes: DFT and ab initio studies of structure, properties and topology.

PubMed

Varadwaj, Pradeep Risikrishna

2010-05-01

Spin-restricted DFT (X3LYP and B3LYP) and ab initio (MP2(fc) and CCSD(fc)) calculations in conjunction with the Aug-CC-pVDZ and Aug-CC-pVTZ basis sets were performed on a series of hydrogen bonded complexes PN...HX (X = F, Cl, Br) to examine the variations of their equilibrium gas phase structures, energetic stabilities, electronic properties, and vibrational characteristics in their electronic ground states. In all cases the complexes were predicted to be stable with respect to the constituent monomers. The interaction energy (Delta E) calculated using a super-molecular model is found to be in this order: PN...HF > PN...HCl > PN...HBr in the series examined. Analysis of various physically meaningful contributions arising from the Kitaura-Morokuma (KM) and reduced variational space self-consistent-field (RVS-SCF) energy decomposition procedures shows that the electrostatic energy has significant contribution to the over-all interaction energy. Dipole moment enhancement (Delta mu) was observed in these complexes expected of predominant dipole-dipole electrostatic interaction and was found to follow the trend PN...HF > PN...HCl > PN...HBr at the CCSD level. However, the DFT (X3LYP and B3LYP) and MP2 levels less accurately determined these values (in this order HF < HCl < HBr). Examination of the harmonic vibrational modes reveals that the PN and HX bands exhibit characteristic blue- and red shifts with concomitant bond contraction and elongation, respectively, on hydrogen bond formation. The topological or critical point (CP) analysis using the static quantum theory of atoms in molecules (QTAIM) of Bader was considered to classify and to gain further insight into the nature of interaction existing in the monomers PN and HX, and between them on H-bond formation. It is found from the analysis of the electron density rho ( c ), the Laplacian of electron charge density nabla(2)rho(c), and the total energy density (H ( c )) at the critical points between the interatomic regions that the interaction N...H is indeed electrostatic in origin (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) > 0 at the BCP) whilst the bonds in PN (rho(c) > 0, nabla(2)rho(c) > 0 and H(c) < 0) and HX ((rho(c) > 0, nabla(2)rho(c) < 0 and H(c) < 0)) are predominantly covalent. A natural bond orbital (NBO) analysis of the second order perturbation energy lowering, E((2)), caused by charge transfer mechanism shows that the interaction N...H is n(N) --> BD*(HX) delocalization.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

2016-04-01

We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

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

Sano, Yukio; Sano, Tomokazu

A quadratic equation for the temperature-independent Grueneisen coefficient {gamma} was derived by a method in which the Walsh-Christian and Mie-Grueneisen equations are combined. Some previously existing ab initio temperature Hugoniots for hexagonal close-packed solid Fe are inaccurate because the constant-volume specific heats on the Hugoniots CVH, which are related uniquely to the solutions of the quadratic equation, have values that are too small. A CVH distribution in the solid phase range was demonstrated to agree approximately with a previous ab initio distribution. In contrast, the corresponding {gamma} distribution was significantly different from the ab initio distribution in the lower pressuremore » region. The causes of these disagreements are clarified.« less

Ab initio study of collective excitations in a disparate mass molten salt.

PubMed

Bryk, Taras; Klevets, Ivan

2012-12-14

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

PubMed

Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

2015-02-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

NASA Astrophysics Data System (ADS)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

NASA Astrophysics Data System (ADS)

Saieswari, A.; Kumar, Sanjay

2007-12-01

An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

Ab initio calculation of one-nucleon halo states

NASA Astrophysics Data System (ADS)

Rodkin, D. M.; Tchuvil'sky, Yu M.

2018-02-01

We develop an approach to microscopic and ab initio description of clustered systems, states with halo nucleon and one-nucleon resonances. For these purposes a basis combining ordinary shell-model components and cluster-channel terms is built up. The transformation of clustered wave functions to the uniform Slater-determinant type is performed using the concept of cluster coefficients. The resulting basis of orthonormalized wave functions is used for calculating the eigenvalues and the eigenvectors of Hamiltonians built in the framework of ab initio approaches. Calculations of resonance and halo states of 5He, 9Be and 9B nuclei demonstrate that the approach is workable and labor-saving.

40 CFR 86.096-7 - Maintenance of records; submittal of information; right of entry.

Code of Federal Regulations, 2010 CFR

2010-07-01

...] (ii) EPA may void ab initio a certificate for a 1994 or 1995 model year light-duty vehicle or light... Administrator upon request. (iii) Any voiding ab initio of a certificate under § 86.091-7(c)(6) and paragraph (h...

40 CFR 80.607 - What are the requirements for obtaining an exemption for diesel fuel or ECA marine fuel used for...

Code of Federal Regulations, 2010 CFR

2010-07-01

... section, will cause the exemption to be void ab initio. (6) If any information required under paragraph (c... void ab initio, and may make the party liable for a violation of this subpart. (f) Effects of exemption...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

The Band Structure of Polymers: Its Calculation and Interpretation. Part 2. Calculation.

ERIC Educational Resources Information Center

Duke, B. J.; O'Leary, Brian

1988-01-01

Details ab initio crystal orbital calculations using all-trans-polyethylene as a model. Describes calculations based on various forms of translational symmetry. Compares these calculations with ab initio molecular orbital calculations discussed in a preceding article. Discusses three major approximations made in the crystal case. (CW)

Ab initio calculations of the lattice dynamics of silver halides

NASA Astrophysics Data System (ADS)

Gordienko, A. B.; Kravchenko, N. G.; Sedelnikov, A. N.

2010-12-01

Based on ab initio pseudopotential calculations, the results of investigations of the lattice dynamics of silver halides AgHal (Hal = Cl, Br, I) are presented. Equilibrium lattice parameters, phonon spectra, frequency densities and effective atomic-charge values are obtained for all types of crystals under study.

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

Iodine Incorporation in Calcite: Insights from Computational and Experimental Study

NASA Astrophysics Data System (ADS)

Feng, X.; Redfern, S. A. T.

2016-12-01

The incorporation of iodine into calcite is important both in the context of radioactive waste disposal (carbonates seem to be the principal host for iodine at the Hnaford site) as well as in paleoproxy methods applied in paleo-oceanography, where iodine content has been proposed as a proxy for fO2. Here, we report on studies of iodine incorporation into calcite carried out by a combination of earlier X-Ray absorption spectroscopy, Raman spectroscopy, X-Ray diffraction and new ab initio DFT calculations (using VASP). Our results show that iodine is principally incorporated into the calcite lattice as IO3, replacing carbon in the carbonate group. The much larger size of iodine, and different outer shell electronic configuration, leads to a distortion of the calcite structure locally. Our DFT results show that the adjacent layers of CO3 groups are significantly distorted, over a length scale of around 0.5 nm, and that this distortion leads to a slight increase in enthalpy associated with the iodine point defect. The relationship to the distorted structure of calcite II is considered, and the role of iodine as an agent of "internal pressure" will be discussed.

Structure of the orthorhombic Al13Co4(100) surface using LEED, STM, and ab initio studies

NASA Astrophysics Data System (ADS)

Shin, Heekeun; Pussi, K.; Gaudry, É.; Ledieu, J.; Fournée, V.; Alarcón Villaseca, S.; Dubois, J.-M.; Grin, Yu.; Gille, P.; Moritz, W.; Diehl, R. D.

2011-08-01

In a combined scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), and density functional theory (DFT) study of the surface of Al13Co4(100), all techniques have found that after annealing to 1165 K, the surface structure is consistent with a dense Al-rich plane with surface Co atom depletion. Various structure models were considered, and in the LEED study, the best agreement was found with a model that consists of Al-rich terminating planes with no Co atoms, and otherwise a structure similar to the bulk puckered layers. This structure was also found to be stable in the DFT study. The best-fit structural parameters are presented for the two domains of this structure, which contain bipentagons that can be related to the pentagonal bipyramidal structures in the bulk, plus additional glue atoms between them. These domains are not strictly related to each other by symmetry, as they have different surface relaxations. The STM study found significant differences in the surfaces of samples grown by different methods and is able to explain a different interpretation made in an earlier study.

Benchmark of Ab Initio Bethe-Salpeter Equation Approach with Numeric Atom-Centered Orbitals

NASA Astrophysics Data System (ADS)

Liu, Chi; Kloppenburg, Jan; Kanai, Yosuke; Blum, Volker

The Bethe-Salpeter equation (BSE) approach based on the GW approximation has been shown to be successful for optical spectra prediction of solids and recently also for small molecules. We here present an all-electron implementation of the BSE using numeric atom-centered orbital (NAO) basis sets. In this work, we present benchmark of BSE implemented in FHI-aims for low-lying excitation energies for a set of small organic molecules, the well-known Thiel's set. The difference between our implementation (using an analytic continuation of the GW self-energy on the real axis) and the results generated by a fully frequency dependent GW treatment on the real axis is on the order of 0.07 eV for the benchmark molecular set. We study the convergence behavior to the complete basis set limit for excitation spectra, using a group of valence correlation consistent NAO basis sets (NAO-VCC-nZ), as well as for standard NAO basis sets for ground state DFT with extended augmentation functions (NAO+aug). The BSE results and convergence behavior are compared to linear-response time-dependent DFT, where excellent numerical convergence is shown for NAO+aug basis sets.

Structural, vibrational, and quasiparticle band structure of 1,1-diamino-2,2-dinitroethelene from ab initio calculations

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

Appalakondaiah, S.; Vaitheeswaran, G., E-mail: gvaithee@gmail.com; Lebègue, S.

The effects of pressure on the structural and vibrational properties of the layered molecular crystal 1,1-diamino-2,2-dinitroethelene (FOX-7) are explored by first principles calculations. We observe significant changes in the calculated structural properties with different corrections for treating van der Waals interactions to Density Functional Theory (DFT), as compared with standard DFT functionals. In particular, the calculated ground state lattice parameters, volume and bulk modulus obtained with Grimme's scheme, are found to agree well with experiments. The calculated vibrational frequencies demonstrate the dependence of the intra and inter-molecular interactions on FOX-7 under pressure. In addition, we also found a significant incrementmore » in the N–H...O hydrogen bond strength under compression. This is explained by the change in bond lengths between nitrogen, hydrogen, and oxygen atoms, as well as calculated IR spectra under pressure. Finally, the computed band gap is about 2.3 eV with generalized gradient approximation, and is enhanced to 5.1 eV with the GW approximation, which reveals the importance of performing quasiparticle calculations in high energy density materials.« less

Photoinduced electron transfer process on emission spectrum of N,N‧-bis(salicylidene)-1,2-phenylenediamine as a Mg2+ cation chemosensor: A first principle DFT and TDDFT study

NASA Astrophysics Data System (ADS)

Taherpour, Avat (Arman); Jamshidi, Morteza; Rezaei, Omid; Belverdi, Ali Rezaei

2018-06-01

The electronic and optical properties of N,N‧-bis(salicylidene)-1,2-phenylenediamine (SPDA) ligand were studied as a chemical sensor of Mg2+ cation in two solvents (water and DMSO) using the ab initio theory through Density Functional Theory (DFT) and Time Dependent Density Functional theory (TDDFT) methods. The results show that the SPDA ligand has a high ability for chemical sensing of Mg2+. The results has also represented that HOMO-LUMO energy gap decreases 0.941 eV after the complex formation between SPDA and Mg2+. In addition, obvious changes are found in the UV-Vis absorption spectrum, optical analyses SPDA ligand and [SPDA.Mg]2+ complex, which it has the capability of detecting Mg2+ via the adsorptive UV-Vis and colorimetric methods. Emission spectrum calculations and photoinduced electron transfer (PET) process in water solution shows different wavelength emission spectrum in amount of 4.6 nm. An analysis of NBO (natural bond orbital) data indicates tangible changes in the electron transfers data from the electron pairs of ligand to the conjugated system, both prior and subsequent to Mg2+addition.

Dehalogenation of persistent halogenated organic compounds: A review of computational studies and quantitative structure-property relationships.

PubMed

Luo, Jin; Hu, Jiwei; Wei, Xionghui; Fu, Liya; Li, Lingyun

2015-07-01

Dehalogenation is one of the highly important degradation reactions for halogenated organic compounds (HOCs) in the environment, which is also being developed as a potential type of the remediation technologies. In combination with the experimental results, intensive efforts have recently been devoted to the development of efficient theoretical methodologies (e.g. multi-scale simulation) to investigate the mechanisms for dehalogenation of HOCs. This review summarizes the structural characteristics of neutral molecules, anionic species and excited states of HOCs as well as their adsorption behavior on the surface of graphene and the Fe cluster. It discusses the key physiochemical properties (e.g. frontier orbital energies and thermodynamic properties) calculated at various levels of theory (e.g. semiempirical, ab initio, density functional theory (DFT) and the periodic DFT) as well as their connections to the reactivity and reaction pathway for the dehalogenation. This paper also reviews the advances in the linear and nonlinear quantitative structure-property relationship models for the dehalogenation kinetics of HOCs and in the mathematical modeling of the dehalogenation processes. Furthermore, prospects of further expansion and exploration of the current research fields are described in this article. Published by Elsevier Ltd.

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

PubMed

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

2015-04-15

A systematic vibrational spectroscopic assignment and analysis of Carbamazepine has been carried out by using FT-IR, FT-Raman and UV spectral data. The vibrational analysis were aided by electronic structure calculations - ab initio (RHF) and hybrid density functional methods (B3LYP) performed with standard basis set 6-31G(d,p). Molecular equilibrium geometries, electronic energies, natural bond order analysis, harmonic vibrational frequencies and IR intensities have been computed. A detailed interpretation of the vibrational spectra of the molecule has been made on the basis of the calculated Potential Energy Distribution (PED) by VEDA program. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λmax were determined by HF/6-311++G(d,p) Time-Dependent method. The thermodynamic functions of the title molecule were also performed using the RHF and DFT methods. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the (13)C and (1)H NMR chemical shifts of Carbamazepine. Copyright © 2015 Elsevier B.V. All rights reserved.

Structures, Energetics, and IR Spectra of Monohydrated Inorganic Acids: Ab initio and DFT Study.

PubMed

Kołaski, Maciej; Zakharenko, Aleksey A; Karthikeyan, S; Kim, Kwang S

2011-10-11

We carried out extensive calculations of diverse inorganic acids interacting with a single water molecule, through a detailed analysis of many possible conformations. The optimized structures were obtained by using density functional theory (DFT) and the second order Møller-Plesset perturbation theory (MP2). For the most stable conformers, we calculated the interaction energies at the complete basis set (CBS) limit using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. The -OH stretching harmonic and anharmonic frequencies are provided as fingerprints of characteristic conformers. The zero-point energy (ZPE) uncorrected/corrected (ΔEe/ΔE0) interaction energies and the enthalpies/free energies (ΔHr/ΔGr at room temperature and 1 bar) are reported. Various comparisons are made between many diverse inorganic acids (HmXOn where X = B/N/P/Cl/Br/I, m = 1-3, and n = 0-4) as well as other simple inorganic acids. In many cases, we find that the dispersion-driven van der Waals interactions between X in inorganic acid molecules and O in water molecules as well as the X(+)···O(-) electrostatic interactions are important.

Theoretical study on the mechanism of a ring-opening reaction of oxirane by the active-site aspartic dyad of HIV-1 protease.

PubMed

Kóna, Juraj

2008-01-21

Two possible mechanisms of the irreversible inhibition of HIV-1 protease by epoxide inhibitors are investigated on an enzymatic model using ab initio (MP2) and density functional theory (DFT) methods (B3LYP, MPW1K and M05-2X). The calculations predict the inhibition as a general acid-catalyzed nucleophilic substitution reaction proceeding by a concerted SN2 mechanism with a reaction barrier of ca. 15-21 kcal mol(-1). The irreversible nature of the inhibition is characterized by a large negative reaction energy of ca. -17-(-24) kcal mol(-1). A mechanism with a direct proton transfer from an aspartic acid residue of the active site onto the epoxide ring has been shown to be preferred compared to one with the proton transfer from the acid catalyst facilitated by a bridging catalytic water molecule. Based on the geometry of the transition state, structural data important for the design of irreversible epoxide inhibitors of HIV-1 protease were defined. Here we also briefly discuss differences between the epoxide ring-opening reaction in HIV-1 protease and epoxide hydrolase, and the accuracy of the DFT method used.

Ab initio study for the IR spectroscopy of PbTiO3 and PbZrO3, primary blocks of PbZr1‑x Ti x O3

NASA Astrophysics Data System (ADS)

Peperstraete, Yoann; Amzallag, Emilie; Tétot, Robert; Roy, Pascale

2018-05-01

PbTiO3 (PT) and PbZrO3 (PZ) are the two primary blocks of the solid solution PbZr1‑x Ti x O3 (PZT). They can be modelled in different ways; but, in order to do comparable DFT calculations on PZT, with different values of x, one must find a unique method that can be used for both PT and PZ. In particular, we want to evaluate their vibrational properties to compare them with experimental data. Density functional theory (DFT) is used to perform structure geometry optimizations and electronic structure calculations, both on low- and high-temperature phase. Then, harmonic vibrational frequencies of their low-temperature phase are determined for transverse and longitudinal optical (TO & LO) phonons. Moreover, a detailed study of the eigenvectors shows that accurate calculations are necessary to correctly interpret and understand the IR spectra. In the end, the comparison of our theoretical results with previous experimental and theoretical data confirm the strong potential of the SOGGA (second-order generalized gradient approximation) functional to correctly describe PT, PZ and, hopefully, PZT; especially their structural and vibrational properties.

Cs diffusion in SiC high-energy grain boundaries

NASA Astrophysics Data System (ADS)

Ko, Hyunseok; Szlufarska, Izabela; Morgan, Dane

2017-09-01

Cesium (Cs) is a radioactive fission product whose release is of concern for Tristructural-Isotropic fuel particles. In this work, Cs diffusion through high energy grain boundaries (HEGBs) of cubic-SiC is studied using an ab-initio based kinetic Monte Carlo (kMC) model. The HEGB environment was modeled as an amorphous SiC, and Cs defect energies were calculated using the density functional theory (DFT). From defect energies, it was suggested that the fastest diffusion mechanism is the diffusion of Cs interstitial in an amorphous SiC. The diffusion of Cs interstitial was simulated using a kMC model, based on the site and transition state energies sampled from the DFT. The Cs HEGB diffusion exhibited an Arrhenius type diffusion in the range of 1200-1600 °C. The comparison between HEGB results and the other studies suggests not only that the GB diffusion dominates the bulk diffusion but also that the HEGB is one of the fastest grain boundary paths for the Cs diffusion. The diffusion coefficients in HEGB are clearly a few orders of magnitude lower than the reported diffusion coefficients from in- and out-of-pile samples, suggesting that other contributions are responsible, such as radiation enhanced diffusion.

Understanding Ferromagnetic Phase Stability, Electronic and Transport Properties of BaPaO3 and BaNpO3 from Ab-Initio Calculations

NASA Astrophysics Data System (ADS)

Khandy, Shakeel Ahmad; Gupta, Dinesh C.

2017-10-01

An extensive study of rare-earth perovskite BaPaO3 and BaNpO3 has been performed by first-principles tactics based on density functional theory (DFT), because the delocalized f-electrons play an important role in the band structure formation, to reveal their impact on the overall physical and chemical properties; it has turned out to be an interesting theme. Along with critical radii and thermoelectric properties, two different theories are employed to calculate the structural properties. The DFT and empirically calculated lattice constants are in rational accord with the experimental results. The critical radius calculations show that the BaPaO3 lattice has a smaller oxygen migration activation energy than the BaNpO3. In addition, we discuss the band profile and magnetic moments for these materials, which demonstrate the half-metallic ferromagnetism with a direct energy gap of 3.91 eV for BaPaO3 and an indirect gap of 3.79 eV for BaNpO3. More interestingly, the integral magnetic moments are in accordance with the Slater-Pauling rule.

Unexpected Competition between Antiferromagnetic and Ferromagnetic States in Hf2MnRu5B2: Predicted and Realized.

PubMed

Shankhari, Pritam; Zhang, Yuemei; Stekovic, Dejan; Itkis, Mikhail E; Fokwa, Boniface P T

2017-11-06

Materials "design" is increasingly gaining importance in the solid-state materials community in general and in the field of magnetic materials in particular. Density functional theory (DFT) predicted the competition between ferromagnetic (FM) and antiferromagnetic (AFM) ground states in a ruthenium-rich Ti 3 Co 5 B 2 -type boride (Hf 2 MnRu 5 B 2 ) for the first time. Vienna ab initio simulation package (VASP) total energy calculations indicated that the FM model was marginally more stable than one of the AFM models (AFM1), indicating very weak interactions between magnetic 1D Mn chains that can be easily perturbated by external means (magnetic field or composition). The predicted phase was then synthesized by arc-melting and characterized as Hf 2 Mn 1-x Ru 5+x B 2 (x = 0.27). Vibrating-scanning magnetometry shows an AFM ground state with T N ≈ 20 K under low magnetic field (0.005 T). At moderate-to-higher fields, AFM ordering vanishes while FM ordering emerges with a Curie temperature of 115 K. These experimental outcomes confirm the weak nature of the interchain interactions, as predicted by DFT calculations.

The origin of anisotropy and high density of states in the electronic structure of Cr2GeC by means of polarized soft x-ray spectroscopy and ab initio calculations

NASA Astrophysics Data System (ADS)

Magnuson, Martin; Mattesini, Maurizio; Bugnet, Matthieu; Eklund, Per

2015-10-01

The anisotropy in the electronic structure of the inherently nanolaminated ternary phase Cr2GeC is investigated by bulk-sensitive and element selective soft x-ray absorption/emission spectroscopy. The angle-resolved absorption/emission measurements reveal differences between the in-plane and out-of-plane bonding at the (0001) interfaces of Cr2GeC. The Cr L 2, 3, C K, and Ge M 1, M 2, 3 emission spectra are interpreted with first-principles density-functional theory (DFT) including core-to-valence dipole transition matrix elements. For the Ge 4s states, the x-ray emission measurements reveal two orders of magnitude higher intensity at the Fermi level than DFT within the General Gradient Approximation (GGA) predicts. We provide direct evidence of anisotropy in the electronic structure and the orbital occupation that should affect the thermal expansion coefficient and transport properties. As shown in this work, hybridization and redistribution of intensity from the shallow 3d core levels to the 4s valence band explain the large Ge density of states at the Fermi level.

The origin of anisotropy and high density of states in the electronic structure of Cr2GeC by means of polarized soft x-ray spectroscopy and ab initio calculations.

PubMed

Magnuson, Martin; Mattesini, Maurizio; Bugnet, Matthieu; Eklund, Per

2015-10-21

The anisotropy in the electronic structure of the inherently nanolaminated ternary phase Cr2GeC is investigated by bulk-sensitive and element selective soft x-ray absorption/emission spectroscopy. The angle-resolved absorption/emission measurements reveal differences between the in-plane and out-of-plane bonding at the (0001) interfaces of Cr2GeC. The Cr L(2, 3), C K, and Ge M1, M(2, 3) emission spectra are interpreted with first-principles density-functional theory (DFT) including core-to-valence dipole transition matrix elements. For the Ge 4s states, the x-ray emission measurements reveal two orders of magnitude higher intensity at the Fermi level than DFT within the General Gradient Approximation (GGA) predicts. We provide direct evidence of anisotropy in the electronic structure and the orbital occupation that should affect the thermal expansion coefficient and transport properties. As shown in this work, hybridization and redistribution of intensity from the shallow 3d core levels to the 4s valence band explain the large Ge density of states at the Fermi level.

Accurate prediction of bond dissociation energies of large n-alkanes using ONIOM-CCSD(T)/CBS methods

NASA Astrophysics Data System (ADS)

Wu, Junjun; Ning, Hongbo; Ma, Liuhao; Ren, Wei

2018-05-01

Accurate determination of the bond dissociation energies (BDEs) of large alkanes is desirable but practically impossible due to the expensive cost of high-level ab initio methods. We developed a two-layer ONIOM-CCSD(T)/CBS method which treats the high layer with CCSD(T) method and the low layer with DFT method, respectively. The accuracy of this method was validated by comparing the calculated BDEs of n-hexane with that obtained at the CCSD(T)-F12b/aug-cc-pVTZ level of theory. On this basis, the C-C BDEs of C6-C20 n-alkanes were calculated systematically using the ONIOM [CCSD(T)/CBS(D-T):M06-2x/6-311++G(d,p)] method, showing a good agreement with the data available in the literature.

Photochemistry and reactivity of the phenyl radical-water system: a matrix isolation and computational study.

PubMed

Mardyukov, Artur; Crespo-Otero, Rachel; Sanchez-Garcia, Elsa; Sander, Wolfram

2010-08-02

The reaction of the phenyl radical 1 with water has been investigated by using matrix isolation spectroscopy and quantum chemical calculations. The primary thermal product of the reaction between 1 and water is a weakly bound complex stabilized by an OH...pi interaction. This complex is photolabile, and visible-light irradiation (lambda>420 nm) results in hydrogen atom transfer from water to radical 1 and the formation of a highly labile complex between benzene and the OH radical. This complex is stable under the conditions of matrix isolation, however, continuous irradiation with lambda>420 nm light results in the complete destruction of the aromatic system and formation of an acylic unsaturated ketene. The mechanisms of all reaction steps are discussed in the light of ab initio and DFT calculations.

Assessment of Molecular Modeling & Simulation

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

None

2002-01-03

This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materialsmore » modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.« less

Vanadium impurity effects on optical properties of Ti3N2 mono-layer: An ab-initio study

NASA Astrophysics Data System (ADS)

Babaeipour, Manuchehr; Eslam, Farzaneh Ghafari; Boochani, Arash; Nezafat, Negin Beryani

2018-06-01

The present work is investigated the effect of vanadium impurity on electronic and optical properties of Ti3N2 monolayer by using density function theory (DFT) implemented in Wien2k code. In order to study optical properties in two polarization directions of photons, namely E||x and E||z, dielectric function, absorption coefficient, optical conductivity, refraction index, extinction index, reflectivity, and energy loss function of Ti3N2 and Ti3N2-V monolayer have been evaluated within GGA (PBE) approximation. Although, Ti3N2 monolayer is a good infrared reflector and can be used as an infrared mirror, introducing V atom in the infrared area will decrease optical conductivity because optical conductivity of a pure form of a material is higher than its doped form.

Half-metallicity in the ferrimagnet [MnII(enH)(H2O)][CrIII(CN)6]·H2O: Ab initio study

NASA Astrophysics Data System (ADS)

Li, N.; Yao, K. L.; Zhong, G. H.; Ching, W. Y.

2013-03-01

The density-functional theory (DFT) within the full potential linearized augmented plane wave (FPLAPW) method is applied to study the two-dimensional achiral soft ferrimagnet [MnII(enH)(H2O)][CrIII(CN)6]·H2O. The phase stability, electronic structure, magnetic and conducting properties are investigated. Our results reveal that the compound has a stable ferrimagnetic ground state in good agreement with the experiment. From the spin density distribution, the spin magnetic moment of the compound is mainly from Cr3+ and Mn2+ ions with small contributions from the oxygen, nitrogen and carbon ions. The calculated electronic band structure predicts the compound to be a half-metal with the spin magnetic moment of 1.000 μB per molecule.

Optical properties of an indium doped CdSe nanocrystal: A density functional approach

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

Salini, K.; Mathew, Vincent, E-mail: vincent@cukerala.ac.in; Mathew, Thomas

2016-05-06

We have studied the electronic and optical properties of a CdSe nanocrystal doped with n-type impurity atom. First principle calculations of the CdSe nanocrystal based on the density functional theory (DFT), as implemented in the Vienna Ab Initio Simulation Package (VASP) was used in the calculations. We have introduced a single Indium impurity atom into CdSe nanocrystal with 1.3 nm diameter. Nanocrystal surface dangling bonds are passivated with hydrogen atom. The band-structure, density of states and absorption spectra of the doped and undopted nanocrystals were discussed. Inclusion of the n-type impurity atom introduces an additional electron in conduction band, and significantlymore » alters the electronic and optical properties of undoped CdSe nanocrystal. Indium doped CdSe nannocrystal have potential applications in optoelectronic devices.« less

Prediction of electronic and optical properties of ZnAl2Te4 defect chalcopyrite semiconductor: an ab-initio study

NASA Astrophysics Data System (ADS)

Mayengbam, Rishikanta; Tripathy, S. K.; Pandey, B. P.

2018-03-01

In this paper, we have investigated the structural, electronic and optical properties of ZnAl2Te4 defect chalcopyrite semiconductor using generalized gradient approximation (GGA) within density functional theory (DFT). We have calculated the optimized lattice constants (a and c) and compared with the available experimental values. The optimized lattice constants have been used to calculate the energy band gap and found to be 1.57 eV. The partial density of states and total density of states have been discussed in detail. The frequency dependent dielectric constant and refractive index have been calculated and plotted in the energy range 0-13 eV. All the above parameters have been compared with the available experimental and theoretical values and found good agreement between them.

Ab-initio calculations of structural, electronic, and optical properties of Zn3(VO4)2

NASA Astrophysics Data System (ADS)

Ahmed, Nisar; Mukhtar, S.; Gao, Wei; Zafar Ilyas, Syed

2018-03-01

The structural, electronic, and optical properties of Zn3(VO4)2 are investigated using full potential linearized augmented plane wave (FP-LAPW) method within the framework of density functional theory (DFT). Various approaches are adopted to treat the exchange and correlation potential energy such as generalized gradient approximation (GGA), GGA+U, and the Tran–Blaha modified Becke–Johnson (TB-mBJ) potential. The calculated band gap of 3.424 eV by TB-mBJ is found to be close to the experimental result (3.3 eV). The optical anisotropy is analyzed through optical constants, such as dielectric function and absorption coefficient along parallel and perpendicular crystal orientations. The absorption coefficient reveals high absorption (1.5× {10}6 {cm}}-1) of photons in the ultraviolet region.

Ab-initio study of electronic and magnetic properties of Co-doped Mo2C monolayer

NASA Astrophysics Data System (ADS)

Mehta, Veenu; Tankeshwar, K.; Saini, Hardev S.

2018-05-01

The spin polarized density functional theory (DFT) based calculations has been performed to investigate the electronic and magnetic properties of pristine and Co-doped Mo2C using VASP code. The calculated results show that the pristine Mo2C is found to be non-magnetic whereas the Co dopant at Mo-site in the Mo2C monolayer generates the ferromagnetism in the resultant compound. The total magnetic moment of the system has been found to be 1.2µB which increases to 2.03µB as the concentration of Co increase from 3% to 8%, respectively. The electronic structure calculations of the pristine and Co-doped Mo2C show its metallic behavior which may found its application in magnetic energy storage devices, magnetic tape etc.

Ab initio study of (Fe, Ni) doped GaAs: Magnetic, electronic properties and Faraday rotation

NASA Astrophysics Data System (ADS)

Sbai, Y.; Ait Raiss, A.; Bahmad, L.; Benyoussef, A.

2017-06-01

The interesting diluted magnetic semiconductor (DMS), Gallium Arsenide (GaAs), was doped with the transition metals magnetic impurities: iron (Fe) and Nickel (Ni), in one hand to study the magnetic and magneto-optical properties of the material Ga(Fe, Ni) As, in the other hand to investigate the effect of the doping on the properties of this material, the calculations were performed within the spin polarized density functional theory (DFT) and generalized gradient approximation (GGA) with AKAI KKR-CPA method, the density of states (DOS) for different doping concentrations were calculated, giving the electronical properties, as well as the magnetic state and magnetic states energy, also the effect of these magnetic impurities on the Faraday rotation as magneto-optical property. Furthermore, we found the stable magnetic state for our doped material GaAs.

Intramolecular addition of cysteine thiyl radical to phenylalanine and tyrosine in model peptides, Phe (CysS•) and Tyr(CysS•): a computational study

PubMed Central

Naumov, Sergej; Schöneich, Christian

2009-01-01

Density Functional Theory (DFT) and ab initio calculations were carried out to evaluate the potential for intramolecular addition of cysteine (Cys) thiyl radicals (CysS•) to aromatic amino acids (Phe and Tyr) in water. These calculations yielded stable cyclic conformations, in which π-complexes were more stable than cyclohexadienyl radicals in water. In these π-complexes, the C2-S distances were significantly shorter compared to the C1-S and C3-S distances. Comparable results on the relative stabilities were obtained for model calculations for the addition of HS•/CH3S• to toluene and para-hydroxytoluene. The adduct of thiyl radicals with Phe was more stable than that with Tyr, and the stabilization energies depended on the C-terminal substituents. PMID:19309133

First-principles studies of electronic, transport and bulk properties of pyrite FeS2

NASA Astrophysics Data System (ADS)

Banjara, Dipendra; Mbolle, Augustine; Malozovsky, Yuriy; Franklin, Lashounda; Bagayoko, Diola

We present results of ab-initio, self-consistent density functional theory (DFT) calculations of electronic, transport, and bulk properties of pyrite FeS2. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO) formalism, following the Bagayoko, Zhao and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method requires successive, self consistent calculations with increasing basis sets to reach the ground state of the system under study. We report the band structure, the band gap, total and partial densities of states, effective masses, and the bulk modulus. Work funded in part by the US Department of Energy (DOE), National Nuclear Security Administration (NNSA) (Award No.DE-NA0002630), the National Science Foundation (NSF) (Award No, 1503226), LaSPACE, and LONI-SUBR.

Raman and infrared spectra and theoretical calculations of dipicolinic acid, dinicotinic acid, and their dianions

NASA Astrophysics Data System (ADS)

McCann, Kathleen; Laane, Jaan

2008-11-01

The Raman and infrared spectra of dipicolinic acid (DPA) and dinicotinic acid (DNic) and their salts (CaDPA, Na 2DPA, and CaDNic) have been recorded and the spectra have been assigned. Ab initio and DFT calculations were carried out to predict the structures and vibrational spectra and were compared to the experimental results. Because of extensive intermolecular hydrogen bonding in the crystals of these molecules, the calculated structures and spectra for the individual molecules agree only moderately well with the experimental values. Theoretical calculations were also carried out for DPA dimers and DPA·2H 2O to better understand the intermolecular interactions. The spectra do show that DPA and its calcium salt, which are present in anthrax spores, can be distinguished from the very similar DNic and CaDNic.

Experimental and theoretical vibrational spectroscopy studies of acetohydroxamic acid and desferrioxamine B in aqueous solution: Effects of pH and iron complexation

NASA Astrophysics Data System (ADS)

Edwards, David C.; Nielsen, Steen B.; Jarzęcki, Andrzej A.; Spiro, Thomas G.; Myneni, Satish C. B.

2005-07-01

The deprotonation and iron complexation of the hydroxamate siderophore, desferrioxamine B (desB), and a model hydroxamate ligand, acetohydroxamic acid (aHa), were studied using infrared, resonance Raman and UV-vis spectroscopy. The experimental spectra were interpreted by a comparison with DFT calculated spectra of aHa (partly hydrated) and desB (reactive groups of unhydrated molecule) at the B3LYP/6-31G* level of theory. The ab initio models include three water molecules surrounding the deprotonation site of aHa to account for partial hydration. Experiments and calculations were also conducted in D 2O to verify spectral assignments. These studies of aHa suggest that the cis-keto-aHa is the dominant form, and its deprotonation occurs at the oxime oxygen atom in aqueous solutions. The stable form of iron-complexed aHa is identified as Fe(aHa) 3 for a wide range of pH conditions. The spectral information of aHa and an ab initio model of desB were used to interpret the chemical state of different functional groups in desB. Vibrational spectra of desB indicate that the oxime and amide carbonyl groups can be identified unambiguously. Vibrational spectral analysis of the oxime carbonyl after deprotonation and iron complexation of desB indicates that the conformational changes between anion and the iron-complexed anion are small. Enhanced electron delocalization in the oxime group of Fe-desB when compared to that of Fe(aHa) 3 may be responsible for higher stability constant of the former.

Ab initio modeling of nonequilibrium electron-ion dynamics of iron in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Ogitsu, T.; Fernandez-Pañella, A.; Hamel, S.; Correa, A. A.; Prendergast, D.; Pemmaraju, C. D.; Ping, Y.

2018-06-01

The spatiotemporal electron and ion relaxation dynamics of iron induced by femtosecond laser pulses was studied using a one-dimensional two-temperature model (1D-TTM) where electron and ion temperature-dependent thermophysical parameters such as specific heat (C ), electron-phonon coupling (G ), and thermal conductivity (K ) were calculated with ab initio density-functional-theory (DFT) simulations. Based on the simulated time evolutions of electron and ion temperature distributions [Te(x ,t ) and Ti(x ,t ) ], the time evolution of x-ray absorption near-edge spectroscopy (XANES) was calculated and compared with experimental results reported by Fernandez-Pañella et al., where the slope of XANES spectrum at the onset of absorption (s ) was used due to its excellent sensitivity to the electron temperature. Our results indicate that the ion temperature dependence on G and C , which is largely neglected in the past studies, is very important for studying the nonequilibrium electron-ion relaxation dynamics of iron in warm dense matter (WDM) conditions. It is also shown that the 1 /s behavior becomes very sensitive to the thermal gradient profile, in other words, to the values of K in a TTM simulation, for target thickness of about two to four times the mean free path of conduction electrons. Our approach based on 1D-TTM and XANES simulations can be used to determine the optimal combination of target geometry and laser fluence for a given target material, which will enable us to tightly constrain the thermophysical parameters under electron-ion nonequilibrium WDM conditions.

Ab initio theories for light nuclei and neutron stars

NASA Astrophysics Data System (ADS)

Gezerlis, Alexandros

2016-09-01

In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).

Ab initio calculation of the shear viscosity of neon in the liquid and hypercritical state over a wide pressure and temperature range

NASA Astrophysics Data System (ADS)

Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc

1992-08-01

The shear viscosity is calculated ab initio for the liquid and hypercritical state, i.e. a previously published potential for Ne 2, obtained from ab initio calculations including electron correlation, is used in classical equilibrium molecular dynamics simulations to obtain the shear viscosity from a Green-Kubo integral. The quality of the results is quite uniform over a large pressure range up to 1000 MPa and a wide temperature range from 26 to 600 K. In most cases the calculated shear viscosity deviates by less than 10% from the experimental value, in general the error being only a few percent.

Ab initio determination of mode coupling in HSSH - The torsional splitting in the first excited S-S stretching state

NASA Technical Reports Server (NTRS)

Herbst, Eric; Winnewisser, G.; Yamada, K. M. T.; Defrees, D. J.; Mclean, A. D.

1989-01-01

A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.

Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations

NASA Astrophysics Data System (ADS)

Fujimori, Mitsuki; Sogawa, Haruki; Ota, Shintaro; Karpov, Pavel; Shulga, Sergey; Blume, Yaroslav; Kurita, Noriyuki

2018-01-01

Filamentous temperature-sensitive Z (FtsZ) protein plays essential role in bacteria cell division, and its inhibition prevents Mycobacteria reproduction. Here we adopted curcumin derivatives as candidates of novel inhibitors and investigated their specific interactions with FtsZ, using ab initio molecular simulations based on protein-ligand docking, classical molecular mechanics and ab initio fragment molecular orbital (FMO) calculations. Based on FMO calculations, we specified the most preferable site of curcumin binding to FtsZ and highlighted the key amino acid residues for curcumin binding at an electronic level. The result will be useful for proposing novel inhibitors against FtsZ based on curcumin derivatives.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

PubMed Central

Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

2015-01-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

One Size Fits All? Learning Conditions and Working Memory Capacity in "Ab Initio" Language Development

ERIC Educational Resources Information Center

Sanz, Cristina; Lin, Hui-Ju; Lado, Beatriz; Stafford, Catherine A.; Bowden, Harriet W.

2016-01-01

The article summarizes results from two experimental studies (N = 23, N = 21) investigating the extent to which working memory capacity (WMC) intervenes in "ab initio" language development under two pedagogical conditions [± grammar lesson + input-based practice + explicit feedback]. The linguistic target is the use of morphosyntax to…