Ab initio structure determination of n-diamond.
Li, Da; Tian, Fubo; Chu, Binhua; Duan, Defang; Sha, Xiaojing; Lv, Yunzhou; Zhang, Huadi; Lu, Nan; Liu, Bingbing; Cui, Tian
2015-01-01
A systematic computational study on the crystal structure of n-diamond has been performed using first-principle methods. A novel carbon allotrope with hexagonal symmetry R32 space group has been predicted. We name it as HR-carbon. HR-carbon composed of lonsdaleite layers and unique C3 isosceles triangle rings, is stable over graphite phase above 14.2 GPa. The simulated x-ray diffraction pattern, Raman, and energy-loss near-edge spectrum can match the experimental results very well, indicating that HR-carbon is a likely candidate structure for n-diamond. HR-carbon has an incompressible atomic arrangement because of unique C3 isosceles triangle rings. The hardness and bulk modulus of HR-carbon are calculated to be 80 GPa and 427 GPa, respectively, which are comparable to those of diamond. C3 isosceles triangle rings are very important for the stability and hardness of HR-carbon. PMID:26299905
Ab initio structure determination of n-diamond
Li, Da; Tian, Fubo; Chu, Binhua; Duan, Defang; Sha, Xiaojing; Lv, Yunzhou; Zhang, Huadi; Lu, Nan; Liu, Bingbing; Cui, Tian
2015-01-01
A systematic computational study on the crystal structure of n-diamond has been performed using first-principle methods. A novel carbon allotrope with hexagonal symmetry R32 space group has been predicted. We name it as HR-carbon. HR-carbon composed of lonsdaleite layers and unique C3 isosceles triangle rings, is stable over graphite phase above 14.2 GPa. The simulated x-ray diffraction pattern, Raman, and energy-loss near-edge spectrum can match the experimental results very well, indicating that HR-carbon is a likely candidate structure for n-diamond. HR-carbon has an incompressible atomic arrangement because of unique C3 isosceles triangle rings. The hardness and bulk modulus of HR-carbon are calculated to be 80 GPa and 427 GPa, respectively, which are comparable to those of diamond. C3 isosceles triangle rings are very important for the stability and hardness of HR-carbon. PMID:26299905
Ab initio Structure Determination of Mg10Ir19B16
Xu, Qiang; Klimczuk, T.; Gortenmulder, T.; Jansen, J.; McGuire, Michael A; Cava, R. J.; Zandbergen, H
2009-01-01
The ab initio structure determination of a novel unconventional noncentro-symmetric superconductor Mg{sub 10}Ir{sub 19}B{sub 16} (T{sub c} = 5 K) has been performed using a method that involves a combination of experimental data and calculations. Electron diffraction, X-ray powder diffraction, phase estimation routines, quantum mechanical calculations, high-resolution electron microscopy, and structural chemistry arguments are used. With the strengths of different methods used to eliminate the ambiguities encountered in others, the complete structure, including a very light B atom, has been determined with a high accuracy from impure polycrystalline powder samples, which suggests that the type of analysis described may be used to successfully address other similar intractable problems. The solved structure of Mg{sub 10}Ir{sub 19}B{sub 16} shows a complex nature that irregular coordination environments preclude a conversional description of compact packing of coordination polyhedra; however, it can be easier understood as ordered in an onion-skin-like series of nested polyhedra.
Gall, D.; Sta''dele, M.; Ja''rrendahl, K.; Petrov, I.; Desjardins, P.; Haasch, R. T.; Lee, T.-Y.; Greene, J. E.
2001-03-15
Experimental and ab initio computational methods are employed to conclusively show that ScN is a semiconductor rather than a semimetal; i.e., there is a gap between the N 2p and the Sc 3d bands. Previous experimental investigators reported, in agreement with band structure calculations showing a band overlap of 0.2 eV, that ScN is a semimetal while others concluded that it is a semiconductor with a band gap larger than 2 eV. We have grown high quality, single crystalline ScN layers on MgO(001) and on TiN(001) buffer layers on MgO(001) by ultrahigh vacuum reactive magnetron sputter deposition. ScN optical properties were determined by transmission, reflection, and spectroscopic ellipsometry while in-situ x-ray and ultraviolet valence band photoelectron spectroscopy were used to determine the density of states (DOS) below the Fermi level. The measured DOS exhibits peaks at 3.8 and 5.2 eV stemming from the N 2p bands and at 15.3 eV due to the N 2s bands. The imaginary part of the measured dielectric function {epsilon}{sub 2} consists of two primary features due to direct X- and {Gamma}-point transitions at photon energies of 2.7 and 3.8 eV, respectively. For comparison, the ScN band structure was calculated using an ab initio Kohn--Sham approach which treats the exchange interactions exactly within density-functional theory. Calculated DOS and the complex dielectric function are in good agreement with our ScN valence-band photoelectron spectra and measured optical properties, respectively. We conclude, combining experimental and computational results, that ScN is a semiconductor with an indirect {Gamma}--X bandgap of 1.3{+-}0.3eV and a direct X-point gap of 2.4{+-}0.3eV.
Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung
2016-01-01
Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380
Yoshimura, Masato; Chen, Nai Chi; Guan, Hong Hsiang; Chuankhayan, Phimonphan; Lin, Chien Chih; Nakagawa, Atsushi; Chen, Chun Jung
2016-07-01
Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380
Bylaska, Eric J.; Dixon, David A.; Felmy, Andrew R.; Tratnyek, Paul G.
2002-12-17
Substituted chloromethyl radicals and anions are potential intermediates in the reduction of substituted chlorinated methanes (CHxCl3-xL, with L- ) F-, OH-, SH-, NO3 -, HCO3 - and (x 0-3). Thermochemical properties, Hf (298.15 K), S(298.15 K,1 bar), and GS(298.15 K, 1 bar), were calculated by using ab initio electronic structure methods for the substituted chloromethyl radicals and anions: CHyCl2-yL and CHyCl2-yL-, for y 0-2. In addition, thermochemical properties were calculated for the aldehyde, ClHCO, and the gemchlorohydrin anions, CCl3O-, CHCl2O-, and CH2ClO-. The thermochemical properties of these additional compounds were calculated because the nitrate-substituted compounds, CHyCl2-y(NO3) and CHyCl2-y(NO3)-,
Ab initio structure determination of novel borate NaSrBO{sub 3}
Wu, L. . E-mail: lwu@nankai.edu.cn; Chen, X.L. . E-mail: xlchen@aphy.iphy.ac.cn; Zhang, Y.; Kong, Y.F.; Xu, J.J.; Xu, Y.P.
2006-04-15
A novel orthoborate, NaSrBO{sub 3}, has been successfully synthesized by standard solid-state reaction, and the crystal structure has been determined from powder X-ray diffraction data. It crystallizes in the monoclinic space group P2{sub 1}/c with lattice parameters: a=5.32446(7)A, b=9.2684(1)A, c=6.06683(8)A, {beta}=100.589(1){sup o}. The fundamental building units are isolated BO{sub 3} groups, which are parallelly distributed along two different directions. Because of the anisotropic polarizations of planar BO{sub 3} groups, a considerable birefringence can be expected in it. The Na atoms are six-coordinated with O atoms to form octahedra, and the Sr atoms are nine-coordinated, forming tri-capped trigonal prisms. Those polyhedra connect with each other by bridging-oxygen atoms, forming infinite three-dimensional network, which indicates that the cleaving problem is expected to be overcome during the course of single-crystal growth. The infrared spectrum has been measured, and the result is consistent with the crystallographic study. Moreover, a comparison of the new structure type with the other known orthoborates is presented here.
Sun, J.; Pohl, K.; Mikkelsen, A.; Fuglsang Jensen, M.; Hofmann, Ph.; Koroteev, Y. M.; Bihlmayer, G.; Chulkov, E. V.
2006-12-15
The surface structure of Bi(110) has been investigated by low-energy electron diffraction intensity analysis and by first-principles calculations. Diffraction patterns at a sample temperature of 110 K and normal incidence reveal a bulk truncated (1x1) surface without indication of any structural reconstruction despite the presence of dangling bonds on the surface layer. Good agreement is obtained between the calculated and measured diffraction intensities for this surface containing only one mirror-plane symmetry element and a buckled bilayer structure. No significant interlayer spacing relaxations are found. The Debye temperature for the surface layer is found to be lower than in the bulk, which is indicative of larger atomic vibrational amplitudes at the surface. Meanwhile, the second layer shows a Debye temperature close to the bulk value. The experimental results for the relaxations agree well with those of our first-principles calculation.
Ab initio nuclear structure theory
NASA Astrophysics Data System (ADS)
Negoita, Gianina Alina
Ab initio no core methods have become major tools for understanding the properties of light nuclei based on realistic nucleon-nucleon (NN) and three-nucleon (NNN) interactions. A brief description is provided for the inter-nucleon interactions that fit two-body scattering and bound state data, as well as NNN interactions. Major new progress, including the goal of applying these interactions to solve for properties of nuclei, is limited by convergence issues. That is, with the goal of obtaining high precision solutions of the nuclear many-body Hamiltonian with no core methods (all nucleons treated on the same footing), one needs to proceed to very large basis spaces to achieve a convergence pattern suitable for extrapolation to the exact result. This thesis investigates (1) the similarity renormalization group (SRG) approach to soften the interaction, while preserving its phase shift properties, and (2) adoption of a realistic basis space using Woods-Saxon (WS) single-particle wavefunctions. Both have their advantages and limitations, discussed here. For (1), SRG was demonstrated by applying it to a realistic NN interaction, JISP16, in a harmonic oscillator (HO) representation. The degree of interaction softening achieved through a regulator parameter is examined. For (2), new results are obtained with the realistic JISP16 NN interaction in ab initio calculations of light nuclei 4He, 6He and 12C, using a WS basis optimized to minimize the ground-state energy within the truncated no core shell model. These are numerically-intensive many-body calculations. Finally, to gain insight into the potential for no core investigations of heavier nuclei, an initial investigation was obtained for the odd mass A = 47 - 49 region nuclei straddling 48Ca. The motivation for selecting these nuclei stems from the aim of preparing for nuclear double beta-decay studies of 48Ca. In these heavier systems, phenomenological additions to the realistic NN interaction determined by previous
van Genderen, E.; Clabbers, M. T. B.; Das, P. P.; Stewart, A.; Nederlof, I.; Barentsen, K. C.; Portillo, Q.; Pannu, N. S.; Nicolopoulos, S.; Gruene, T.; Abrahams, J. P.
2016-01-01
Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014). PMID:26919375
Development of Novel Analytical Method for Ab Initio Powder Structural Analysis
NASA Astrophysics Data System (ADS)
Sakata, Makoto; Nishibori, Eiji; Sawa, Hiroshi
Genetic Algorithm (GA) applied to ab initio structure determination from synchrotron powder diffraction is described. It seems to have an advantage over other real space methods for ab initio structure determination because of the existence of schema theorem. As an example, the case of Prednisolone Succinate is shown in some detail. Future development of GA in crystallography is briefly described.
Strak, Pawel; Sakowski, Konrad; Kempisty, Pawel
2015-09-07
Properties of bare and nitrogen-covered Al-terminated AlN(0001) surface were determined using density functional theory (DFT) calculations. At a low nitrogen coverage, the Fermi level is pinned by Al broken bond states located below conduction band minimum. Adsorption of nitrogen is dissociative with an energy gain of 6.05 eV/molecule at a H3 site creating an overlap with states of three neighboring Al surface atoms. During this adsorption, electrons are transferred from Al broken bond to topmost N adatom states. Accompanying charge transfer depends on the Fermi level. In accordance with electron counting rule (ECR), the DFT results confirm the Fermi level is not pinned at the critical value of nitrogen coverage θ{sub N}(1) = 1/4 monolayer (ML), but it is shifted from an Al-broken bond state to Np{sub z} state. The equilibrium thermodynamic potential of nitrogen in vapor depends drastically on the Fermi level pinning being shifted by about 4 eV for an ECR state at 1/4 ML coverage. For coverage above 1/4 ML, adsorption is molecular with an energy gain of 1.5 eV at a skewed on-top position above an Al surface atom. Electronic states of the admolecule are occupied as in the free molecule, no electron transfer occurs and adsorption of a N{sub 2} molecule does not depend on the Fermi level. The equilibrium pressure of molecular nitrogen above an AlN(0001) surface depends critically on the Fermi level position, being very low and very high for low and high coverage, respectively. From this fact, one can conclude that at typical growth conditions, the Fermi level is not pinned, and the adsorption and incorporation of impurities depend on the position of Fermi level in the bulk.
NASA Astrophysics Data System (ADS)
Strak, Pawel; Sakowski, Konrad; Kempisty, Pawel; Krukowski, Stanislaw
2015-09-01
Properties of bare and nitrogen-covered Al-terminated AlN(0001) surface were determined using density functional theory (DFT) calculations. At a low nitrogen coverage, the Fermi level is pinned by Al broken bond states located below conduction band minimum. Adsorption of nitrogen is dissociative with an energy gain of 6.05 eV/molecule at a H3 site creating an overlap with states of three neighboring Al surface atoms. During this adsorption, electrons are transferred from Al broken bond to topmost N adatom states. Accompanying charge transfer depends on the Fermi level. In accordance with electron counting rule (ECR), the DFT results confirm the Fermi level is not pinned at the critical value of nitrogen coverage θN(1) = 1/4 monolayer (ML), but it is shifted from an Al-broken bond state to Npz state. The equilibrium thermodynamic potential of nitrogen in vapor depends drastically on the Fermi level pinning being shifted by about 4 eV for an ECR state at 1/4 ML coverage. For coverage above 1/4 ML, adsorption is molecular with an energy gain of 1.5 eV at a skewed on-top position above an Al surface atom. Electronic states of the admolecule are occupied as in the free molecule, no electron transfer occurs and adsorption of a N2 molecule does not depend on the Fermi level. The equilibrium pressure of molecular nitrogen above an AlN(0001) surface depends critically on the Fermi level position, being very low and very high for low and high coverage, respectively. From this fact, one can conclude that at typical growth conditions, the Fermi level is not pinned, and the adsorption and incorporation of impurities depend on the position of Fermi level in the bulk.
Ab initio determination of light hadron masses.
Dürr, S; Fodor, Z; Frison, J; Hoelbling, C; Hoffmann, R; Katz, S D; Krieg, S; Kurth, T; Lellouch, L; Lippert, T; Szabo, K K; Vulvert, G
2008-11-21
More than 99% of the mass of the visible universe is made up of protons and neutrons. Both particles are much heavier than their quark and gluon constituents, and the Standard Model of particle physics should explain this difference. We present a full ab initio calculation of the masses of protons, neutrons, and other light hadrons, using lattice quantum chromodynamics. Pion masses down to 190 mega-electron volts are used to extrapolate to the physical point, with lattice sizes of approximately four times the inverse pion mass. Three lattice spacings are used for a continuum extrapolation. Our results completely agree with experimental observations and represent a quantitative confirmation of this aspect of the Standard Model with fully controlled uncertainties. PMID:19023076
Többens, Daniel M; Kahlenberg, Volker; Kaindl, Reinhard
2005-12-12
The crystal structure of a sodium yttrium silicate with composition NaYSi2O6 has been determined from laboratory X-ray powder diffraction data by simulated annealing, and has been subsequently refined with the Rietveld technique. The compound is monoclinic with space group P2(1)/c and unit cell parameters of a=5.40787(2) A, b=13.69784(5) A, c=7.58431(3) A, and beta=109.9140(3) degrees at 23.5 degrees C (Z=4). The structure was found to be a single-chain silicate with a chain periodicity of four. The two symmetry dependent [Si4O12] chains in the unit cell are parallel to c. A prominent feature is the strong folding of the crankshaft-like chains within the b,c-plane resulting in intrachain Si-Si-Si angles close to 90 degrees. The coordination of the Y3+ ions by O2- is 7-fold in the form of slightly irregular pentagonal bipyramids, with oxygen atoms from four different chains contributing to the coordination polyhedron. Na+ ions are irregularly coordinated by 10 oxygens from two neighboring chains. No disorder of Na+ and Y3+ between the two nontetrahedral cation sites could be observed. Furthermore, micro-Raman spectra have been obtained from the polycrystalline material. PMID:16323944
Ab Initio Structure Analysis Using Laboratory Powder Diffraction Data
NASA Astrophysics Data System (ADS)
Sasaki, Akito
Today, laboratory X-ray diffractometers are seeing increasingly wide use in the ab initio crystal structure analysis of organic powder samples. This is because optics and optical devices have been improved, making it possible to obtain precise integrated intensities of reflections in high 2-theta ranges. Another reason is that one can use direct-space methods, which do not require “high-resolution diffraction data”, much more easily than before. Described here are some key points to remember when performig ab initio crystal structure analysis using powder diffraction data from organic compounds.
NASA Astrophysics Data System (ADS)
Cremer, Dieter; Dorofeeva, Olga V.; Mastryukov, Vladimir S.
1981-09-01
Restricted Hartree—Fock calculations on 21 planar and puckered conformers of azetidine have been done employing a split valence basis augmented by d functions. Complete geometry optimizations have been performed for eight conformers. In this way the puckering potential of azetidine is explored over the range -40° < ø (puckering angle) < 40°, for both sp3 and sp2 hybridization of the nitrogen atom. In its equatorial form, azetidine is slightly more puckered than cyclobutane. This is because of a decrease of van der Waals' repulsion between H atoms. Charge effects lead to destabilization of the axial forms. There is only moderate coupling between puckering and methylene group rocking. Previously published electron diffraction (ED) data are reinvestigated using vibrational corrections and information from the ab initio calculations. On the basis of this MO constrained ED (MOCED) analysis a puckering angle φ = 35.1(1.8)° is found. Observed rg and re bond distances are compared with ab initio values.
D Saldin; H Poon; M Bogan; S Marchesini; D Sahpiro; R Kirian; U Weierstall; J Spence
2011-12-31
We report on the first experimental ab initio reconstruction of an image of a single particle from fluctuations in the scattering from an ensemble of copies, randomly oriented about an axis. The method is applicable to identical particles frozen in space or time (as by snapshot diffraction from an x-ray free electron laser). These fluctuations enhance information obtainable from an experiment such as conventional small angle x-ray scattering.
NASA Astrophysics Data System (ADS)
D'Yachkov, P. N.; Makaev, D. V.
2007-11-01
Every carbon single-walled nanotube (SWNT) can be generated by first mapping only two nearest-neighbor C atoms onto a surface of a cylinder and then using the rotational and helical symmetry operators to determine the remainder of the tubule [C. T. White , Phys. Rev. B 47, 5485 (1993)]. With account of these symmetries, we developed a symmetry-adapted version of a linear augmented cylindrical wave method. In this case, the cells contain only two carbon atoms, and the ab initio theory becomes applicable to any SWNT independent of the number of atoms in a translational unit cell. The approximations are made in the sense of muffin-tin (MT) potentials and local-density-functional theory only. An electronic potential is suggested to be spherically symmetrical in the regions of atoms and constant in an interspherical region up to the two essentially impenetrable cylinder-shaped potential barriers. To construct the basis wave functions, the solutions of the Schrödinger equation for the interspherical and MT regions of the tubule were sewn together using a theorem of addition for cylindrical functions, the resulting basis functions being continuous and differentiable anywhere in the system. With account of analytical equations for these functions, the overlap and Hamiltonian integrals are calculated, which permits determination of electronic structure of nanotube. We have calculated the total band structures and densities of states of the chiral and achiral, semiconducting, semimetallic, and metallic carbon SWNTs (13, 0), (12, 2), (11, 3), (10, 5), (9, 6), (8, 7), (7, 7), (12, 4), and (100, 99) containing up to the 118 804 atoms per translational unit cell. Even for the (100, 99) system with huge unit cell, the band structure can be easily calculated and the results can be presented in the standard form of four curves for the valence band plus one curve for the low-energy states of conduction band. About 150 functions produce convergence of the band structures better then
Ab initio molecular crystal structures, spectra, and phase diagrams.
Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni
2014-09-16
Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling
Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung
2014-09-01
A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ{sub 1} and ϕ{sub 2}) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ{sub DS} list as a criterion to select optimized phases ϕ{sub am} from ϕ{sub 1} or ϕ{sub 2} of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ{sub SAD} has been developed. Based on this work, reflections with an angle θ{sub DS} in the range 35–145° are selected for an optimized improvement, where θ{sub DS} is the angle between the initial phase ϕ{sub SAD} and a preliminary density-modification (DM) phase ϕ{sub DM}{sup NHL}. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.
Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals
NASA Astrophysics Data System (ADS)
Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano
2015-03-01
Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.
Ab initio modelling: Genesis of crystal structures
NASA Astrophysics Data System (ADS)
van de Walle, Axel
2005-05-01
Genetic algorithms prove useful to distil a complex quantum mechanical calculation of interatomic interactions down to its simplest mathematical expression. This makes it possible to predict the structure of new compounds from first principles.
NASA Astrophysics Data System (ADS)
Canè, E.; Di Lonardo, G.; Fusina, L.; Jerzembeck, W.; Bürger, H.; Breidung, J.; Thiel, W.
2006-01-01
The high resolution infrared spectrum of 121SbD 3, recorded between 20 and 350 cm -1 and in the regions of bending and stretching fundamental bands, centred at 600 and 1350 cm -1, has been analysed. Splittings of the K″=3, 6 lines have been observed both in the rotation and ro-vibration spectra. A large number of 'perturbation allowed' transitions with selection rules Δ(k-ℓ)=±3, ±6 and ±9 have been identified in all fundamental bands. Accurate ground state molecular parameters have been determined fitting simultaneously the rotational transitions and about 9000 ground state combination differences obtained from lines assigned in the ro-vibrational spectra. The A and B reductions of the rotational Hamiltonian have been applied in the analysis of the ground state. They provided almost equivalent results. The molecular parameters of the 1 1, 2 1, 3 1 and 4 1 states have been obtained from the simultaneous analysis of the ν1 ( A1)/ ν3 ( E) stretching and of the ν2 ( A1)/ ν4 ( E) bending dyads. In fact, the corresponding excited states are affected by strong perturbations due to Coriolis and k-type rovibrational interactions that have been treated explicitly in the model adopted for the analysis. Improved effective ground state and equilibrium geometries have been determined and compared to those of 121SbH 3 and of 123SbD 3. Ab initio calculations at the coupled cluster CCSD(T) level with an energy-consistent large-core pseudopotential and large basis sets have been carried out to determine the equilibrium structure, the anharmonic force field, and the associated spectroscopic constants of 121-stibine. The theoretical constants and structural parameters are in good agreement with the experimental data.
Ab initio Hadron structure from lattice QCD
J.D. Bratt; R.G. Edwards; M. Engelhardt; G.T. Fleming; Ph. Hägler; B. Musch; J.W. Negele; K. Orginos; A.V. Pochinsky; D.B. Renner; D.G. Richards; W. Schroers
2007-06-01
Early scattering experiments revealed that the proton was not a point particle but a bound state of many quarks and gluons. Deep inelastic scattering (DIS) experiments have accurately determined the probability of struck quarks carrying a fraction of the proton's momentum. The current generation of experiments and Lattice QCD calculations will provide detailed multi-dimensional pictures of the distributions of quarks and gluons inside the proton.
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Draayer, Jerry P.
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Macromolecular ab initio phasing enforcing secondary and tertiary structure
Millán, Claudia; Sammito, Massimo; Usón, Isabel
2015-01-01
Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors’ approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a ‘still-life’, but some are correct enough for density modification and main-chain tracing to reveal the protein’s true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631
Unified ab initio approaches to nuclear structure and reactions
NASA Astrophysics Data System (ADS)
Navrátil, Petr; Quaglioni, Sofia; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo
2016-05-01
The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Be {({{p}},γ )}8{{B}} radiative capture. Finally, we highlight our efforts to describe transfer reactions including the 3H{({{d}},{{n}})}4He fusion.
Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones
NASA Astrophysics Data System (ADS)
Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng
2004-04-01
A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (Δ G#) and also free energy differences (Δ G0) for benzodiazepines are reported.
Structure and lattice dynamics of PrFe3(BO3)4: Ab initio calculation
NASA Astrophysics Data System (ADS)
Chernyshev, V. A.; Nikiforov, A. E.; Petrov, V. P.
2016-06-01
The crystal structure and phonon spectrum of PrFe3(BO3)4 are ab initio calculated in the context of the density functional theory. The ion coordinates in the unit cell of a crystal and the lattice parameters are evaluated from the calculations. The types and frequencies of the fundamental vibrations, as well as the line intensities of the IR spectrum, are determined. The elastic constants of the crystal are calculated. A "seed" frequency of the vibration strongly interacting with the electron excitation on the praseodymium ion is obtained for low-frequency A 2 mode. The calculated results are in agreement with the known experimental data.
Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules
NASA Astrophysics Data System (ADS)
Zheng, Haoping
The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with precise calculations. Thus the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule has become a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), will be presented in this paper. The reactive sites of the inhibitors are determined and explained. The accuracy of structure determination of the inhibitors are tested theoretically.
Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules
NASA Astrophysics Data System (ADS)
Zheng, Haoping
2003-04-01
The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with unchanged calculation precision. So the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule becomes a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the Ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), are presented. The reactive sites of the inhibitors are determined and explained. The precision of structure determination of inhibitors are tested theoretically.
Ab-initio study of magnetism behavior in TiO2 semiconductor with structural defects
NASA Astrophysics Data System (ADS)
Zarhri, Z.; Houmad, M.; Ziat, Y.; El Rhazouani, O.; Slassi, A.; Benyoussef, A.; El Kenz, A.
2016-05-01
Magnetic, electronic and structural properties of titanium dioxide material with different structural defects are studied using the first-principles ab-initio calculations and the Korringa-Kohn-Rostoker method (KKR) combined with the coherent potential approximation (CPA) method in connection with the local density approximation (LDA). We investigated all structural defects in rutile TiO2 such as Titanium interstitial (Tii), Titanium anti-sites (Tio), Titanium vacancies (VTi), Oxygen interstitial (Oi), Oxygen anti-sites (OTi) and oxygen vacancies (Vo). Mechanisms of hybridization and interaction between magnetic atoms are investigated. The transition temperature is computed using the Mean Field Approximation (MFA).Magnetic stability energy of ferromagnetic and disordered local moment states is calculated to determine the most stable state. Titanium anti-sites have a half-metallic aspect. We also studied the change type caused by structural defects in this material.
Ab initio simulations for the ion-ion structure factor of warm dense aluminum.
Rüter, Hannes R; Redmer, Ronald
2014-04-11
We perform ab initio simulations based on finite-temperature density functional theory in order to determine the static and dynamic ion-ion structure factor in aluminum. We calculate the dynamic structure factor via the intermediate scattering function and extract the dispersion relation for the collective excitations. The results are compared with available experimental x-ray scattering data. Very good agreement is obtained for the liquid metal domain. In addition we perform simulations for warm dense aluminum in order to obtain the ion dynamics in this strongly correlated quantum regime. We determine the sound velocity for both liquid and warm dense aluminum which can be checked experimentally using narrow-bandwidth free electron laser radiation. PMID:24765982
Kostadinova, O.; Chrissanthopoulos, A.; Petkova, T.; Petkov, P.; Yannopoulos, S.N.
2011-02-15
We report an investigation of the structure and vibrational modes of (AgI){sub x} (AsSe){sub 100-x}, bulk glasses using Raman spectroscopy and first principles calculations. The short- and medium-range structural order of the glasses was elucidated by analyzing the reduced Raman spectra, recorded at off-resonance conditions. Three distinct local environments were revealed for the AsSe glass including stoichiometric-like and As-rich network sub-structures, and cage-like molecules (As{sub 4}Se{sub n}, n=3, 4) decoupled from the network. To facilitate the interpretation of the Raman spectra ab initio calculations are employed to study the geometric and vibrational properties of As{sub 4}Se{sub n} molecular units that are parts of the glass structure. The incorporation of AgI causes appreciable structural changes into the glass structure. AgI is responsible for the population reduction of molecular units and for the degradation of the As-rich network-like sub-structure via the introduction of As-I terminal bonds. Ab initio calculations of mixed chalcohalide pyramids AsSe{sub m}I{sub 3-m} provided useful information augmenting the interpretation of the Raman spectra. -- Graphical abstract: Raman scattering and ab initio calculations are employed to study the structure of AgI-AsSe superionic glasses. The role of mixed chalcohalide pyramidal units as illustrated in the figure is elucidated. Display Omitted Research highlights: {yields} Doping binary As-Se glasses with AgI cause dramatic changes in glass structure. {yields} Raman scattering and ab initio calculations determine changes in short- and medium-range order. {yields} Three local environments exist in AsSe glass including a network sub-structure and cage-like molecules. {yields} Mixed chalcohalide pyramids AsSe{sub m}I{sub 3-m} dominate the AgI-doped glass structure.
Peterson, Charles; Penchoff, Deborah A.; Wilson, Angela K.
2015-11-21
An effective approach for the determination of lanthanide energetics, as demonstrated by application to the third ionization energy (in the gas phase) for the first half of the lanthanide series, has been developed. This approach uses a combination of highly correlated and fully relativistic ab initio methods to accurately describe the electronic structure of heavy elements. Both scalar and fully relativistic methods are used to achieve an approach that is both computationally feasible and accurate. The impact of basis set choice and the number of electrons included in the correlation space has also been examined.
Ab initio electronic structure study for TTF-TCNQ under uniaxial compression
NASA Astrophysics Data System (ADS)
Ishibashi, Shoji; Hashimoto, Tamotsu; Kohyama, Masanori; Terakura, Kiyoyuki
2004-04-01
We have investigated the electronic structure of TTF-TCNQ under uniaxial compression with ab initio plane-wave pseudopotential calculations within the local-density approximation and generalized gradient approximation. Depending on the compression direction, the constituent molecules are deformed in different ways. Along with these structural deformations, quasi-one-dimensional Fermi surfaces show dramatic changes in their shapes and sizes.
An improved ab initio structure for fluorine peroxide (FOOF)
NASA Astrophysics Data System (ADS)
Mack, Hans-Georg; Oberhammer, Heinz
1988-03-01
Ab initio calculations with the 6-31G* and Dunning (9s5p/4s2p) basis sets augmented with p and d functions at various levels of theory (RHF, MP2, MP3, and MP4) were carried out on F 2O 2. The best result was obtained at the MP2 level with the Dunning basis plus one set of d functions on fluorine and two sets of d functions on oxygen. These calculations reproduce the experimental bond lengths to within 0.01 Å and the angles to within the experimental uncertainties.
Xu, Dong; Zhang, Yang
2012-01-01
Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565
NASA Astrophysics Data System (ADS)
Durig, J. R.; Shen, S.; Guirgis, G. A.
2001-01-01
The far infrared spectrum from 370 to 50 cm -1 of gaseous 2-bromoethanol, BrCH 2CH 2OH, was recorded at a resolution of 0.10 cm -1. The fundamental O-H torsion of the more stable gauche ( Gg') conformer, where the capital G refers to internal rotation around the C-C bond and the lower case g to the internal rotation around the C-O bond, was observed as a series of Q-branch transitions beginning at 340 cm -1. The corresponding O-H torsional modes were observed for two of the other high energy conformers, Tg (285 cm -1) and Tt (234 cm -1). The heavy atom asymmetric torsion (rotation around C-C bond) for the Gg' conformer has been observed at 140 cm -1. Variable temperature (-63 to -100°C) studies of the infrared spectra (4000-400 cm -1) of the sample dissolved in liquid xenon have been recorded. From these data the enthalpy differences have been determined to be 411±40 cm -1 (4.92±0.48 kJ/mol) for the Gg'/ Tt and 315±40 cm -1 (3.76±0.48 kJ/mol) for the Gg'/ Tg, with the Gg' conformer the most stable form. Additionally, the infrared spectrum of the gas, and Raman spectrum of the liquid phase are reported. The structural parameters, conformational stabilities, barriers to internal rotation and fundamental frequencies have been obtained from ab initio calculations utilizing different basis sets at the restricted Hartree-Fock or with full electron correlation by the perturbation method to second order. The theoretical results are compared to the experimental results when appropriate. Combining the ab initio calculations with the microwave rotational constants, r0 adjusted parameters have been obtained for the three 2-haloethanols (F, Cl and Br) for the Gg' conformers.
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction
Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin
2014-01-01
Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test data set of 198 proteins, achieving a Q3 accuracy of 80.7% and a Sov accuracy of 74.2%. PMID:25750595
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.
Spencer, Matt; Eickholt, Jesse; Jianlin Cheng
2015-01-01
Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent. PMID:25750595
2014-01-01
Background The advent of human genome sequencing project has led to a spurt in the number of protein sequences in the databanks. Success of structure based drug discovery severely hinges on the availability of structures. Despite significant progresses in the area of experimental protein structure determination, the sequence-structure gap is continually widening. Data driven homology based computational methods have proved successful in predicting tertiary structures for sequences sharing medium to high sequence similarities. With dwindling similarities of query sequences, advanced homology/ ab initio hybrid approaches are being explored to solve structure prediction problem. Here we describe Bhageerath-H, a homology/ ab initio hybrid software/server for predicting protein tertiary structures with advancing drug design attempts as one of the goals. Results Bhageerath-H web-server was validated on 75 CASP10 targets which showed TM-scores ≥0.5 in 91% of the cases and Cα RMSDs ≤5Å from the native in 58% of the targets, which is well above the CASP10 water mark. Comparison with some leading servers demonstrated the uniqueness of the hybrid methodology in effectively sampling conformational space, scoring best decoys and refining low resolution models to high and medium resolution. Conclusion Bhageerath-H methodology is web enabled for the scientific community as a freely accessible web server. The methodology is fielded in the on-going CASP11 experiment. PMID:25521245
DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering
Franke, Daniel; Svergun, Dmitri I.
2009-01-01
DAMMIF, a revised implementation of the ab-initio shape-determination program DAMMIN for small-angle scattering data, is presented. The program was fully rewritten, and its algorithm was optimized for speed of execution and modified to avoid limitations due to the finite search volume. Symmetry and anisometry constraints can be imposed on the particle shape, similar to DAMMIN. In equivalent conditions, DAMMIF is 25–40 times faster than DAMMIN on a single CPU. The possibility to utilize multiple CPUs is added to DAMMIF. The application is available in binary form for major platforms.
Ab initio studies of equations of state and chemical reactions of reactive structural materials
NASA Astrophysics Data System (ADS)
Zaharieva, Roussislava
subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated
Quarti, Claudio; Mosconi, Edoardo; De Angelis, Filippo
2015-04-14
The last two years have seen the unprecedentedly rapid emergence of a new class of solar cells, based on hybrid organic-inorganic halide perovskites. The success of this class of materials is due to their outstanding photoelectrochemical properties coupled to their low cost, mainly solution-based, fabrication techniques. Solution processed materials are however often characterized by an inherent flexible structure, which is hardly mapped into a single local minimum energy structure. In this perspective, we report on the interplay between structural and electronic properties of hybrid lead iodide perovskites investigated using ab initio molecular dynamics (AIMD) simulations, which allow the dynamical simulation of disordered systems at finite temperature. We compare the prototypical MAPbI3 (MA = methylammonium) perovskite in its cubic and tetragonal structure with the trigonal phase of FAPbI3 (FA = formamidinium), investigating different starting arrangements of the organic cations. Despite the relatively short time scale amenable to AIMD, typically a few tens of ps, this analysis demonstrates the sizable structural flexibility of this class of materials, showing that the instantaneous structure could significantly differ from the time and thermal averaged structure. We also highlight the importance of the organic-inorganic interactions in determining the fluxional properties of this class of materials. A peculiar spatial localization of the valence and conduction band edges is also found, with a dynamics in the range of 0.1 ps, which is associated with the positional dynamics of the organic cations within the cubo-octahedral perovskite cage. This asymmetry in the spatial localization of the band edges is expected to ease exciton dissociation and assist the initial stages of charge separation, possibly constituting one of the key factors for the impressive photovoltaic performances of hybrid lead-iodide perovskites. PMID:25766785
Nekrashevich, S. S. Gritsenko, V. A.; Klauser, R.; Gwo, S.
2010-10-15
Charge transfer {Delta}Q = 0.35e at the Si-N bond in silicon nitride is determined experimentally using photoelectron spectroscopy, and the ionic formula of silicon nitride Si{sub 3}{sup +1.4}N{sub 4}{sup -1.05} is derived. The electronic structure of {alpha}-Si{sub 3}N{sub 4} is studied ab initio using the density functional method. The results of calculations (partial density of states) are compared with experimental data on X-ray emission spectroscopy of amorphous Si{sub 3}N{sub 4}. The electronic structure of the valence band of amorphous Si{sub 3}N{sub 4} is studied using synchrotron radiation at different excitation energies. The electron and hole effective masses m{sub e}{sup *} {approx} m{sub h}{sup *} {approx} 0.5m{sub e} are estimated theoretically. The calculated values correspond to experimental results on injection of electrons and holes into silicon nitride.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil
2015-05-15
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.
Structural stability of nitrogen-doped ultrathin single-walled boron nanotubes: an ab initio study
NASA Astrophysics Data System (ADS)
Jain, Sandeep Kumar; Srivastava, Pankaj
2012-09-01
Ab initio calculations have been performed for determining structural stabilities of nitrogen-doped ultrathin single-walled boron nanotube. We have considered ultrathin boron nanotubes of diameters <0.5 nm, which include mainly three conformations of BNTs viz. zigzag (5,0), armchair (3,3) and chiral (4,2) with diameters 4.60, 4.78 and 4.87 Å, respectively. It has been investigated that α-BNTs are highly stable, while hexagonal BNTs are found to be least stable. In view of increasing structural stability of hexagonal BNTs, substitutional doping of foreign atoms, i.e. nitrogen is chosen. The nitrogen atoms substitute the host atoms at the middle of the tubes. The substitution doping is made with all the three conformations. The structural stabilities of BNTs have been investigated by using density functional theory (DFT). Subsequently, the cohesive energy is calculated, which directly measures the structural stability. The cohesive energy of BNTs has been calculated for different nitrogen concentrations. We found that the structures get energetically more stable with increasing nitrogen concentration. Moreover, it is also revealed that all the three BNTs are almost equally stable for single-atom doping, while the armchair BNT (3,3) is highly stable followed by zigzag (5,0) and chiral (4,2) BNTs for two- and three-atom doping. The structural stability is an important factor for realization of any physical device. Thus, these BNTs can be used for field emission, semiconducting and highly conducting devices at nanoscale.
Polysiloxanes: ab initio force field and structural, conformational and thermophysical properties
NASA Astrophysics Data System (ADS)
Sun, Huai; Rigby, David
1997-07-01
Various levels of ab initio calculation have been performed to determine the optimum strategy for parameterization of the valence parameters of a CFF-type force field for siloxanes and polysiloxanes. Electrostatic nonbond parameters have been determined using scaled electrostatic potential (ESP) charges adjusted for known systematic differences between ab initio and experimental data, while van der Waals nonbond parameters have been determined using a classical approach involving fitting to experimental liquid density and cohesive energy density data measured at atmospheric pressure and a single temperature for a set of four small molecules. Simulations have been performed on molecular crystals, liquids and isolated molecules, yielding results which agree favorably with available experimental data. Properties calculated include unit cell parameters and crystal densities, liquid densities from 303-473 K and 0-1800 bar, dependence of oligomer density and solubility parameters on chain length and temperature, gas-phase geometries and vibrational frequencies, and gas and liquid-phase conformational behavior.
Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam
2015-01-01
Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568
Predicting crystal structures ab initio: group 14 nitrides and phosphides.
Hart, Judy N; Allan, Neil L; Claeyssens, Frederik
2010-08-14
Crystal structures are predicted for a range of group 14 nitrides and phosphides with 1 : 1 stoichiometry, following our method of starting from the known structures for a range of binary compounds and looking for trends in the preferred local bonding environments in the optimised structures. We have previously applied this method to predict the structures of carbon nitride and phosphorus carbide. Here, we use a similar approach to predict the structures of silicon and germanium nitrides and phosphides with 1 : 1 stoichiometry. We find that the local bonding environments in the preferred structures for the nitrides are the same as those for the 3 : 4 stoichiometry. For the phosphides, we have found several possible structures with similar energies. Structures containing hypervalent phosphorus must be considered as these are often low in energy, particularly for GeP; these have not been included in previous work. The greater tendency to form hypervalent phosphorus in GeP than SiP can be rationalised by considering the bond enthalpies for the two compositions. PMID:20603659
Ab Initio determination of Cu 3d orbital energies in layered copper oxides
Hozoi, Liviu; Siurakshina, Liudmila; Fulde, Peter; van den Brink, Jeroen
2011-01-01
It has long been argued that the minimal model to describe the low-energy physics of the high Tc superconducting cuprates must include copper states of other symmetries besides the canonical one, in particular the orbital. Experimental and theoretical estimates of the energy splitting of these states vary widely. With a novel ab initio quantum chemical computational scheme we determine these energies for a range of copper-oxides and -oxychlorides, determine trends with the apical Cu–ligand distances and find excellent agreement with recent Resonant Inelastic X-ray Scattering measurements, available for La2CuO4, Sr2CuO2Cl2, and CaCuO2. PMID:22355584
Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation
NASA Astrophysics Data System (ADS)
Correa, J. D.; Cisternas, E.
2016-09-01
By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.
Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.
2013-12-12
Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.
Kurova, N. V. Burdov, V. A.
2013-12-15
The results of ab initio calculations of the electronic structure of Si nanocrystals doped with shallow donors (Li, P) are reported. It is shown that phosphorus introduces much more significant distortions into the electronic structure of the nanocrystal than lithium, which is due to the stronger central cell potential of the phosphorus ion. It is found that the Li-induced splitting of the ground state in the conduction band of the nanocrystal into the singlet, doublet, and triplet retains its inverse structure typical for bulk silicon.
Synthesis, crystal structure and ab initio/DFT calculations of a derivative of dithiophosphonates
NASA Astrophysics Data System (ADS)
Karakus, M.; Solak, S.; Hökelek, T.; Dal, H.; Bayrakdar, A.; Özdemir Kart, S.; Karabacak, M.; Kart, H. H.
2014-03-01
The compound 2 has been synthesized from the reaction of 2,4-Bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2,4-disulfide and (R)-1-[3,5-Bis(trifloromethyl)phenyl]ethanol in toluene. The obtained crude dithiophosphonic acid 1 has been treated with the excess of N(C2H5)3 to give rise to 2, [(+HN(C2H5)3][(O-CH3CH-C6H3(CF3)2)(CH3OC6H4)PS2-]. The compound 2 has been characterized by using the spectroscopic methods such as IR, 1H, 13C, 31P NMR and structural analysing method such as X-ray crystallography. It crystallizes in the orthorhombic system, whose space group is P212121. It consists of a dithiophosphonate bridged methoxyphenyl and bis(triflorophenylethyl) groups and a triethylammonium moiety linked by Nsbnd H⋯S and Csbnd H⋯F hydrogen bonds. In the crystal structure, the C17H14F6O2PS2 molecule is elongated along the b-axis and stacked along the a-axis. The triethylammonium, N(CH2CH3)3, molecule fill in the cavities between the C17H14F6O2PS2 molecule. Moreover, ab initio methods based on Hartree-Fock (HF) and Density Functional Theory (DFT) calculations with the basis set of 6-31G(d) are also carried out to determine the molecular structural properties and to calculate FT-IR and NMR spectrum of the compound 2. The experimental results and theoretical calculations have been compared, and they are found to be in good agreement.
Knockout reactions from p-shell nuclei : tests of ab initio structure models.
Grinyer, G. F.; Bazin, D.; Gade, A.; Tostevin, J. A.; Adrich, P.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; McDaniel, S.; Navratil, P.; Obertelli, A.; Quaglioni, S.; Siwek, K.; Terry, J. R.; Weisshaar, D.; Wiringa, R. B.
2011-04-22
Absolute cross sections have been determined following single neutron knockout reactions from {sup 10}Be and {sup 10}C at intermediate energy. Nucleon density distributions and bound-state wave function overlaps obtained from both variational Monte Carlo (VMC) and no core shell model (NCSM) ab initio calculations have been incorporated into the theoretical description of knockout reactions. Comparison to experimental cross sections demonstrates that the VMC approach, with the inclusion of 3-body forces, provides the best overall agreement while the NCSM and conventional shell-model calculations both overpredict the cross sections by 20% to 30% for {sup 10}Be and by 40% to 50% for {sup 10}C, respectively. This study gains new insight into the importance of 3-body forces and continuum effects in light nuclei and provides a sensitive technique to assess the accuracy of ab initio calculations for describing these effects.
Knockout Reactions from p-Shell Nuclei: Tests of Ab Initio Structure Models
Grinyer, G. F.; Bazin, D.; Adrich, P.; Obertelli, A.; Weisshaar, D.; Gade, A.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; McDaniel, S.; Siwek, K.; Terry, J. R.; Tostevin, J. A.; Navratil, P.; Quaglioni, S.; Wiringa, R. B.
2011-04-22
Absolute cross sections have been determined following single neutron knockout reactions from {sup 10}Be and {sup 10}C at intermediate energy. Nucleon density distributions and bound-state wave function overlaps obtained from both variational Monte Carlo (VMC) and no core shell model (NCSM) ab initio calculations have been incorporated into the theoretical description of knockout reactions. Comparison to experimental cross sections demonstrates that the VMC approach, with the inclusion of 3-body forces, provides the best overall agreement while the NCSM and conventional shell-model calculations both overpredict the cross sections by 20% to 30% for {sup 10}Be and by 40% to 50% for {sup 10}C, respectively. This study gains new insight into the importance of 3-body forces and continuum effects in light nuclei and provides a sensitive technique to assess the accuracy of ab initio calculations for describing these effects.
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
Kaplan, Tommy; Friedman, Nir; Margalit, Hanah
2005-01-01
Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structure-based approach applicable to transcription factors with no prior binding data. Our approach combines sequence data and structural information to infer context-specific amino acid–nucleotide recognition preferences. These are used to predict binding sites for novel transcription factors from the same structural family. We demonstrate our approach on the Cys2His2 Zinc Finger protein family, and show that the learned DNA-recognition preferences are compatible with experimental results. We use these preferences to perform a genome-wide scan for direct targets of Drosophila melanogaster Cys2His2 transcription factors. By analyzing the predicted targets along with gene annotation and expression data we infer the function and activity of these proteins. PMID:16103898
Determination of absolute configuration using ab initio calculation of optical rotation.
Stephens, P J; Devlin, F J; Cheeseman, J R; Frisch, M J; Bortolini, O; Besse, P
2003-01-01
Ab initio Density Functional Theory (DFT) calculations of transparent spectral region, discrete frequency specific rotations were used to assign the absolute configurations (ACs) of: 1, 2H-naphtho[1,8-bc]thiophene 1-oxide; 2, m-F-phenyl glycidic acid methyl ester; 3, o-Br-phenyl glycidic acid methyl ester; 4, p-CH(3)-phenyl glycidic acid methyl ester; 5, 2-(1-hydroxyethyl)-chromen-4-one; and 6, 6-Br-2-(1-hydroxyethyl)-chromen-4-one. The ACs of 5 and 6 were previously determined via X-ray crystallography to be: 5, R(-)/S(+); 6, R(+)/S(-). The ACs obtained using [alpha](D) are the same for both 5 and 6: R(+)/S(-). We conclude that the previously reported AC of 5 is incorrect. PMID:12884375
Ab initio determination of the instability growth rate of warm dense beryllium-deuterium interface
NASA Astrophysics Data System (ADS)
Wang, Cong; Li, Zi; Li, DaFang; Zhang, Ping
2015-10-01
Accurate knowledge about the interfacial unstable growth is of great importance in inertial confinement fusion. During implosions, the deuterium-tritium capsule is driven by laser beams or X-rays to access the strongly coupled and partially degenerated warm dense matter regime. At this stage, the effects of dissipative processes, such as diffusion and viscosity, have significant impact on the instability growth rates. Here, we present ab initio molecular dynamics simulations to determine the equations of state and the transport coefficients. Several models are used to estimate the reduction in the growth rate dispersion curves of Rayleigh-Taylor and Richtmyer-Meshkov instabilities with considering the presence of these dissipative effects. We show that these instability growth rates are effectively reduced when considering diffusion. The findings provide significant insights into the microscopic mechanism of the instability growth at the ablator-fuel interface and will refine the models used in the laser-driven hydrodynamic instability experiments.
Ab initio determination of the instability growth rate of warm dense beryllium-deuterium interface
Wang, Cong; Zhang, Ping; Li, Zi; Li, DaFang
2015-10-15
Accurate knowledge about the interfacial unstable growth is of great importance in inertial confinement fusion. During implosions, the deuterium-tritium capsule is driven by laser beams or X-rays to access the strongly coupled and partially degenerated warm dense matter regime. At this stage, the effects of dissipative processes, such as diffusion and viscosity, have significant impact on the instability growth rates. Here, we present ab initio molecular dynamics simulations to determine the equations of state and the transport coefficients. Several models are used to estimate the reduction in the growth rate dispersion curves of Rayleigh-Taylor and Richtmyer-Meshkov instabilities with considering the presence of these dissipative effects. We show that these instability growth rates are effectively reduced when considering diffusion. The findings provide significant insights into the microscopic mechanism of the instability growth at the ablator-fuel interface and will refine the models used in the laser-driven hydrodynamic instability experiments.
Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface
NASA Technical Reports Server (NTRS)
Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)
1997-01-01
A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.
Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations.
Monastyrskii, Liubomyr S; Boyko, Yaroslav V; Sokolovskii, Bogdan S; Potashnyk, Vasylyna Ya
2016-12-01
An investigation of the model of porous silicon in the form of periodic set of silicon nanowires has been carried out. The electronic energy structure was studied using a first-principle band method-the method of pseudopotentials (ultrasoft potentials in the basis of plane waves) and linearized mode of the method of combined pseudopotentials. Due to the use of hybrid exchange-correlation potentials (B3LYP), the quantitative agreement of the calculated value of band gap in the bulk material with experimental data is achieved. The obtained results show that passivation of dangling bonds with hydrogen atoms leads to substantial transformation of electronic energy structure. At complete passivation of the dangling silicon bonds by hydrogen atoms, the band gap value takes the magnitude which substantially exceeds that for bulk silicon. The incomplete passivation gives rise to opposite effect when the band gap value decreases down the semimetallic range. PMID:26768147
Ab initio nuclear structure from lattice effective field theory
Lee, Dean
2014-11-11
This proceedings article reviews recent results by the Nuclear Lattice EFT Collaboration on an excited state of the {sup 12}C nucleus known as the Hoyle state. The Hoyle state plays a key role in the production of carbon via the triple-alpha reaction in red giant stars. We discuss the structure of low-lying states of {sup 12}C as well as the dependence of the triple-alpha reaction on the masses of the light quarks.
Hydration structure of salt solutions from ab initio molecular dynamics.
Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L
2013-01-01
The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed. PMID:23298049
Hydration structure of salt solutions from ab initio molecular dynamics
Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.
2013-01-07
The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
Hydration structure of salt solutions from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.
2013-01-01
The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
NASA Astrophysics Data System (ADS)
Matsuda, Yuki
This dissertation focuses on ab-initio quantum mechanical calculations of nanoelectronics in three research topics: contact resistance properties of carbon nanotubes and graphenes (Chapters 1 through 3), electrical properties of carbon nanotubes (Chapter 4) and silicon nanowires (Chapter 5). Through all the chapters, the aim of the research is to provide useful guidelines for experimentalists. Chapter 1 presents the contact resistance of metal electrode-carbon nanotube and metal electrode-graphene interfaces for various deposited metals, based on first-principles quantum mechanical density functional and matrix Green's function methods. Chapters 2 and 3 describe inventive ways to enhance contact resistance properties as well as mechanical stabilities using "molecular anchors" (Chapter 2) or using "end-contacted" (or end-on) electrodes (Chapter 3). Chapters 1 through 3 also provide useful guidelines for nanotube assembly process which is one of the main obstacles in nanoelectronics. Chapter 4 shows accurate and detailed band structure properties of single-walled carbon nanotubes using B3LYP hybrid functional, which are critical parameters in determining the electronic properties such as small band gaps (˜0.1 eV) and effective masses. Chapter 5 details both structural and electronic properties of silicon nanowires. These results lead to the findings controlling the diameter and surface coverage by adsorbates (e.g., hydrogen) of silicon nanowires can be effectively used to optimize their properties for various applications. All the theoretical results are compared with other theoretical studies and experimental data. Notably, electronic studies using B3LYP show excellent agreement with experimental studies quantitatively, which previous quantum mechanical calculations had failed. These studies show how quantum mechanical predictions of complex phenomena can be effectively investigated computationally in nanomaterials and nanodevices. Given the difficulty, expense
Ab initio prediction of protein structure with both all-atom and simplified force fields
NASA Astrophysics Data System (ADS)
Scheraga, Harold
2004-03-01
Using only a physics-based ab initio method, and both all-atom (ECEPP/3) and simplified united-residue (UNRES) force fields, global optimization of both potential functions with Monte Carlo-plus-Minimization (MCM) and Conformational Space Annealing (CSA), respectively, provides predicted structures of proteins without use of knowledge-based information. The all-atom approach has been applied to the 46-residue protein A, and the UNRES approach has been applied to larger CASP targets. The predicted structures will be described.
Ramsdellite-structured LiTiO 2: A new phase predicted from ab initio calculations
NASA Astrophysics Data System (ADS)
Koudriachova, M. V.
2008-06-01
A new phase of highly lithiated titania with potential application as an anode in Li-rechargeable batteries is predicted on the basis of ab initio calculations. This phase has a composition LiTiO2 and may be accessed through electrochemical lithiation of ramsdellite-structured TiO2 at the lowest potential reported for titanium dioxide based materials. The potential remains constant over a wide range of Li-concentrations. The new phase is metastable with respect to a tetragonally distorted rock salt structure, which hitherto has been the only known polymorph of LiTiO2.
Ab initio analysis of the defect structure of ceria
NASA Astrophysics Data System (ADS)
Zacherle, T.; Schriever, A.; De Souza, R. A.; Martin, M.
2013-04-01
We calculated the formation energies of all simple point defects in cubic fluorite structured CeO2 using density functional theory within the GGA+U approximation. All possible defect charge states were considered, and also polarons CeCe' and associates of polarons with oxygen vacancies: (VO··-CeCe')· and (CeCe'-VO··-CeCe')×. From the individual defect energies, we extracted Schottky, Frenkel, and anti-Frenkel energies: we find that anti-Frenkel disorder has the lowest energy in ceria. Energies for the reduction and the hydration of ceria are also computed, and the results are in good agreement with experiment. Finally, point-defect concentrations and conductivities are predicted for undoped and donor-doped systems as a function of oxygen partial pressure and temperature. The characteristic slopes found in experiment are reproduced.
Ab-initio study on crystal structure of α-RuCl3
NASA Astrophysics Data System (ADS)
Kee, Hae-Young; Kim, Heung-Sik
α -RuCl3 was recently proposed as a candidate system for materialization of Kitaev model, but precise structural information of the compound has remained elusive. For the clarification of the full three-dimensional crystal structure of α-RuCl3, we performed ab-initio electronic structure calculations including effects of spin-orbit coupling (SOC) and electron correlations. We found that SOC prevents dimerization between Ru atoms, and keeps the system close to honeycomb lattice. The ground state crystal structure has monoclinic C 2 / m -type layer stacking, but trigonal P31 12 -and orthorhombic Cmc21 -type stacking orders are comparable to the C 2 / m structure in energy, so that stacking faults can be easily introduced. The electronic structure and the jeff=1/2 pseudospin exchange interactions and possible magnetic states in α-RuCl3 will be presented.
Timoshenko, J.; Shivhare, A.; Scott, R. W.; Lu, D.; Frenkel, A. I.
2016-06-30
We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.
NASA Astrophysics Data System (ADS)
Zhou, Liangcai; Körmann, Fritz; Holec, David; Bartosik, Matthias; Grabowski, Blazej; Neugebauer, Jörg; Mayrhofer, Paul H.
2014-11-01
The dynamical and thermodynamic phase stabilities of the stoichiometric compound CrN including different structural and magnetic configurations are comprehensively investigated using a first-principles density functional theory (DFT) plus U (DFT +U ) approach in conjunction with experimental measurements of the thermal expansion. Comparing DFT and DFT +U results with experimental data reveals that the treatment of electron correlations using methods beyond standard DFT is crucial. The nonmagnetic face-centered cubic B1-CrN phase is both elastically and dynamically unstable, even under high pressure, while CrN phases with nonzero local magnetic moments are predicted to be dynamically stable within the framework of the DFT +U scheme. Furthermore, the impact of different treatments for the exchange-correlation (xc)-functional is investigated by carrying out all computations employing the local density approximation and generalized gradient approximation. To address finite-temperature properties, both magnetic and vibrational contributions to the free energy have been computed employing our recently developed spin-space averaging method. The calculated phase transition temperature between low-temperature antiferromagnetic and high-temperature paramagnetic (PM) CrN variants is in excellent agreement with experimental values and reveals the strong impact of the choice of the xc-functional. The temperature-dependent linear thermal expansion coefficient of CrN is experimentally determined by the wafer curvature method from a reactive magnetron sputter deposited single-phase B1-CrN thin film with dense film morphology. A good agreement is found between experimental and ab initio calculated linear thermal expansion coefficients of PM B1-CrN. Other thermodynamic properties, such as the specific heat capacity, have been computed as well and compared to previous experimental data.
Ab initio study of the structure and dynamics of bulk liquid Fe
NASA Astrophysics Data System (ADS)
Marqués, M.; González, L. E.; González, D. J.
2015-10-01
Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.
Cormary, Benoît; Malfant, Isabelle; Valade, Lydie; Buron-Le Cointe, Marylise; Buron-Le Cointe, Marylize; Toupet, Loïc; Todorova, Teodora; Delley, Bernard; Schaniel, Dominik; Mockus, Nicholas; Woike, Theo; Fejfarová, Karla; Petrícek, Václav; Dusek, Michal
2009-10-01
Structure analysis of ground state (GS) and two light-induced (SI and SII) metastable linkage NO isomers of [Ru(py)4Cl(NO)](PF6)2.0.5H2O is presented. Illumination of the crystal by a laser with lambda = 473 nm at T = 80 K transfers around 92% of the NO ligands from Ru-N-O into the isomeric configuration Ru-O-N (SI). A subsequent irradiation with lambda = 980 nm generates about 48% of the side-on configuration Ru<(N)(O) (SII). Heating to temperatures above 200 K or irradiation with light in the red spectral range transfers both metastable isomers reversibly back to the GS. Photodifference maps clearly show the N-O configurations for both isomers and they could be used to find a proper starting model for subsequent refinements. Both metastable isomers have slightly but significantly different cell parameters with respect to GS. The main structural changes besides the Ru-O-N and RU<(N)(O) linkage are shortenings of the trans Ru-Cl bonds and the equatorial Ru-N bonds. The experimental results are compared with solid-state calculations based on density functional theory (DFT), which reproduce the observed structures with high accuracy concerning bond lengths and angles. The problem of how the different occupancies of SI and GS could affect refinement results was solved by a simulation procedure using the DFT data as starting values. PMID:19767684
NASA Technical Reports Server (NTRS)
Komornicki, A.; Jaffe, R. L.
1979-01-01
The infrared spectral intensities for HOCl and HO2 have been calculated using a new ab initio technique. Theoretical results for the geometries, vibrational frequencies, and the dipole moments of these species are also reported. All of the calculations were performed at the SCF level using near Hartree-Fock quality basis sets. The results for the molecular geometries and the vibrational frequencies are in good agreement with available experimental data. It is believed that the computed intensities are accurate to at least 50%. The results should be helpful in attempts to determine the stratospheric abundance of HOCl and HO2 by in situ infrared spectroscopic measurements.
Electronic Structures of Anti-Ferromagnetic Tetraradicals: Ab Initio and Semi-Empirical Studies.
Zhang, Dawei; Liu, Chungen
2016-04-12
The energy relationships and electronic structures of the lowest-lying spin states in several anti-ferromagnetic tetraradical model systems are studied with high-level ab initio and semi-empirical methods. The Full-CI method (FCI), the complete active space second-order perturbation theory (CASPT2), and the n-electron valence state perturbation theory (NEVPT2) are employed to obtain reference results. By comparing the energy relationships predicted from the Heisenberg and Hubbard models with ab initio benchmarks, the accuracy of the widely used Heisenberg model for anti-ferromagnetic spin-coupling in low-spin polyradicals is cautiously tested in this work. It is found that the strength of electron correlation (|U/t|) concerning anti-ferromagnetically coupled radical centers could range widely from strong to moderate correlation regimes and could become another degree of freedom besides the spin multiplicity. Accordingly, the Heisenberg-type model works well in the regime of strong correlation, which reproduces well the energy relationships along with the wave functions of all the spin states. In moderately spin-correlated tetraradicals, the results of the prototype Heisenberg model deviate severely from those of multi-reference electron correlation ab initio methods, while the extended Heisenberg model, containing four-body terms, can introduce reasonable corrections and maintains its accuracy in this condition. In the weak correlation regime, both the prototype Heisenberg model and its extended forms containing higher-order correction terms will encounter difficulties. Meanwhile, the Hubbard model shows balanced accuracy from strong to weak correlation cases and can reproduce qualitatively correct electronic structures, which makes it more suitable for the study of anti-ferromagnetic coupling in polyradical systems. PMID:26963572
Symmetry-Adapted Ab Initio Shell Model for Nuclear Structure Calculations
NASA Astrophysics Data System (ADS)
Draayer, J. P.; Dytrych, T.; Launey, K. D.; Langr, D.
2012-05-01
An innovative concept, the symmetry-adapted ab initio shell model, that capitalizes on partial as well as exact symmetries that underpin the structure of nuclei, is discussed. This framework is expected to inform the leading features of nuclear structure and reaction data for light and medium mass nuclei, which are currently inaccessible by theory and experiment and for which predictions of modern phenomenological models often diverge. We use powerful computational and group-theoretical algorithms to perform ab initio CI (configuration-interaction) calculations in a model space spanned by SU(3) symmetry-adapted many-body configurations with the JISP16 nucleon-nucleon interaction. We demonstrate that the results for the ground states of light nuclei up through A = 16 exhibit a strong dominance of low-spin and high-deformation configurations together with an evident symplectic structure. This, in turn, points to the importance of using a symmetry-adapted framework, one based on an LS coupling scheme with the associated spatial configurations organized according to deformation.
Structure and Raman spectra in cryolitic melts: simulations with an ab initio interaction potential.
Cikit, Serpil; Akdeniz, Zehra; Madden, Paul A
2014-01-30
The Raman spectra of cryolitic melts have been calculated from molecular dynamics computer simulations using a polarizable ionic potential obtained by force-fitting to ab initio electronic structure calculations. Simulations which made use of this ab initio derived polarizable interaction potential reproduced the structure and dynamical properties of crystalline cryolite, Na3AlF6, rather well. The transferability of the potential model from solid state to the molten state is tested by comparing results for the Raman spectra of melts of various compositions with those previously obtained with empirically developed potentials and with experimental data. The shapes of the spectra and their evolution with composition in the mixtures conform quite well to those seen experimentally, and we discuss the relationship between the bands seen in the spectra and the vibrational modes of the AlFn((3–n)) coordination complexes which are found in the NaF/AlF3 mixtures. The simulations thus enable a link between the structure of the melt as derived through Raman spectroscopy and through diffraction experiments. We report results for quantities which relate to the degree of cross-linking between these coordination complexes and the diffusive properties of ions. PMID:24432905
Klevets, Ivan; Bryk, Taras
2014-12-07
Electron-ion structure factors, calculated in ab initio molecular dynamics simulations, are reported for several binary liquids with different kinds of chemical bonding: metallic liquid alloy Bi–Pb, molten salt RbF, and liquid water. We derive analytical expressions for the long-wavelength asymptotes of the partial electron-ion structure factors of binary systems and show that the analytical results are in good agreement with the ab initio simulation data. The long-wavelength behaviour of the total charge structure factors for the three binary liquids is discussed.
The Crystal Structure of Impurity Centers Tm^{2+} and Eu^{2+} in SrCl2 : Ab Initio Calculations
NASA Astrophysics Data System (ADS)
Chernyshev, V. A.; Serdcev, A. V.; Petrov, V. P.; Nikiforov, A. E.
2016-01-01
Ab initio calculations of the impurity centers Tm^{2+} thulium and europium Eu^{2+} in SrCl2 and MeF2 (Me = Ca, Sr, Ba) were carried out at low (zero) temperature. The crystal structure of impurity centers was investigated. Charge density maps show that the bonds formed by the rare-earth ions have an ionic character. The crystal structures, lattice dynamics, and band structures of MeF2 and SrCl2 were calculated at low temperature. Ab initio calculations were performed in periodic CRYSTAL code within the framework of the MO LCAO approach by using hybrid DFT functionals.
Ab Initio Calculation of Structure and Thermodynamic Properties of Zintl Aluminide SrAl2
NASA Astrophysics Data System (ADS)
Fu, Zhi-Jian; Jia, Li-Jun; Xia, Ji-Hong; Tang, Ke; Li, Zhao-Hong; Sun, Xiao-Wei; Chen, Qi-Feng
2015-12-01
The structural and thermodynamic properties of the orthorhombic and cubic structure SrAl2 at pressure and temperature are investigated by using the ab initio plane-wave pseudopotential density functional theory methodwithin the generalised gradient approximation (GGA). The calculated lattice parameters are in agreement with the available experimental data and other theoretical results. The phase transition predicted takes place at 0.5 GPa from the orthorhombic to the cubic structure at zero temperature. The thermodynamic properties of the zinc-blende structure SrAl2 are calculated by the quasi-harmonic Debye model. The pressure-volume relationship and the variations inthe thermal expansion α are obtained systematically in the pressure and temperature ranges of 0-5 GPa and 0-500 K, respectively.
Ab initio study of pressure induced structural and electronic properties in TmPo
Makode, Chandrabhan Pataiya, Jagdish; Sanyal, Sankar P.; Panwar, Y. S.; Aynyas, Mahendra
2015-06-24
We report an ab initio calculation of pressure induced structural phase transition and electronic properties of Thulium Polonide (TmPo).The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). It is found that TmPo is stable in NaCl-type (B{sub 1}-phase) structure to CsCl-type (B{sub 2}-phase) structure of this compound in the pressure range of 7.0 GPa. We also calculate the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure and density of states. From energy diagram it is observed that TmPo exhibit metallic behavior. The calculated values of equilibrium lattice parameter and bulk modulus are in general good agreement.
Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study
Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z
2014-04-01
The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
NASA Astrophysics Data System (ADS)
Baba, Masaak
2009-06-01
Polycyclic aromatic hydrocarbons (PAHs) are fascinating objects of basic studies on molecular structure and excited-state dynamics. We have observed and analyzed rotationally resolved ultrahigh-resolution spectra of the S_1 ← S_0 transition of naphthalene, anthracene, pyrene and perylene (all D_{2h} symmetry) in collimated supersonic jets. We conclude that radiationless transitions are all slow in the S_1 zero-vibrational level of the isolated PAH molecule. Possible radiationless processes are intersystem crossing (ISC), internal conversion (IC), and predissociation. Predissociation does not take place because all of the bond energies are larger than the S_1 ← S_0 excitation energy. The observed radiationless process has been presumed to be ISC so far. However, it is inconsistent with El-Sayed's rule that spin-orbit interaction is very weak between the ^1ππ^* and ^3ππ^* states. We have observed Zeeman splitting of each rotational line and shown that the magnetic moment is very small in the S_1 state. Therefore, the main radiationless process is not ISC to the triplet state, but IC to the hot ground state. IC is caused by non-Born-Oppenheimer vibronic interaction, which is expected to be very weak if the molecular structure is identical for both electronic states. The experimentally determined rotational constants are almost identical for the S_0 and S_1 states. It is consistent with the observed long lifetime and high fluorescence quantum yield of PAHs. We carried out ab initio calculation, and the resultant values of rotational constants of the S_0 state are in extremely good coincidence with the experimental ones for naphthalene and anthracene. On the contrary, for the excited state, it is necessary to perform huge SAC-CI calculation to obtain satisfactory results. Fast IC has been found, for instance, in high vibrational levels of benzene (channel 3), which is due to unavoided potential crossing (conical intersection). However, it is not likely in large
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Rice, Julia E.
1992-01-01
The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.
NASA Astrophysics Data System (ADS)
Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.
From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.
Ab initio theory for ultrafast magnetization dynamics with a dynamic band structure
NASA Astrophysics Data System (ADS)
Mueller, B. Y.; Haag, M.; Fähnle, M.
2016-09-01
Laser-induced modifications of magnetic materials on very small spatial dimensions and ultrashort timescales are a promising field for novel storage and spintronic devices. Therefore, the contribution of electron-electron spin-flip scattering to the ultrafast demagnetization of ferromagnets after an ultrashort laser excitation is investigated. In this work, the dynamical change of the band structure resulting from the change of the magnetization in time is taken into account on an ab initio level. We find a large influence of the dynamical band structure on the magnetization dynamics and we illustrate the thermalization and relaxation process after laser irradiation. Treating the dynamical band structure yields a demagnetization comparable to the experimental one.
NASA Astrophysics Data System (ADS)
Autrey, Daniel; Choo, Jaebum; Laane, Jaan
2000-10-01
The ring-twisting vibration of 1,3-cyclohexadiene has been studied using Raman and infrared spectroscopy of the molecule in the vapor phase. The Raman spectrum shows five ring-twisting transitions in the 150 - 200 cm-1 region. The far-infrared spectrum shows only two transitions for this vibration, which is infrared forbidden in the C_2v (planar) approximation. Three ring-twisting combination bands were also observed off a fundamental vibration at 926.1 cm-1. A coordinate dependent kinetic energy expansion for the ring-twisting motion was calculated, and this was used to determine the ring-twisting potential function. Ab initio calculations were performed using Moller-Plesset perturbation theory (MP2) using different basis sets. The barrier to planarity of 1150 cm-1 was determined from the spectroscopic data. The various ab initio calculations gave barriers to planarity in the 1197 - 1593 cm-1 range.
Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W
2015-01-28
X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range. PMID:25524926
Ab-initio crystal structure prediction. A case study: NaBH{sub 4}
Caputo, Riccarda; Tekin, Adem
2011-07-15
Crystal structure prediction from first principles is still one of the most challenging and interesting issue in condensed matter science. we explored the potential energy surface of NaBH{sub 4} by a combined ab-initio approach, based on global structure optimizations and quantum chemistry. In particular, we used simulated annealing (SA) and density functional theory (DFT) calculations. The methodology enabled the identification of several local minima, of which the global minimum corresponded to the tetragonal ground-state structure (P4{sub 2}/nmc), and the prediction of higher energy stable structures, among them a monoclinic (Pm) one was identified to be 22.75 kJ/mol above the ground-state at T=298 K. In between, orthorhombic and cubic structures were recovered, in particular those with Pnma and F4-bar 3m symmetries. - Graphical abstract: The total electron energy difference of the calculated stable structures. Here, the tetragonal (IT 137) and the monoclinic (IT 6) symmetry groups corresponded to the lowest and the highest energy structures, respectively. Highlights: > Potential energy surface of NaBH{sub 4} is investigated. > This is done a combination of global structure optimizations based on simulated annealing and density functional calculations. > We successfully reproduced experimentally found tetragonal and orthorhombic structures of NaBH{sub 4}. > Furthermore, we found a new stable high energy structure.
Atomic and Electronic Structures of C_60+BN Nanopeapods from ab initio Pseudopotential Calculations
NASA Astrophysics Data System (ADS)
Trave, Andrea; Ribeiro, Filipe; Louie, Steven G.; Cohen, Marvin L.
2004-03-01
Nanopeapods are structures of nanometric size consisting of an external carbon nanotube encapsulating a chain or complex array of fullerenes. Recent calculations and experiments have proven that nanopeapods can be obtained assembling fullerenes within boron nitride nanotubes, creating novel materials of possible interest for electronic transport applications. To improve the understanding of the properties of these composite systems, as compared to empty nanotubes and carbon nanopeapods, ab-initio total energy calculations have been performed within the pseudopotential Density Functional Theory in local density approximation. Results of these calculations on the energetics and geometrical deformations involved in the encapsulation will be presented, followed by a discussion of the consequences on the electronic structures of these systems, with particular focus on aspects relevant to electronic transport phenomena. This work is supported by NFS (Grant DMR00-87088) and DOE (Contract DE-AC03-76SF00098), using computational resources at NERSC and NPACI.
Pressure-induced structural transitions in BN from ab initio metadynamics
NASA Astrophysics Data System (ADS)
Hromadová, Liliana; Martoňák, Roman
2011-12-01
We report here results of ab initio metadynamics simulations of structural transitions in boron nitride at high pressures. Transitions starting from sp2 bonded (graphite-like) structures are studied in a temperature range from 300 to 3000 K and pressures from 20 to 31 GPa. Rhombohedral boron nitride (r-BN) was found to directly transform at all temperatures into cubic boron nitride (c-BN). Hexagonal boron nitride (h-BN) transforms at T<700 K into wurtzite boron nitride (w-BN). At higher temperatures we found a possible transformation pathway resulting in the fully tetrahedrally (sp3) bonded metastable structure. This structure is tetragonal (P42/mnm) and is an analog of the “bct C4” (I4/mmm) structure recently discussed for carbon. The P42/mnm structure has been predicted theoretically for BN but so far not reported experimentally. We calculate structural, elastic, and electronic properties of this structure and discuss the transition mechanism. We also study the transitions at extreme pressures in the tera-pascal range starting from sp3 bonded c-BN and w-BN structures.
NASA Astrophysics Data System (ADS)
Aarset, Kirsten; Hagen, Kolbjørn; Stølevik, Reidar
1997-09-01
Gas-phase electron diffraction data obtained at 23°C, together with results from ab initio molecular orbital calculations ( {HF}/{6-31 G(d)}). were used to determine the structure and conformational composition of 1,1-dichlorobutane. Of the five distinguishable conformers (AA, G + A, AG +, G + G + and G + G -), the G + A conformer was found to be the low-energy form, and the investigation also indicated that certain amounts of the AA and G + G - conformers might be present. The symbols describing the conformers refer to torsion about the C 1C 2 and C 2C 3 bonds, anti (A) with H 5C 1C 2C 3 and C 1C 2C 3C 4 torsion angles of 180° and gauche (G + or G -) with torsion angles of + 60° or 300° (-60°) respectively. The results for the principal distances ( rg) and angles (∠ α) from the combined electron diffraction/ab initio study for the G + A conformer, with estimated 2σ uncertainties, were as follows: r( C1 C2) = 1.521(4) Å, r( C2 C3) = 1.539(4) Å, r( C3 C4) = 1.546(4) Å, r( C Cl6) = 1.782(3) Å, r( CCl7) = 1.782(3) Å,
NASA Astrophysics Data System (ADS)
Mogulkoc, Y.; Ciftci, Y. O.; Kabak, M.; Colakoglu, K.
2014-07-01
The structural, elastic, thermodynamic, electronic and vibrational properties of CsCl-type TbMg have been studied by performing ab initio calculations based on density functional theory using the Vienna Ab initio Simulation Package (VASP). The exchange correlation potential within the generalized-gradient approximation (GGA) of projector augmented wave (PAW) method is used. The calculated structural parameters, such as the lattice constant, bulk modulus, its pressure derivative, formation energy and second-order elastic constants are presented in this paper. The obtained results are compared with related experimental and theoretical studies. The electronic band calculations, total density of states (DOS), partial DOS and charge density are also presented. Formation enthalpy and Cauchy pressure are determined. In order to obtain more information the elastic properties such as Zener anisotropy factor, Poisson’s ratio, Young modulus, isotropic shear modulus, Debye temperature and melting point have been carried out. The elastic constants are calculated in zero and different pressure ranges (0-50 GPa) with bulk modulus. We have performed the thermodynamic properties of TbMg by using quasi-harmonic Debye model. The temperature and pressure variation of the volume, bulk modulus, and thermal expansion coefficient have been predicted over a pressure range of 0-25 GPa for of TbMg. Pressure dependence of the anisotropy factors, Young’s modulus, Poisson’s ratios, bulk modulus and axis compressibility of TbMg are presented along different directions and planes. Finally, the phonon dispersion curves are presented for TbMg.
NASA Astrophysics Data System (ADS)
Stepanian, S. G.; Reva, I. D.; Radchenko, E. D.; Latajka, Z.; Wierzejewska, M.; Ratajczak, H.
1999-06-01
The molecular structure of 1-methylaminophosphinic acid (AMPA) was investigated with the matrix isolation IR spectroscopy and ab initio calculations performed with RHF, MP2, MP3, MP4(DQ), MP4(SDQ) and MP4(SDTQ) methods. Three pseudopotential basis sets designed as CEP-31G were used in the calculations: Basis Set I-CEP-31G with the d-functions on phosphorus; Basis Set II-CEP-31G with the d-functions on all heavy atoms; Basis Set III-CEP-31G with the d-functions on all heavy atoms and p-functions on hydrogens. Four stable molecular and four stable zwitterion conformers of aminophosphinic acid were found via ab initio calculations. According to the calculations, molecular conformers are always more stable than the zwitterion conformers, irrespective of the basis set size and level of theory. This result is in good agreement with matrix IR spectrum of the AMPA. The presence of the bands of OH stretching and NH 2 bending vibrations and the absence of the bands of POO - and NH 3+ vibrations are the evidence of molecular structure of AMPA in the isolated state. An increased number of vibrational bands is found in the IR spectrum. It is explained by the high conformation lability of AMPA molecules which is related to very low barrier of rotation about C-P bond. The IR spectrum is actually determined by multiple sites of AMPA molecule packed in the Ar crystal, which considerably increases the number of bands in the IR spectrum.
NASA Astrophysics Data System (ADS)
Liang, Wenkel
This dissertation consists of two general parts: (I) developments of optimization algorithms (both nuclear and electronic degrees of freedom) for time-independent molecules and (II) novel methods, first-principle theories and applications in time dependent molecular structure modeling. In the first part, we discuss in specific two new algorithms for static geometry optimization, the eigenspace update (ESU) method in nonredundant internal coordinate that exhibits an enhanced performace with up to a factor of 3 savings in computational cost for large-sized molecular systems; the Car-Parrinello density matrix search (CP-DMS) method that enables direct minimization of the SCF energy as an effective alternative to conventional diagonalization approach. For the second part, we consider the time dependence and first presents two nonadiabatic dynamic studies that model laser controlled molecular photo-dissociation for qualitative understandings of intense laser-molecule interaction, using ab initio direct Ehrenfest dynamics scheme implemented with real-time time-dependent density functional theory (RT-TDDFT) approach developed in our group. Furthermore, we place our special interest on the nonadiabatic electronic dynamics in the ultrafast time scale, and presents (1) a novel technique that can not only obtain energies but also the electron densities of doubly excited states within a single determinant framework, by combining methods of CP-DMS with RT-TDDFT; (2) a solvated first-principles electronic dynamics method by incorporating the polarizable continuum solvation model (PCM) to RT-TDDFT, which is found to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. (3) applications of the PCM-RT-TDDFT method to study the intramolecular charge-transfer (CT) dynamics in a C60 derivative. Such work provides insights into the
Brain, Paul T.; Cowie, Jill; Donohoe, David J.; Hnyk, Drahomír; Rankin, David W. H.; Reed, David; Reid, Bruce D.; Robertson, Heather E.; Welch, Alan J.; Hofmann, Matthias; Schleyer, Paul von Ragué
1996-03-13
The compound 1-phenyl-1,2-dicarba-closo-dodecaborane(12), 1-C(6)H(5)-1,2-closo-C(2)B(10)H(11) (1), has been synthesized and characterized by a complete assignment of its (11)B NMR spectrum via (11)B{(1)H}/(11)B{(1)H} (COSY), (1)H{(11)B(selective)} and (1)H{(11)B}/(1)H{(11)B} (COSY) spectroscopy. An electron- and X-ray diffraction investigation of 1, complemented by ab initio calculations, has been undertaken. The gas-phase electron-diffraction (GED) data can be fitted by several models describing conformations which differ in the position of the phenyl ring with respect to the carborane cage. Local symmetries ofC(2)(v)() and D(6)(h)() for the 1,2-C(2)B(10) and C(6) moieties, respectively, were adopted in the GED model in order to simplify the problem. In addition, constraints among the close-lying C-C and B-B bonds were employed. However, even though such simplifications led to satisfactory refinements (R(G) = 0.069-0.071), a unique, definitive solution could not be gained. The (C-C)(mean), (C-B)(mean) and (B-B)(mean) bond lengths,r(a), are ca. 1.44, 1.72, and 1.78 Å, respectively. The C(6) hexagon, with r(a)(C-C) = ca. 1.394 Å, either eclipses the C(1)-C(2) vector (overall C(s)() symmetry) or more or less eclipses the C(1)-B(4) cluster bond (overall C(1) symmetry). In contrast, in the solid at 199 K, the ring lies at a position intermediate between the two GED positions, as determined by X-ray crystallography [C(8)H(16)B(10), monoclinic P2(1)/a: a = 12.047(3) Å, b = 18.627(4) Å, c = 12.332(5) Å, beta = 110.09(4) degrees, Z = 8]. The C-B distances span the range 1.681(6)-1.743(5) Å, and B-B lengths lie between 1.756(6) and 1.795(6) Å. A similar conformation was found for the theoretical (RHF/6-31G level) structure which was fully optimized in C(1) symmetry. The r(e) distances are consistent with the dimensions derived in the experimental studies. IGLO calculations of the (11)B chemical shifts, in addition to SCF single-point energies of the GED structures
NASA Astrophysics Data System (ADS)
Ford, Thomas A.
2014-09-01
The molecular structures, vibrational spectra and atomic charges of the alicyclic ethers containing from two to five carbon atoms have been determined by means of ab initio calculations, at the level of second order Møller-Plesset perturbation theory and using Dunning's augmented correlation-consistent polarized valence triple-zeta basis set. Two isomers of the oxetane, tetrahydrofuran and tetrahydropyran molecules have been identified and their relative energies determined. Structural properties, such as the COC bond angles and the CH bond lengths, are found to increase steadily with increasing ring size and with decreasing ionization energy. The mean CH2 stretching and bending wavenumbers exhibit the reverse behaviour, while the mean wavenumbers of the CH2 wagging and twisting modes follow the same trend as the structural features. The ring mode wavenumbers vary in a less regular way. The charges of the oxygen, α-carbon and axial and equatorial α- and β-hydrogen atoms also do not show systematic dependences on ring size or ionization energy. The trends in the values of these properties have been rationalized.
NASA Astrophysics Data System (ADS)
Erba, A.
2014-09-01
A general-purpose, fully automated, computationally efficient implementation is presented of a series of techniques for the simultaneous description of pressure and temperature effects on structural properties of materials, by means of standard ab initio simulations. Equilibrium volume, bulk modulus, thermal expansion coefficient, equation-of-state, Grüneisen parameter, constant-pressure and constant-volume specific heats are computed as a function of temperature and pressure for the simple crystal of diamond and compared with accurate experimental data. Convergence of computed properties with respect to super-cell size is critically discussed. The effect on such properties of the adopted exchange-correlation functional of the density-functional-theory is discussed by considering three different levels of approximation (including hybrids): it is found to be rather small for the temperature dependence of equilibrium volume and bulk modulus, whereas it is quite large as regards their absolute values.
Erba, A
2014-09-28
A general-purpose, fully automated, computationally efficient implementation is presented of a series of techniques for the simultaneous description of pressure and temperature effects on structural properties of materials, by means of standard ab initio simulations. Equilibrium volume, bulk modulus, thermal expansion coefficient, equation-of-state, Grüneisen parameter, constant-pressure and constant-volume specific heats are computed as a function of temperature and pressure for the simple crystal of diamond and compared with accurate experimental data. Convergence of computed properties with respect to super-cell size is critically discussed. The effect on such properties of the adopted exchange-correlation functional of the density-functional-theory is discussed by considering three different levels of approximation (including hybrids): it is found to be rather small for the temperature dependence of equilibrium volume and bulk modulus, whereas it is quite large as regards their absolute values. PMID:25273420
Numerical criteria for the evaluation of ab initio predictions of protein structure.
Zemla, A; Venclovas, C; Reinhardt, A; Fidelis, K; Hubbard, T J
1997-01-01
As part of the CASP2 protein structure prediction experiment, a set of numerical criteria were defined for the evaluation of "ab initio" predictions. The evaluation package comprises a series of electronic submission formats, a submission validator, evaluation software, and a series of scripts to summarize the results for the CASP2 meeting and for presentation via the World Wide Web (WWW). The evaluation package is accessible for use on new predictions via WWW so that results can be compared to those submitted to CASP2. With further input from the community, the evaluation criteria are expected to evolve into a comprehensive set of measures capturing the overall quality of a prediction as well as critical detail essential for further development of prediction methods. We discuss present measures, limitations of the current criteria, and possible improvements. PMID:9485506
Ab Initio study of multiple exciton generation in layered structure quantum dots
NASA Astrophysics Data System (ADS)
Zhang, Zhiyong; Zimmerman, Paul; Cui, Yi; Musgrave, Charles
2011-03-01
Multiple Exciton Generation (MEG) can potentially increase the photovoltaic conversion efficiency significantly and has been reported in a large number of systems and has been extensively studies theoretically and experimentally. Here we report our study of the MEG process in inorganic layered structure quantum dots using high level Ab Initio methods that are capable of electronic states of multi-exciton in character. Our results show that multiple states that are of multi-exciton character exist in quantum dots and different mechanisms govern the MEG process in quantum dots: (1) MEG through an internal crossing mechanism from a optically active state to an optically dark multi-exciton state, as in the singlet fission process of pentacene; and (2) direct multi-exciton generation through an optically active excited state. We also discuss detailed structure evolution of quantum dots, from stable molecular like structures of various shapes and sizes, to larger quantum dots of bulk like bonding motifs with distinctive surface structures and illustrate the correlation between structure and the multi-exciton states.
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. PMID:23742495
Vázquez-Mayagoitia, Alvaro; Huertas, Oscar; Brancolini, Giorgia; Migliore, Agostino; Sumpter, Bobby G; Orozco, Modesto; Luque, F Javier; Di Felice, Rosa; Fuentes-Cabrera, Miguel
2009-10-29
The structural, tautomeric, hydrogen-bonding, stacking, and electronic properties of a seleno-derivative of thymine (T), denoted here as 4SeT and created by replacing O4 in T with Se, are investigated by means of ab initio computational techniques. The structural properties of T and 4SeT are very similar, and the geometrical differences are mainly limited to the adjacent environment of the C-Se bond. The canonical "keto" form is the most stable tautomer, in the gas phase and in aqueous solution, for both T and 4SeT. It is argued that the competition between two opposite trends, i.e., a decrease in the base-pairing ability and an increase of the stacking interaction upon incorporation of 4SeT into a duplex, likely explains the similar experimental melting points of a seleno-derivative duplex (Se-DNA) and its native counterpart. Interestingly, the underlying electronic structure shows that replacement of O4 with Se promotes a reduction in the HOMO-LUMO gap and an increase in interplane coupling, which suggests that Se-DNA could be potentially useful for nanodevice applications. This finding is further supported by the fact that transfer integrals between 4SeT...A stacked base pairs are larger than those determined for similarly stacked natural T...A pairs. PMID:19813710
NASA Astrophysics Data System (ADS)
Pereira Silva, Pedro S.; Ghalib, Raza Murad; Mehdi, Sayed Hasan; Hashim, Rokiah; Sulaiman, Othman; Silva, Manuela Ramos
2011-05-01
A new polymorph of N', N″, N″'-triphenylbiuret, C 20H 17N 3O 2 (form II), has been synthesized and the structure has been solved by X-ray diffraction. The crystals are monoclinic, space group P2 1/ c, with a = 7.6966 (3) Å, b = 12.5490 (4) Å, c = 18.5996 (6) Å, β = 107.632(2)°, Mr = 331.37, V = 1712.04 (10) Å 3, Z = 4 and R = 0.0454. The hydrogen bonding of this polymorph is considerably different from that of the previously known structure. The molecules are linked in infinite chains, via C-H⋯O hydrogen bonds and there is also an intramolecular N-H⋯O hydrogen bond. The intermolecular interactions present in this polymorph, and on the previously reported polymorph, were analysed by means of the fingerprint plots derived from the Hirshfeld surfaces. The fingerprint plots evidenced the different packing modes of the two structures. Quantum-mechanical ab initio calculations for the free molecule were performed using the Hartree-Fock and DFT/B3LYP methods with the 6-31G(d,p) basis set of wave functions. The solid-state conformations compared with those obtained theoretically from DFT calculations for the isolated molecules show significant differences. Some difficulties of using quantum-mechanical calculations for the determination of relative conformational energies are also discussed.
NASA Astrophysics Data System (ADS)
Zemen, J.; Mašek, J.; Kučera, J.; Mol, J. A.; Motloch, P.; Jungwirth, T.
2014-04-01
An empirical multiorbital (spd) tight binding (TB) model including magnetism and spin-orbit coupling is applied to calculations of magnetic anisotropy energy (MAE) in CoPt L10 structure. A realistic Slater-Koster parametrisation for single-element transition metals is adapted for the ordered binary alloy. Spin magnetic moment and density of states are calculated using a full-potential linearised augmented plane-wave (LAPW) ab initio method and our TB code with different variants of the interatomic parameters. Detailed mutual comparison of this data allows for determination of a subset of the compound TB parameters tuning of which improves the agreement of the TB and LAPW results. MAE calculated as a function of band filling using the refined parameters is in broad agreement with ab initio data for all valence states and in quantitative agreement with ab initio and experimental data for the natural band filling. Our work provides a practical basis for further studies of relativistic magnetotransport anisotropies by means of local Green's function formalism which is directly compatible with our TB approach.
Ab initio molecular dynamics studies of the structure and dynamics of molten SexTe1-x alloys
NASA Astrophysics Data System (ADS)
Lomba, E.; Katcho, N. A.; Otero-Díaz, L. C.
2005-10-01
We calculate the microscopic structure and dynamics of molten SexTe1-x alloys ( x=0.3 , 0.5, 0.7) at 748 K by means of ab initio molecular dynamics. We present results for the static and dynamic structure factors, diffusion coefficients, and frequency spectra, in addition to the electronic density of states. Both the results for the structural and dynamic properties are in relatively good agreement with the available experimental data, despite the known shortcomings of ab initio techniques for the limiting case x=0 . The results also indicate that, as expected, the increase in the number of Te atoms augments the metallic character of the sample in close connection with a corresponding disruption of the Se chain network that dominates the structure of the condensed phases of pure selenium.
Ab initio calculation of structural stability, electronic and optical properties of Ag{sub 2}Se
Rameshkumar, S.; Jayalakshmi, V.; Jaiganesh, G.; Palanivel, B.
2015-06-24
The structural stability, electronic and optical properties of Ag{sub 2}Se compound is studied using ab initio packages. Ag{sub 2}Se is found to crystallize in orthorhombic structure with two different space groups i.e. P2{sub 1}2{sub 1}2{sub 1} (No. 19) and P222{sub 1} (No. 17). For this compound in these two space groups, the total energy has been computed as a function of volume. Our calculated results suggest that the P2{sub 1}2{sub 1}2{sub 1}–phase is more stable than that of the P222{sub 1}–phase. The band structure calculation show that Ag{sub 2}Se is semimetallic with an overlap of about 0.014 eV in P2{sub 1}2{sub 1}2{sub 1}–phase whereas is metallic in nature in P222{sub 1}–phase. Moreover, the optical properties including the dielectric function, energy loss spectrum are obtained and analysed.
NASA Astrophysics Data System (ADS)
Padilha, José Eduardo; Pontes, Renato Borges
2016-01-01
Ab initio electronic structure and transport calculations of 2D hexagonal germanium with four possible structural defects were performed. The considered defects were Stone-Wales (SW), single vacancy (5-9) and two divacancies (5-8-5 and 555-777). We showed that these defects present a local reconstruction that can be clearly identified by STM images. Among the investigated defects, we verified that the SW defect has the lowest formation energy. We showed that in the presence of structural defects the 2D hexagonal germanium maintains its Dirac cone feature only for the single vacancy. The divacancies and the SW defect destroy the linear dispersion relation of the electrons, near the Fermi level, in this system. Moreover, we verified that these defects create scattering centers, which can lead to diminishing of the current by roughly 42% for the Stone-Wales and single vacancy, 55% for the divacancy 5-8-5 and 68% for the 555-777 divacancy.
Local Structure in Ab Initio Liquid Water: Signatures of Amorphous Phases
NASA Astrophysics Data System (ADS)
Santra, Biswajit; Distasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto
Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyze the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I), was unimodal with most water molecules characterized by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water This work was supported by the DOE: DE-SC0008626, DE-SC0005180.
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions
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 to 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.
AB Initio Study of the Structure and Spectroscopic Properties of Halogenated Thioperoxy Radicals
NASA Technical Reports Server (NTRS)
Munoz, Luis A.; Binning, R. C., Jr.; Weiner, Brad R.; Ishikawa, Yasuyuki
1997-01-01
Thioperoxy (XSO or XOS) radicals exist in a variety of chemical environments, and they have as a consequence drawn some interest. HSO, an important species in the chemistry of the troposphere, has been examined both experimentally. The halogenated (X = F, Cl or Br) peroxy species and isovalent thioperoxy species have been studied less, but they too are potentially interesting because oxidized sulfur species and halogen sources are present in the atmosphere. Learning the fate of XSO and XOS radicals is important to understanding the atmospheric oxidation chemistry of sulfur compounds. Of these, FSO and ClSO are particularly interesting because they have been directly detected spectroscopically. Recent studies in our laboratory on the photochemistry of thionyl halides (X2SO; where X = F or Cl) have suggested new ways to generate XSO species. The laser-induced photodissociation of thionyl fluoride, F2SO, at 193 nm and thionyl chloride, ClSO, at 248 nm is characterized by a radical mechanism, X2SO -> XSO + X. The structure of FSO has been characterized experimentally by Endo et cd. employing microwave spectroscopy. Using the unrestricted Hartree-Fock (UHF) self-consistent field (SCF) method, Sakai and Morokuma computed the electronic structure of the ground (sup 2)A" and the first excited (sup 2)A' states of FSO. Electron correlation was not taken into account in their study. In a laser photodissociation experiment, Huber et al. identified ClSO mass spectromctrically. ClSO has also been detected in low temperature matrices by EPR and in the gas phase by far IR laser magnetic resonance. Although the structure of FSO is known in detail, the only study, experimental or theoretical, of CISO has been an ab initio HFSCF study by Hinchliffe. Electron correlation corrections were also excluded from this study. In order to better understand the isomerization and dissociation dynamics of the radical species, we have performed ab initio correlated studies of the potential energy
Crystal structure and magnetism in α -RuCl3 : An ab initio study
NASA Astrophysics Data System (ADS)
Kim, Heung-Sik; Kee, Hae-Young
2016-04-01
α -RuCl3 has been proposed recently as an excellent playground for exploring Kitaev physics on a two-dimensional (2D) honeycomb lattice. However, structural clarification of the compound has not been completed, which is crucial in understanding the physics of this system. Here, using ab initio electronic structure calculations, we study a full three-dimensional (3D) structure of α -RuCl3 , including the effects of spin-orbit coupling (SOC) and electronic correlations. The three major results are as follows: (i) SOC suppresses dimerization of Ru atoms, which exists in other Ru compounds such as isostructural Li2RuO3 , and makes the honeycomb closer to an ideal one. (ii) The nearest-neighbor Kitaev exchange interaction between the jeff=1 /2 pseudospin strongly depends on the Ru-Ru distance and the Cl position, originating from the nature of the edge-sharing geometry. (iii) The optimized 3D structure without electronic correlations has P 3 ¯1 m space-group symmetry independent of SOC, but including electronic correlation changes the optimized 3D structure to either C 2 /m or C m c 21 within 0.1 meV per formula unit (f.u.) energy difference. The reported P 3112 structure is also close in energy. The interlayer spin-exchange coupling is a few percent of the in-plane spin-exchange terms, confirming that α -RuCl3 is close to a 2D system. We further suggest how to increase the Kitaev term via tensile strain, which sheds light in realizing the Kitaev spin-liquid phase in this system.
High Resolution Powder Diffraction and Structure Determination
Cox, D. E.
1999-04-23
It is clear that high-resolution synchrotrons X-ray powder diffraction is a very powerful and convenient tool for material characterization and structure determination. Most investigations to date have been carried out under ambient conditions and have focused on structure solution and refinement. The application of high-resolution techniques to increasingly complex structures will certainly represent an important part of future studies, and it has been seen how ab initio solution of structures with perhaps 100 atoms in the asymmetric unit is within the realms of possibility. However, the ease with which temperature-dependence measurements can be made combined with improvements in the technology of position-sensitive detectors will undoubtedly stimulate precise in situ structural studies of phase transitions and related phenomena. One challenge in this area will be to develop high-resolution techniques for ultra-high pressure investigations in diamond anvil cells. This will require highly focused beams and very precise collimation in front of the cell down to dimensions of 50 {micro}m or less. Anomalous scattering offers many interesting possibilities as well. As a means of enhancing scattering contrast it has applications not only to the determination of cation distribution in mixed systems such as the superconducting oxides discussed in Section 9.5.3, but also to the location of specific cations in partially occupied sites, such as the extra-framework positions in zeolites, for example. Another possible application is to provide phasing information for ab initio structure solution. Finally, the precise determination of f as a function of energy through an absorption edge can provide useful information about cation oxidation states, particularly in conjunction with XANES data. In contrast to many experiments at a synchrotron facility, powder diffraction is a relatively simple and user-friendly technique, and most of the procedures and software for data analysis
Ab initio electron affinity and hyperfine structure constants of ^231Pa:
NASA Astrophysics Data System (ADS)
Dinov, Konstantin D.; Beck, Donald R.
1996-05-01
We have performed valence shell Relativistic Configuration Interaction calculations(Konstantin D. Dinov and Donald R. Beck, Electron affinity and hyperfine structure constants of Pa^-: 7p attachment.) Submitted to Phys. Rev. A for the Electron Affinity (EA) of ^231Pa. Our result of 0.222 eV for the binding energy of the Pa^- 5f^2 6d 7s^2 7p J=6 state is consistent with the experimental yield(X-L. Zhao, M-J. Nadeau, M.A. Garwan, L.R. Kilius and A.E. Litherland, Nuc. Instr. Meth. B 92), 258-64 (1994). Our result for the hyperfine structure constants of Pa^-, is the first available ab initio result. No other bound states were found for the 7p attachment. We didn't find evidence to support possible 5d attachment in this system. This work extends our previous calculations for the Rare Earth negative ions(K.D. Dinov and D.R. Beck, Phys. Rev. A 52) , 2632-37 (1995); K. Dinov and D.R. Beck, Phys. Rev. A 51 (2), 1680-82 (1995); K. Dinov, D.R. Beck and D. Datta, Phys. Rev. A 50 (2), 1144-48 (1994).
NASA Astrophysics Data System (ADS)
Binev, I. G.; Tsenov, J. A.; Velcheva, E. A.; Juchnovski, I. N.
1995-01-01
The structures of phenylacetonitrile and of its carbanion have been studied on the basis of IR spectroscopic data (including literature results) and of ab initio force field calculations. The assignment (D. Croisat et al., J. Org. Chem., 157 (1992) 6435) of the IR bands of phenylacetonitrile, its d5 analogue, and their carbanions has been confirmed. An excellent linear correlation ( R = 0.999) has been found between the theoretical and experimental IR frequencies of the species studied. The calculations predict well the strong increase in intensity (five to 42 fold) of the vCN, vS8 and vI9 bands which accompanies the conversion of the phenylacetonitrile molecule to its carbanion. The structures of both sodium and potassium derivatives of phenylacetonitrile in dimethyl sulfoxide are close to that of the kinetically free phenylacetonitrile carbanion. The carbanionic center is practically planar; the cyano group carries a considerable negative charge, but its influence on the carbanionic center is mainly inductive. The carbanionic charge is delocalized over the phenyl ring (0.42 e -), methide (0.30 e -), and cyano (0.28 e -) groups.
Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott
2012-02-13
Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.
Hegde, Ganesh Bowen, R. Chris
2015-10-15
The accuracy of a single s-orbital representation of Cu towards enabling multi-thousand atom ab initio calculations of electronic structure is evaluated in this work. If an electrostatic compensation charge of 0.3 electron per atom is used in this basis representation, the electronic transmission in bulk and nanocrystalline Cu can be made to compare accurately to that obtained with a Double Zeta Polarized basis set. The use of this representation is analogous to the use of single band effective mass representation for semiconductor electronic structure. With a basis of just one s-orbital per Cu atom, the representation is extremely computationally efficient and can be used to provide much needed ab initio insight into electronic transport in nanocrystalline Cu interconnects at realistic dimensions of several thousand atoms.
Origin of the Hadži ABC structure: An ab initio study
NASA Astrophysics Data System (ADS)
Van Hoozen, Brian L.; Petersen, Poul B.
2015-11-01
Medium and strong hydrogen bonds are well known to give rise to broad features in the vibrational spectrum often spanning several hundred wavenumbers. In some cases, these features can span over 1000 cm-1 and even contain multiple broad peaks. One class of strongly hydrogen-bonded dimers that includes many different phosphinic, phosphoric, sulfinic, and selenic acid homodimers exhibits a three-peaked structure over 1500 cm-1 broad. This unusual feature is often referred to as the Hadži ABC structure. The origin of this feature has been debated since its discovery in the 1950s. Only a couple of theoretical studies have attempted to interpret the origin of this feature; however, no previous study has been able to reproduce this feature from first principles. Here, we present the first ab initio calculation of the Hadži ABC structure. Using a reduced dimensionality calculation that includes four vibrational modes, we are able to reproduce the three-peak structure and much of the broadness of the feature. Our results indicate that Fermi resonances of the in-plane bend, out-of-plane bend, and combination of these bends play significant roles in explaining this feature. Much of the broadness of the feature and the ability of the OH stretch mode to couple with many overtone bending modes are captured by including an adiabatically separated dimer stretch mode in the model. This mode modulates the distance between the monomer units and accordingly the strength of the hydrogen-bonds causing the OH stretch frequency to shift from 2000 to 3000 cm-1. Using this model, we were also able to reproduce the vibrational spectrum of the deuterated isotopologue which consists of a single 500 cm-1 broad feature. Whereas previous empirical studies have asserted that Fermi resonances contribute very little to this feature, our study indicates that while not appearing as a separate peak, a Fermi resonance of the in-plane bend contributes substantially to the feature.
A Initio Lcao Electronic Structure Calculations of Layered Transition Metal Compounds.
NASA Astrophysics Data System (ADS)
Dawson, William G.
1987-09-01
Available from UMI in association with The British Library. In this work the electronic structure of three systems of layered transition metal compounds are examined using an ab initio tight binding (LCAO) method using the Xalpha exchange/correlation approximation: group VI ditellurides, group IV trichalcogenides and quaternary copper oxide defect-perovskites. A chemical pseudopotential argument is presented in order to justify the use of a small basis set of atomic orbitals. The group VI transition metal compounds MoTe_2 and WTe _2 show strong metal-metal interactions and MoTe_2 undergoes an unusual phase transition with the lattice parameter perpendicular to the layers decreasing with increasing temperature. The group IV transition metal trichalcogenides provide a useful series for study due to their quasi-1-dimensional character and the occurrence of two closely related structural variants. The atypical compound ZrTe_3 is given special attention because of its apparent semimetallic nature. The final group of compounds studied are the high Tc superconducting ceramics Ba-La-Cu-O and Ba-Y-Cu-O. The technological importance of compounds with zero resistance and showing the Meissner effect (expelling magnetic fields) above liquid nitrogen temperatures and the, as yet, undefined nature of the mechanism of superconductivity stresses the need to carefully examine the electronic structure of these materials. The role of oxygen vacancies, the charge state of the copper ions and the possibility of structural phase transitions are some of the topics considered here. The use of an atomic-orbital basis allows a comparatively straightforward description of the chemical bonding in a crystal--especially useful when the unit cell contains a large number of atoms.
Dynamics and Structure of Point Defects in Forsterite: ab initio calculations
NASA Astrophysics Data System (ADS)
Churakov, S.; Khisina, N.; Urusov, V.; Wirth, R.
2001-12-01
OH-bearing fluid inclusions in Fo92 forsterite samples from peridotite nodule 9206 (Udachnaja kimberlite pipe)[1] were documented recently based on TEM and IR studies. The Fourier transform of diffraction pattern from the inclusions exhibited a pattern, which is interpreted as ordered planar (2H)xMg defects. In this study the structure and dynamics of protons associated with Mg(1), Mg(2) vacancies and interstitial polyhedrons ordered in a (100) plane corresponding to double unite cell periodicity of the forsterite lattice has been investigated by ab initio quantum mechanic calculations. Static structure optimizations and ab-initio molecular dynamics (MD) simulations have been performed using the CPMD density functional code[2]. The calculations were accomplished with the BLYP-functional utilizing the generalized gradient approximation. Non-local Goedecker-type pseudopotentials[3] have been applied to account for core electrons. Valence electron orbitals were approximated by plane wave expansion up to 70 Ry energy cutoff. The energy of static structures was sampled on 2x2x2 Monkhorst-Pack mesh[4]. During the structure relaxation parameters of an orthorhombic 2x1x2 supercell contaning 116 atoms corresponding to Mg28Si16O64H8 hydrous olivine was fixed at experimental values of a=9.524Å b=10.225Å and c=11.988Å relative to the Pbnm space group. Series of NVT-MD calculations were performed at 1000 K on 2x1x1 supercell with 58 atoms using four chain Nose thermostat. Randomly disturbed optimized structures were used as initial configuration for MD runs. The 1ps system equilibration is followed by trajectory production over 5 ps interval. A point energy sampling was applied in all MD calculations. A series of geometry optimizations, starting with various initial position of protons in Mg(1), Mg(2) and interstitial sites were carried out to obtain a structure with the lowest lattice energy. It was found that structures with protons completely located within the M1
Rahal-Sekkal, Majda; Sekkal, Nezha; Kleb, Dirk C; Bleckmann, Paul
2003-05-01
Optimized geometries and total energies of some conformers of alpha- and beta-D-galactose have been calculated using the RHF/6-31G* ab initio method. Vibrational frequencies were computed at the 6-31G* level for the conformers that favor internal hydrogen bonding, in order to evaluate their enthalpies, entropies, Gibbs free energies, and then their structural stabilities. The semiempirical AM1, PM3, MNDO methods have also been performed on the conformers GG, GT, and TG of alpha- and beta-D-galactose. In order to test the reliability of each semiempirical method, the obtained structures and energies from the AM1, PM3, and MNDO methods have been compared to those achieved using the RHF/6-31G* ab initio method. The MNDO method has not been investigated further, because of the large deviation in the structural parameters compared with those obtained by the ab initio method for the galactose. The semiempirical method that has yielded the best results is AM1, and it has been chosen to perform structural and energy calculations on the galabiose molecule (the disaccharides constituted by two galactose units alpha 1,4 linked). The goal of such calculations is to draw the energy surface maps for this disaccharide. To realize each map, 144 different possible conformations resulting from the rotations of the two torsional angles psi and phi of the glycosidic linkage are considered. In each calculation, at each increment of psi and phi, using a step of 30 degrees from 0 to 330 degrees, the energy optimization is employed. In this article, we report also calculations concerning the galabiose molecule using different ab initio levels such as RHF/6-31G*, RHF/6-31G**, and B3Lyp/6-31G*. PMID:12692790
NASA Astrophysics Data System (ADS)
Bacca, Sonia
2016-04-01
A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.
Ab initio molecular orbital study of the structures of purine hydrates
Colson, A.O.; Sevilla, M.D.
1996-03-14
The structures of the isomers of purine hydrates [4(5)-hydroxy-5(4)-hydropurines] have been geometry optimized with ab initio quantum chemical methods at the 6-31G{sup *} basis set and with the semiempirical method PM3. These hydrates which can result from reduction of radical species formed by attack of hydroxyl radical at the 4,5 double bond in the purines, show significant geometrical distortion when compared to the natural bases. More specifically, the cis isomers adopt a `butterfly` conformation, while in the trans isomers, the pyrimidine and imidazole rings tilt opposite to each other. Our results predict the cis purine hydrate isomers are far more stable than the trans isomers by 10-18 kcal/mol at the 6-31G{sup *} level, whereas the 4-hydroxy-5-hydropurines are found to be slightly more energetically stable than the 5-hydroxy-4-hydropurines. The `butterfly` conformation of the cis isomers constitutes a bulky lesion which will result in a significant distortion of the DNA helix. 33 refs., 2 figs., 3 tabs.
Monteseguro, V.; Rodríguez-Hernández, P.; Muñoz, A.
2015-12-28
The structural, elastic, and vibrational properties of yttrium aluminum garnet Y{sub 3}Al{sub 5}O{sub 12} are studied under high pressure by ab initio calculations in the framework of the density functional theory. The calculated ground state properties are in good agreement with the available experimental data. Pressure dependences of bond length and bulk moduli of the constituent polyhedra are reported. The evolution of the elastic constants and the major elastic properties, Young and shear modulus, Poisson's ratios, and Zener anisotropy ratio, are described. The mechanical stability is analyzed, on the light of “Born generalized stability criteria,” showing that the garnet is mechanically unstable above 116 GPa. Symmetries, frequencies, and pressure coefficients of the Raman-active modes are discussed on the basis of the calculated total and partial phonon density of states, which reflect the dynamical contribution of each atom. The relations between the phonon modes of Y{sub 3}Al{sub 5}O{sub 12} and the internal and external molecular modes of the different polyhedra are discussed. Infrared-active modes, as well as the silent modes, and their pressure dependence are also investigated. No dynamical instabilities were found below 116 GPa.
Ab initio quasiparticle band structure of ABA and ABC-stacked graphene trilayers
NASA Astrophysics Data System (ADS)
Menezes, Marcos G.; Capaz, Rodrigo B.; Louie, Steven G.
2014-01-01
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 self-energy 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 self-energy corrections. Finally, other effects, such as trigonal warping, electron-hole asymmetry, and energy gaps, are discussed in terms of the associated parameters.
PSI3: an open-source Ab Initio electronic structure package.
Crawford, T Daniel; Sherrill, C David; Valeev, Edward F; Fermann, Justin T; King, Rollin A; Leininger, Matthew L; Brown, Shawn T; Janssen, Curtis L; Seidl, Edward T; Kenny, Joseph P; Allen, Wesley D
2007-07-15
PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License. PMID:17420978
NASA Astrophysics Data System (ADS)
Bučko, Tomáš; Šimko, František
2016-02-01
Ab initio molecular dynamics simulations in isobaric-isothermal ensemble have been performed to study the low- and the high-temperature crystalline and liquid phases of cryolite. The temperature induced transitions from the low-temperature solid (α) to the high-temperature solid phase (β) and from the phase β to the liquid phase have been simulated using a series of MD runs performed at gradually increasing temperature. The structure of crystalline and liquid phases is analysed in detail and our computational approach is shown to reliably reproduce the available experimental data for a wide range of temperatures. Relatively frequent reorientations of the AlF6 octahedra observed in our simulation of the phase β explain the thermal disorder in positions of the F- ions observed in X-ray diffraction experiments. The isolated AlF63-, AlF52-, AlF4-, as well as the bridged Al 2 Fm 6 - m ionic entities have been identified as the main constituents of cryolite melt. In accord with the previous high-temperature NMR and Raman spectroscopic experiments, the compound AlF5 2 - has been shown to be the most abundant Al-containing species formed in the melt. The characteristic vibrational frequencies for the AlFn 3 - n species in realistic environment have been determined and the computed values have been found to be in a good agreement with experiment.
Bučko, Tomáš; Šimko, František
2016-02-14
Ab initio molecular dynamics simulations in isobaric-isothermal ensemble have been performed to study the low- and the high-temperature crystalline and liquid phases of cryolite. The temperature induced transitions from the low-temperature solid (α) to the high-temperature solid phase (β) and from the phase β to the liquid phase have been simulated using a series of MD runs performed at gradually increasing temperature. The structure of crystalline and liquid phases is analysed in detail and our computational approach is shown to reliably reproduce the available experimental data for a wide range of temperatures. Relatively frequent reorientations of the AlF6 octahedra observed in our simulation of the phase β explain the thermal disorder in positions of the F(-) ions observed in X-ray diffraction experiments. The isolated AlF6(3-), AlF5(2-), AlF4(-), as well as the bridged Al2Fm(6-m) ionic entities have been identified as the main constituents of cryolite melt. In accord with the previous high-temperature NMR and Raman spectroscopic experiments, the compound AlF5(2-) has been shown to be the most abundant Al-containing species formed in the melt. The characteristic vibrational frequencies for the AlFn(3-n) species in realistic environment have been determined and the computed values have been found to be in a good agreement with experiment. PMID:26874492
Ab initio simulation of the electronic structure of Ta{sub 2}O{sub 5} crystal modifications
Perevalov, T. V. Shaposhnikov, A. V.
2013-06-15
Ab initio simulation of the electronic structure crystalline {beta} and {delta} phases of tantalum(V) oxide (Ta{sub 2}O{sub 5}), representing a promising dielectric material for microelectronics, has been carried out. Both ideal crystals and those with neutral oxygen vacancies in various coordination positions have been studied. The simulation has been performed using the density functional theory with hybrid functionals involving the Hartree-Fock exchange energy. This approach gives a correct description of the bandgap width: 4.1 eV for {beta}-Ta{sub 2}O{sub 5} and 3.1 eV for {delta}-Ta{sub 2}O{sub 5}. The energy levels related to oxygen vacancies in various positions have been determined for the spectra of electron states in {beta}- and {delta}-Ta{sub 2}O{sub 5} polymorphs. It is established that the presence of oxygen vacancies in Ta{sub 2}O{sub 5} crystal modifications leads to the formation of characteristic absorption peaks in their electron energy loss spectra.
NASA Astrophysics Data System (ADS)
Emül, Y.; Erbahar, D.; Açıkgöz, M.
2014-11-01
The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.
Matrix-isolation study and ab initio calculations of the structure and spectra of hydroxyacetone.
Sharma, Archna; Reva, Igor; Fausto, Rui
2008-07-01
The structure of hydroxyacetone (HA) isolated in an argon matrix (at 12 K) and in a neat solid phase (at 12-175 K) was characterized by using infrared (IR) spectroscopy. The interpretation of the experimental results was supported by high-level quantum chemical calculations, undertaken by using both ab initio (MP2) and density functional theory methods. A potential-energy surface scan, carried out at the MP2/6-311++G(d,p) level of theory, predicted four nonequivalent minima, Cc, Tt, Tg, and Ct, all of them doubly degenerate by symmetry. The energy barriers for conversion between most of the symmetrically related structures and also between some of the nonequivalent minima (e.g., Tg --> Tt and Ct --> Tt) are very small and stay below the zero-point vibrational level associated with the isomerization coordinate in the higher-energy form in each pair. Therefore, only Cc and Tt conformers have physical significance, with populations of 99 and 1%, respectively, in gas phase at room temperature. For the matrix-isolated compound, only the most stable Cc conformer was observed. On the other hand, the polarizable continuum model calculations indicated that in water solution, the population of Tt and Ct conformers might be high enough (ca. 6 and 11%, respectively) to enable their experimental detection, thus supporting the conclusions of a previous IR spectroscopy study [ Spectrochim. Acta A 2005, 61, 477] in which the presence of more than one HA conformer in aqueous solution was postulated. The signatures of these minor conformers, however, do not appear in the spectra of the neat HA crystal, and the crystal structure was rationalized in terms of centrosymmetric hydrogen-bonded dimers consisting of two Cc-like units. Finally, we calculated (1)H, (13)C, and (17)O NMR chemical shifts at different levels of theory and found them to agree with available experimental data. PMID:18537231
NASA Astrophysics Data System (ADS)
Ottonello, Giulio; Zuccolini, Marino Vetuschi
2009-11-01
The hexa-aqua complexes [Fe(H 2O) 6-m-n(OH) n] (2-n)+n = 0 → 3, m = 0 → 6 - n; [Fe(H 2O) 6-m-n(OH) n] (3-n)+n = 0 → 4, m = 0 → 6 - n were investigated by ab-initio methods with the aim of determining their ground-state geometries, total energies and vibrational properties by treating their inner solvation shell as part of their gaseous precursor (or " hybrid approach"). After a gas-phase energy optimization within the Density Functional Theory (DFT), the molecules were surrounded by a dielectric representing the Reaction Field through an implicit Polarized Continuum Model (PCM). The exploration of several structural ligand arrangements allowed us to quantify the relative stabilities of the various ionic species and the role of the various forms of energy (solute-solvent electronic interaction, cavitation, dispersion, repulsion, liberation free energy) that contribute to stabilize the aqueous complexes. A comparison with experimental thermochemistries showed that ab-initio gas-phase + solvation energies are quite consistent with experimental evidence and allow the depiction of the most stable form in solution and the eventual configurational disorder of water/hydroxyl species around central cations. A vibrational analysis performed on the 54Fe, 56Fe, 57Fe and 58Fe isotopomers indicated important separative effects systematically affected by the extent of deprotonation. The role of the system's redox state (fO 2) and acidity (pH) on the isotopic imprinting of the aqueous species in solution was investigated by coupling the separative effects with speciation calculations. The observed systematics provided a tool of general utility in the interpretation of the iron isotopic signature of natural waters. Applications to the interpretation of isotopic fractionation in solution dictated by redox equilibria and to the significance of the Fe-isotopic imprinting of Banded Iron Formations are given. With "gaseous precursor" it is intended here the isolated gaseous
NASA Astrophysics Data System (ADS)
Suter, James L.; Kabalan, Lara; Khader, Mahmoud; Coveney, Peter V.
2015-11-01
Ab initio molecular dynamics simulations have been performed to gain an understanding of the interfacial microscopic structure and reactivity of fully hydrated clay edges. The models studied include both micropore and interlayer water. We identify acidic sites through dissociation mechanisms; the resulting ions can be stabilized by both micropore and interlayer water. We find clay edges possess a complex amphoteric behavior, which depends on the face under consideration and the location of isomorphic substitution. For the neutral (1 1 0) surface, we do not observe any dissociation on the timescale accessible. The edge terminating hydroxyl groups participate in a hydrogen bonded network of water molecules that spans the interlayer between periodic images of the clay framework. With isomorphic substitutions in the tetrahedral layer of the (1 1 0) clay edge, we find the adjacent exposed apical oxygen behaves as a Brönsted base and abstracts a proton from a nearby water molecule, which in turn removes a proton from an AlOH2 group. With isomorphic substitutions in the octahedral layer of the (1 1 0) clay edge the adjacent exposed apical oxygen atom does not abstract a proton from the water molecules, but increases the number of hydrogen bonded water molecules (from one to two). Acid treated clays are likely to have both sites protonated. The (0 1 0) surface does not have the same interfacial hydrogen bonding structure; it is much less stable and we observe dissociation of half the terminal SiOH groups (tbnd Sisbnd Osbnd H → tbnd Sisbnd O- + H+) in our models. The resulting anions are stabilized by solvation from both micropore and interlayer water molecules. This suggests that, when fully hydrated, the (0 1 0) surface can act as a Brönsted acid, even at neutral pH.
Input/Output of ab-initio nuclear structure calculations for improved performance and portability
Laghave, Nikhil
2010-01-01
Many modern scientific applications rely on highly computation intensive calculations. However, most applications do not concentrate as much on the role that input/output operations can play for improved performance and portability. Parallelizing input/output operations of large files can significantly improve the performance of parallel applications where sequential I/O is a bottleneck. A proper choice of I/O library also offers a scope for making input/output operations portable across different architectures. Thus, use of parallel I/O libraries for organizing I/O of large data files offers great scope in improving performance and portability of applications. In particular, sequential I/O has been identified as a bottleneck for the highly scalable MFDn (Many Fermion Dynamics for nuclear structure) code performing ab-initio nuclear structure calculations. We develop interfaces and parallel I/O procedures to use a well-known parallel I/O library in MFDn. As a result, we gain efficient I/O of large datasets along with their portability and ease of use in the down-stream processing. Even situations where the amount of data to be written is not huge, proper use of input/output operations can boost the performance of scientific applications. Application checkpointing offers enormous performance improvement and flexibility by doing a negligible amount of I/O to disk. Checkpointing saves and resumes application state in such a manner that in most cases the application is unaware that there has been an interruption to its execution. This helps in saving large amount of work that has been previously done and continue application execution. This small amount of I/O provides substantial time saving by offering restart/resume capability to applications. The need for checkpointing in optimization code NEWUOA has been identified and checkpoint/restart capability has been implemented in NEWUOA by using simple file I/O.
Structure and mechanical properties of cement and intermetallic compounds via ab-initio simulations
NASA Astrophysics Data System (ADS)
Dharmawardhana, Chamila Chathuranga
Calcium silicate hydrates comprise a class of minerals formed synthetically during Portland cement hydration or naturally through various geological processes. The importance of these minerals is immense since they are the primary binding phases for Portland cement derived construction materials. Efforts spanning centuries have been devoted to understand the structural aspects of cohesion in these minerals. In recent years, the focus has progressively turned to atomic level comprehension. Structurally these minerals can range from crystalline to highly disordered amorphous phases. This thesis focuses upon unraveling the nature of chemical bonding in a large subset of calcium silicate hydrate (CSH) crystals. Thus their electronic structure was calculated and bonding mechanisms were investigated quantitatively. Results highlight a wide range of contributions from each type of bonding (Si-O, Ca-O, O-H and hydrogen bond) with respect to silicate polymerization, crystal symmetry, water and OH content. Consequently, total bond order density (TBOD) was designated as the overall single criterion for characterizing crystal cohesion. The TBOD categorization indicates that a rarely known orthorhombic phase Suolunite is closest to the ideal composition and structure of cement. Present work finds the relationship of partial bond order density (PBOD) of each bond species, especially HBs to the mechanical properties of CSH crystals. This can be used as a basis to validate existing C-S-H models and to build improved ones. This work goes further and validates the recently proposed models (2014) for C-S-H (I) phase on the same basis of proposed electronic structure parameters. Then the respective Calcium aluminosilicate hydrates C-A-S-H (I) phase models are proposed. Finally, these results lead to improved interpretations and construction of realistic atomistic models of cement hydrates. Ab initio molecular dynamics (AIMD) could be vital to solve critical problems in complex
Observation and Structure Determination of an Oxide Quasicrystal Approximant.
Förster, S; Trautmann, M; Roy, S; Adeagbo, W A; Zollner, E M; Hammer, R; Schumann, F O; Meinel, K; Nayak, S K; Mohseni, K; Hergert, W; Meyerheim, H L; Widdra, W
2016-08-26
We report on the first observation of an approximant structure to the recently discovered two-dimensional oxide quasicrystal. Using scanning tunneling microscopy, low-energy electron diffraction, and surface x-ray diffraction in combination with ab initio calculations, the atomic structure and the bonding scheme are determined. The oxide approximant follows a 3^{2}.4.3.4 Archimedean tiling. Ti atoms reside at the corners of each tiling element and are threefold coordinated to oxygen atoms. Ba atoms separate the TiO_{3} clusters, leading to a fundamental edge length of the tiling 6.7 Å. PMID:27610863
Ab initio determination of effective electron-phonon coupling factor in copper
NASA Astrophysics Data System (ADS)
Ji, Pengfei; Zhang, Yuwen
2016-04-01
The electron temperature Te dependent electron density of states g (ε), Fermi-Dirac distribution f (ε), and electron-phonon spectral function α2 F (Ω) are computed as prerequisites before achieving effective electron-phonon coupling factor Ge-ph. The obtained Ge-ph is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing Ge-ph from ab initio calculation shows a faster decrease of Te and increase of Tl than those using Ge-ph from phenomenological treatment. The approach of calculating Ge-ph and its implementation into MD-TTM simulation is applicable to other metals.
Ab initio determination of the proton affinities of small neutral and anionic molecules
NASA Technical Reports Server (NTRS)
DeFrees, D. J.; McLean, A. D.
1986-01-01
The proton affinity of a molecule in the gas phase is a fundamental measure of its basicity and is the factor controlling the course of many ion-molecule reactions. In this article, ab initio molecular orbital theory at the MP4/6-311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol-1. Furthermore, the errors are random, indicating that there are likely no systematic errors in either the experimental or theoretical PA's. Also, this level of theory is used to calibrate less sophisticated theoretical models which are suitable for larger molecules; the MP4/6-311 ++ G(2d, 2p) and MP2/6-311 ++ G(d, p) theoretical models should be particularly useful. A procedure for predicting the vibrational frequencies for anion is proposed and applied to CH3-, NH2-, OH-, and CN-.
Ab initio study of the electronic structures of lithium containing diatomic molecules and ions
NASA Astrophysics Data System (ADS)
Boldyrev, Alexander I.; Simons, Jack; Schleyer, Paul von R.
1993-12-01
Ab initio calculations are used to provide bond lengths, harmonic frequencies, and dissociation energies of low-lying electronic states for LiX, LiX+, and LiX- (with X=Li through F and Na through Cl). Most of these species represent hitherto experimentally unknown molecules or ions, which provides the focus of the work presented here. All of these species are stable to dissociation and the anions are stable to loss of an electron. Differences among the electronic structures of the valence isoelectronic LiX; and HX, LiX+, and HX+; and LiX- and HX- species are analyzed. Optimized geometries, dissociation energies, ionization potentials, and electron affinities were calculated for the following ground states of the respective species: 1Σ+ for Li2(1Σ+g) LiNa, LiBe+, LiBe-, LiMg+, LiMg-, LiF, LiAl, LiS-, and LiCl; 2Σ+ for Li+2(2Σ+g), Li-2(2Σ+u) LiBe, LiB+, LiF-, LiNa+, LiNa-, LiMg, LiAl+, and LiCl-; 2Πr for LiB-, LiAl-; 2Πi for LiO, LiF+, LiS, and LiCl+; 3Πr for LiB, LiC+, and LiSi+; 3Σ- for LiN, LiO+, LiSi-, LiP, and LiS+; 4Σ- for LiC, LiN+, LiN-, LiSi, LiP+, and LiP-; and 5Σ- for LiC-.
Origin of the Hadži ABC structure: An ab initio study
Van Hoozen, Brian L.; Petersen, Poul B.
2015-11-14
Medium and strong hydrogen bonds are well known to give rise to broad features in the vibrational spectrum often spanning several hundred wavenumbers. In some cases, these features can span over 1000 cm{sup −1} and even contain multiple broad peaks. One class of strongly hydrogen-bonded dimers that includes many different phosphinic, phosphoric, sulfinic, and selenic acid homodimers exhibits a three-peaked structure over 1500 cm{sup −1} broad. This unusual feature is often referred to as the Hadži ABC structure. The origin of this feature has been debated since its discovery in the 1950s. Only a couple of theoretical studies have attempted to interpret the origin of this feature; however, no previous study has been able to reproduce this feature from first principles. Here, we present the first ab initio calculation of the Hadži ABC structure. Using a reduced dimensionality calculation that includes four vibrational modes, we are able to reproduce the three-peak structure and much of the broadness of the feature. Our results indicate that Fermi resonances of the in-plane bend, out-of-plane bend, and combination of these bends play significant roles in explaining this feature. Much of the broadness of the feature and the ability of the OH stretch mode to couple with many overtone bending modes are captured by including an adiabatically separated dimer stretch mode in the model. This mode modulates the distance between the monomer units and accordingly the strength of the hydrogen-bonds causing the OH stretch frequency to shift from 2000 to 3000 cm{sup −1}. Using this model, we were also able to reproduce the vibrational spectrum of the deuterated isotopologue which consists of a single 500 cm{sup −1} broad feature. Whereas previous empirical studies have asserted that Fermi resonances contribute very little to this feature, our study indicates that while not appearing as a separate peak, a Fermi resonance of the in-plane bend contributes substantially to
Xiao, Hai Yan; Gao, Fei; Zu, Xiaotao T.; Weber, William J.
2010-02-04
High-pressure induced zinc blende to rocksalt phase transition in GaN has been investigated by ab initio molecular dynamics method to characterize the transformation mechanism at the atomic level. It was shown that at 100 GPa GaN passes through tetragonal and monoclinic states before rocksalt structure is formed. The transformation mechanism is consistent with that for other zinc blende semiconductors obtained from the same method. Detailed structural analysis showed that there is no bond breaking involved in the phase transition.
Determining structural performance
NASA Technical Reports Server (NTRS)
Ernst, Michael A.; Kiraly, Louis J.
1987-01-01
An overview is given of the methods and concepts developed to enhance and predict structural dynamic characteristics of advanced aeropropulsion systems. Aeroelasticity, Vibration Control, Dynamic Systems, and Computational Structural Methods are four disciplines that make up the research program at NASA/Lewis Research Center. The Aeroelasticity program develops analytical and experimental methods to minimize flutter and forced vibration of aerospace propulsion systems. Both frequency domain and time domain methods have been developed for applications on the turbofan, turbopump, and advanced turboprop. To improve life and performance, the Vibration Control program conceives, analyzes, develops, and demonstrates new methods to control vibrations in aerospace systems. Active and passive vibration control is accomplished with electromagnetic dampers, magnetic bearings, and piezoelectric crystals to control rotor vibrations. The Dynamic Systems program analyzes and verifies the dynamics of interacting systems, as well as develops concepts and methods for high-temperature dynamic seals. The Computational Structural Methods program uses computer science to improve solutions of structural problems.
Aruguete, Deborah A.; Marcus, Matthew A.; Li, Liang-shi; Williamson, Andrew; Fakra, Sirine; Gygi, Francois; Galli, Giulia; Alivisatos, A. Paul
2006-01-27
We report orientation-specific, surface-sensitive structural characterization of colloidal CdSe nanorods with extended X-ray absorption fine structure spectroscopy and ab-initio density functional theory calculations. Our measurements of crystallographically-aligned CdSe nanorods show that they have reconstructed Cd-rich surfaces. They exhibit orientation-dependent changes in interatomic distances which are qualitatively reproduced by our calculations. These calculations reveal that the measured interatomic distance anisotropy originates from the nanorod surface.
Amokrane, S.; Ayadim, A.; Levrel, L.
2015-11-21
We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.
Determining structural performance
NASA Technical Reports Server (NTRS)
Ernst, Michael A. (Editor); Brown, Gerald; Dirusso, Eliseo; Fleming, David; Janetzke, David; Kascak, Albert; Kaza, Krishna; Kielb, Robert; Kiraly, Louis J.; Lawrence, Charles
1990-01-01
An overview of the methods and concepts developed to enhance and predict structural dynamic characteristics of advanced aeropropulsion systems is presented. Aeroelasticity, vibration control, dynamic systems, and computational structural methods are four disciplines that make up the structural dynamic effort at LeRC. The aeroelasticity program develops analytical and experimental methods for minimizing flutter and forced vibration of aerospace propulsion systems. Both frequency domain and time domain methods were developed for applications on the turbofan, turbopump, and advanced turboprop. In order to improve life and performance, the vibration control program conceives, analyzes, develops, and demonstrates new methods for controlling vibrations in aerospace systems. Active and passive vibration control is accomplished with electromagnetic dampers, magnetic bearings, and piezoelectric crystals to control rotor vibrations. The dynamic systems program analyzes and verifies the dynamics of interacting systems, as well as develops concepts and methods for high-temperature dynamic seals. Work in this field involves the analysis and parametric identification of large, nonlinear, damped, stochastic systems. The computational structural methods program exploits modern computer science as an aid to the solutions of structural problems.
Determination of a silane intermolecular force field potential model from an ab initio calculation
Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng
2010-12-15
Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.
NASA Astrophysics Data System (ADS)
Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.; Zakir'yanov, D. O.
2015-06-01
The effect of hydrostatic compression on the lattice structure and dynamics of elpasolites Cs2NaYbF6 and Cs2NaYF6 (sp. gr. 225) has been investigated ab initio. The frequencies and types of fundamental oscillations are determined, and elastic constants are calculated. The computation is performed within the molecular orbitals-linear combinations of atomic orbitals (MO LCAO) approach using the density functional theory (DFT) method with hybrid functionals B3LYP and PBE0 in the CRYSTAL09 program. The rare-earth ion was described by representing the inner (in particular, 4 f) orbitals in the form of a pseudopotential. The outer 5 s and 5 p orbitals, which determine chemical bonding, were described using valence basis sets.
Specific force field parameters determination for the hybrid ab initio QM/MM LSCF method.
Ferré, Nicolas; Assfeld, Xavier; Rivail, Jean-Louis
2002-04-30
The pure quantum mechanics method, called Local Self-Consistent Field (LSCF), that allows to optimize a wave function within the constraint that some predefined spinorbitals are kept frozen, is discussed. These spinorbitals can be of any shape, and their occupation numbers can be 0 or 1. Any post-Hartree-Fock method, based on the restricted or unrestricted Hartree-Fock Slater determinant, and Kohn-Sham-based DFT method are available. The LSCF method is easily applied to hybrid quantum mechanics/molecular mechanics (QM/MM) procedure where the quantum and the classical parts are covalently bonded. The complete methodology of our hybrid QM/MM scheme is detailed for studies of macromolecular systems. Not only the energy but also the gradients are derived; thus, the full geometry optimization of the whole system is feasible. We show that only specific force field parameters are needed for a correct description of the molecule, they are given for some general chemical bonds. A careful analysis of the errors induced by the use of molecular mechanics in hybrid computation show that a general procedure can be derived to obtain accurate results at low computation effort. The methodology is applied to the structure determination of the crambin protein and to Menshutkin reactions between primary amines and chloromethane. PMID:11939595
NASA Astrophysics Data System (ADS)
Trevisanutto, Paolo E.; Vignale, Giovanni
2016-05-01
Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is "native" to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basic tools of ab initio electronic structure theory — density functional theory, GW approximation and Bethe-Salpeter equation — are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields.
Trevisanutto, Paolo E; Vignale, Giovanni
2016-05-28
Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is "native" to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basic tools of ab initio electronic structure theory - density functional theory, GW approximation and Bethe-Salpeter equation - are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields. PMID:27250294
Rio, Beatriz G del; González, Luis E
2014-11-19
We have performed a comprehensive study of the properties of liquid Be, Ca and Ba, through the use of orbital free ab initio simulations. To this end we have developed a force-matching method to construct the necessary local pseudopotentials from standard ab initio calculations. The structural magnitudes are analyzed, including the average and local structures and the dynamic properties are studied. We find several common features, like an asymmetric second peak in the structure factor, a large amount of local structures with five-fold symmetry, a quasi-universal behaviour of the single-particle dynamic properties and a large degree of positive dispersion in the propagation of collective density fluctuations, whose damping is dictated by slow thermal relaxations and fast viscoelastic ones. Some peculiarities in the dynamic properties are however observed, like a very high sound velocity and a large violation of the Stokes-Einstein relation for Be, or an extremely high positive dispersion and a large slope in the dispersion relation of shear waves at the onset of the wavevector region where they are supported for Ba. PMID:25347355
NASA Astrophysics Data System (ADS)
Kritayakornupong, Chinapong; Hannongbua, Supot
2007-01-01
The structural and dynamical properties of high-spin Ru 2+ in aqueous solution have been theoretically studied using molecular dynamics (MD) simulations. The conventional MD simulation based on pair potentials gives the overestimated average first shell coordination number of 9, whereas the value of 5.9 was observed when the three-body corrected function was included. A combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation has been performed to take into account the many-body effects on the hydration shell structure of Ru 2+. The most important region, the first hydration shell, was treated by ab initio quantum mechanics at UHF level using the SBKJC VDZ ECP basis set for Ru 2+ and the 6-31G ∗ basis sets for water. An exact coordination number of 6 for the first hydration shell was obtained from the QM/MM simulation. The QM/MM simulation predicts the average Ru 2+-O distance of 2.42 Å for the first hydration shell, whereas the values of 2.34 and 2.46 Å are resulted from the pair potentials without and with the three-body corrected simulations, respectively. Several other structural properties representing position and orientation of the solvate molecules were evaluated for describing the hydration shell structure of the Ru 2+ ion in dilute aqueous solution. A mean residence time of 7.1 ps was obtained for water ligands residing in the second hydration shell.
NASA Astrophysics Data System (ADS)
Siraleartmukul, Krisana; Siriwong, Khatcharin; Remsungnen, Tawun; Muangsin, Nongnuj; Udomkichdecha, Werasak; Hannongbua, Supot
2004-09-01
The solvation structure of glucosamine in aqueous solution was investigated using Monte Carlo simulation at 298 K. The MCY rigid water model and ab initio glucosamine-water fitted potential were applied. The first hydration shell appears at 4.6 Å from the center of glucosamine with a coordination number of seven water molecules where one water lies in the ligand's plane while two and four of them are about 2-4 Å above and below the plane, respectively. Furthermore, the mobility distribution and orientation of the water molecules around the ligand have been intensively investigated and reported.
A Nonparametrized Ab Initio Determination of the Heat of Formation of Hydroxylamine, NH2OH
Feller, David F.; Dixon, David A.
2003-12-04
Large basis set coupled cluster calculations through noniterative triple excitations were used to compute optimized structures, harmonic vibrational frequencies, atomization energies at 0 K and heats of formation at 298 K for hydroxylamine (NH2OH) and three related compounds (NH3, HNO and H2O2). The use of basis sets as large as augmented sextuple zeta resulted in small extrapolations to the complete basis set limit in order to achieve chemical accuracy ( 1 kcal/mol) in the thermodynamic properties. Complete basis set estimates were determined from several simple extrapolation formulas. In addition, four other corrections were applied to the frozen core atomization energies, (1) a zero point vibrational correction: (2) a core/valence correlation correction; (3) a Douglas-Kroll-Hess scalar relativistic correction; and (4) a first order atomic spin-orbit correction. For NH3 and HNO we incorporated a fifth correction term intended to approximate the difference between coupled cluster theory and the full configuration interact result. This correction was based on coupled cluster theory through iterative quadruple excitations (CCSDTQ). Excellent agreement with experiment was found for the heats of formation of NH3, HNO and H2O2. For NH2OH the best current estimate of the heat of formation at 298 K is 10.1 0.3 kcal/mol, which falls roughly midway between two experimental values at 12.0 2.4 and 7.9 1.5 kcal/mol.
NASA Astrophysics Data System (ADS)
Durandurdu, Murat
2009-03-01
Ab initio constant pressure molecular dynamics simulations within a generalized gradient approximation (GGA) are carried out to study the structural phase transformation of ZnSe under hydrostatic and nonhydrostatic conditions. ZnSe undergoes a first-order phase transition from the zinc-blende structure to a rocksalt structure having practically identical transformation mechanisms under hydrostatic and nonhydrostatic compressions. This phase transformation is also analyzed using the enthalpy calculations. Our transition parameters and bulk properties are comparable with experimental and theoretical data. Furthermore, the influence of pressure on the electronic structure of ZnSe is investigated. It is found that the band gap energy increases nonlinearly under both hydrostatic and nonhydrostatic conditions and the effect of stress deviations on the band gap energy is small. The computed pressure coefficients and deformation potential of the band gap are in good agreement with experiments.
MOTOR: model assisted software for NMR structure determination.
Schieborr, Ulrich; Sreeramulu, Sridhar; Elshorst, Bettina; Maurer, Marcus; Saxena, Krishna; Stehle, Tanja; Kudlinzki, Denis; Gande, Santosh Lakshmi; Schwalbe, Harald
2013-11-01
Eukaryotic proteins with important biological function can be partially unstructured, conformational flexible, or heterogenic. Crystallization trials often fail for such proteins. In NMR spectroscopy, parts of the polypeptide chain undergoing dynamics in unfavorable time regimes cannot be observed. De novo NMR structure determination is seriously hampered when missing signals lead to an incomplete chemical shift assignment resulting in an information content of the NOE data insufficient to determine the structure ab initio. We developed a new protein structure determination strategy for such cases based on a novel NOE assignment strategy utilizing a number of model structures but no explicit reference structure as it is used for bootstrapping like algorithms. The software distinguishes in detail between consistent and mutually exclusive pairs of possible NOE assignments on the basis of different precision levels of measured chemical shifts searching for a set of maximum number of consistent NOE assignments in agreement with 3D space. Validation of the method using the structure of the low molecular-weight-protein tyrosine phosphatase A (MptpA) showed robust results utilizing protein structures with 30-45% sequence identity and 70% of the chemical shift assignments. About 60% of the resonance assignments are sufficient to identify those structural models with highest conformational similarity to the real structure. The software was benchmarked by de novo solution structures of fibroblast growth factor 21 (FGF21) and the extracellular fibroblast growth factor receptor domain FGFR4 D2, which both failed in crystallization trials and in classical NMR structure determination. PMID:23852655
Puzzarini, Cristina; Taylor, Peter R
2005-02-01
Highly accurate ab initio computations of the molecular structure and properties, torsional potential energy function, and harmonic force field of disilane and ethane have been carried out. Equilibrium parameters as well as vibrational corrections have been evaluated. In addition, for these systems a vibrational averaging procedure has been employed for calculating the dipole moment of molecules which have no permanent dipole moment, i.e., SiH(3)SiD(3) and CH(3)CD(3). The molecular and spectroscopic properties calculated for ethane and its isotopomers provide a calibration against known experimental data, allowing us to estimate the reliability of our computed results for disilane for which there is much less experimental data. The goal of the present study is to predict the molecular parameters, with estimated uncertainties, that determine the microwave spectrum of SiH(3)SiD(3). PMID:15740330
NASA Astrophysics Data System (ADS)
Puzzarini, Cristina; Taylor, Peter R.
2005-02-01
Highly accurate ab initio computations of the molecular structure and properties, torsional potential energy function, and harmonic force field of disilane and ethane have been carried out. Equilibrium parameters as well as vibrational corrections have been evaluated. In addition, for these systems a vibrational averaging procedure has been employed for calculating the dipole moment of molecules which have no permanent dipole moment, i.e., SiH3SiD3 and CH3CD3. The molecular and spectroscopic properties calculated for ethane and its isotopomers provide a calibration against known experimental data, allowing us to estimate the reliability of our computed results for disilane for which there is much less experimental data. The goal of the present study is to predict the molecular parameters, with estimated uncertainties, that determine the microwave spectrum of SiH3SiD3.
NASA Astrophysics Data System (ADS)
Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha
2011-11-01
Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.
Hoy, Erik P.; Mazziotti, David A.
2015-08-14
Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.
Hoy, Erik P; Mazziotti, David A
2015-08-14
Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory. PMID:26277123
NASA Technical Reports Server (NTRS)
Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)
1994-01-01
Conformational energy contours of perfluoroalkanes, determined from ab initio calculations, confirm the well-known spitting of trans states into two minima at plus or minus 17 degrees but also show that the gauche states split as well, with minima at plus or minus 124 degrees and plus or minus 84 in order to relieve steric crowding. The directions of such split distortions from the perfectly staggered states are strongly coupled for adjacent pairs of bonds in a manner identical to the intradyad pair for poly (isobutylene) chains. These conformational characteristics are fully represented by a six-state rotational isomeric state (RIS) model for PTFE comprised of t(+), t(-), g(sup +)+, g(sup +)-, g(sup -) + and g(sup -)-states, located at the split energy minima. The resultant 6 x 6 statistical weight matrix is described by first-order interaction parameters for the g+(+) (ca. 0.6 kcal/mol) and g+- (ca. 2.0 kcal/mol) states, and second order parameters for the g(sup +)+g(sup +)+ (ca 0.6 kcal/mol) and g(sup +)+g(sup -)+ (ca. 1.0 kcal/mol) states. This six-state RIS model, without adjustment of the geometric or energy parameters as determined from the ab initio calculations, predicts the unperturbed chain dimensions and the fraction of gauche bonds as a function of temperature for PTFE in good agreement with available experimental values.
Ab initio investigations of A-site doping on the structure and electric polarization of HoMnO3
NASA Astrophysics Data System (ADS)
S, Sathya Sheela; C, Kanagaraj; Natesan, Baskaran
2015-06-01
We have investigated the effect of A-site doping on the structure and electric polarization of orthorhombic HoMnO3 using ab initio density functional theory calculations. We find that the substitution of rare earth ions, such as Lu, Y and La in place of Ho in orthorhombic HoMnO3 modifies the local structure around Mn ions drastically, and leads to the formation of two distinct Mn sites Mn(0) and Mn(1). As a result, large variance between Mn(0)O6 and Mn(1)O6 octahedral distortions arises. This variance in the octahedral distortions drives the disparate hopping of electrons between the eg orbitals enhancing the electronic polarization with increasing rare earth ion radius. The largest polarization of 7 µC/cm2 is obtained for La doped HoMnO3. This increase in polarization has been explained on the basis of radius mismatch induced local structural effects.
NASA Astrophysics Data System (ADS)
Binev, Ivan G.; Binev, Yuri I.; Stamboliyska, Bistra A.; Juchnovski, Ivan N.
1997-12-01
The potassium cyanide, alkali-metal methoxide and heptylamine adducts of benzylidenemalononitrile were prepared as dimethyl sulphoxide (DMSO) and DMSO- d6 solutions; their structures were studied by IR spectroscopy and ab initio force field calculations. The cyanide and methoxide adducts have a carbanionic structure, whereas heptylamine forms a zwitterion. The IR spectra of the adducts studied are characterized by very intense, low-frequency νCN bands with a strong νCNs- νCNas splitting. The changes in the structure and force field of benzylidenemalononitrile accompanying its conversion into the adducts studied are essential and are spread over the whole molecule. The anionic charge is localized mainly within the dicyanomethide groups of the adducts.
Jakse, N.; Pasturel, A.
2014-12-21
In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.
NASA Astrophysics Data System (ADS)
Carrera, Juan J.; Son, Sang-Kil; Chu, Shih-I.
2007-06-01
We present an ab initio quantum investigation of the frequency comb structure formed within each high harmonic generation (HHG) power spectrum driven by a train of equal- spacing short laser pulses. The HHG power spectrum of atomic hydrogen is calculated by solving the time-dependent Schr"o dinger equation accurately and efficiently by means of the time- dependent generalized pseudospectral method. We found that the frequency comb structure is preserved within each harmonic. In addition, the repetition frequency of the comb laser depends upon the pulse separation τ and the spectral width of each individual comb fringe is inversely proportional to the number of pulses (n) used. However, the global HHG power spectrum pattern depends only upon the laser frequency and intensity used and is not sensitive to the τ and n parameters. Finally, the frequency comb structure persists even in the presence of appreciable ionization.
NASA Astrophysics Data System (ADS)
Senent, M. L.; Moule, D. C.; Smeyers, Y. G.
1995-04-01
We have calculated the potential energy hypersurface of dimethyl ether with respect to the COC bending coordinate α and the torsional angles of the two methyl groups, θ1 and θ2. Two sets of ab initio calculations were carried out. The first was made at the level MP2/6-31G(d,p) in which the structural coordinates were fully relaxed except for the grid points on the hypersurface. More extensive calculation were carried out with MP4 corrections for electron correlation with the same molecular structure. The torsional bending Hamiltonian matrix was symmetrized by the operations of the G36 nonrigid group and was solved variationally. The effect of explicitly considering the bending mode in the three-dimensional treatment was determined by a comparison to the two-dimensional model in which the flexibility of the frame was absorbed into the calculation by the fully relaxed method. It was found that the three-dimensional calculation gave a much better account of the sin(3θ1)sin(θ2) intermode coupling than the two-dimensional treatment.
Putungan, Darwin Barayang; Lin, Shi-Hsin; Kuo, Jer-Lai
2016-07-27
We systematically investigated the potential of single-layer VS2 polytypes as Na-battery anode materials via density functional theory calculations. We found that sodiation tends to inhibit the 1H-to-1T structural phase transition, in contrast to lithiation-induced transition on monolayer MoS2. Thus, VS2 can have better structural stability in the cycles of charging and discharging. Diffussion of Na atom was found to be very fast on both polytypes, with very small diffusion barriers of 0.085 eV (1H) and 0.088 eV (1T). Ab initio random structure searching was performed in order to explore stable configurations of Na on VS2. Our search found that both the V top and the hexagonal center sites are preferred adsorption sites for Na, with the 1H phase showing a relatively stronger binding. Notably, our random structures search revealed that Na clusters can form as a stacked second layer at full Na concentration, which is not reported in earlier works wherein uniform, single-layer Na adsorption phases were assumed. With reasonably high specific energy capacity (232.91 and 116.45 mAh/g for 1H and 1T phases, respectively) and open-circuit voltage (1.30 and 1.42 V for 1H and 1T phases, respectively), VS2 is a promising alternative material for Na-ion battery anodes with great structural sturdiness. Finally, we have shown the capability of the ab initio random structure searching in the assessment of potential materials for energy storage applications. PMID:27373121
NASA Astrophysics Data System (ADS)
Pietrucci, Fabio; Andreoni, Wanda
2011-08-01
Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.
Phosphine adsorption and dissociation on the Si(001) surface: An ab initio survey of structures
NASA Astrophysics Data System (ADS)
Warschkow, O.; Wilson, H. F.; Marks, N. A.; Schofield, S. R.; Curson, N. J.; Smith, P. V.; Radny, M. W.; McKenzie, D. R.; Simmons, M. Y.
2005-09-01
We report a comprehensive ab initio survey of possible dissociation intermediates of phosphine (PH3) on the Si(001) surface. We assign three scanning tunneling microscopy (STM) features, commonly observed in room-temperature dosing experiments, to PH2+H , PH+2H , and P+3H species, respectively, on the basis of calculated energetics and STM simulation. These assignments and a time series of STM images which shows these three STM features converting into another, allow us to outline a mechanism for the complete dissociation of phosphine on the Si(001) surface. This mechanism closes an important gap in the understanding of the doping process of semiconductor devices.
NASA Astrophysics Data System (ADS)
Kumar, Anupriya; Kołaski, Maciej; Kim, Kwang S.
2008-01-01
Structures of the ground state pyrrole-(H2O)n clusters are investigated using ab initio calculations. The charge-transfer driven femtosecond scale dynamics are studied with excited state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field method for pyrrole-(H2O)n clusters. Upon the excitation of these clusters, the charge density is located over the farthest water molecule which is repelled by the depleted π-electron cloud of pyrrole ring, resulting in a highly polarized complex. For pyrrole-(H2O), the charge transfer is maximized (up to 0.34a.u.) around ˜100fs and then oscillates. For pyrrole-(H2O)2, the initial charge transfer occurs through the space between the pyrrole and the π H-bonded water molecule and then the charge transfer takes place from this water molecule to the σ H-bonded water molecule. The total charge transfer from the pyrrole to the water molecules is maximized (up to 0.53a.u.) around ˜100fs.
Ab initio, density functional theory and structural studies of 4-amino-2-methylquinoline.
Arjunan, V; Saravanan, I; Ravindran, P; Mohan, S
2009-10-01
The Fourier transform infrared (FTIR) and FT-Raman spectra of 4-amino-2-methylquinoline (AMQ) have been recorded in the range 4000-400 and 4000-100 cm(-1), respectively. The experimental vibrational frequency was compared with the wavenumbers obtained theoretically by ab initio HF and DFT-B3LYP gradient calculations employing the standard 6-31 G** and high level 6-311 ++G** basis sets for optimised geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the experimental FTIR and FT-Raman data, and quantum mechanical studies. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The potential energy distribution of the fundamental modes was calculated with ab initio force fields utilising Wilson's FG matrix method. The NH-pi interactions and the influence of amino and methyl groups on the skeletal modes are investigated. PMID:19581121
Ab initio, density functional theory and structural studies of 4-amino-2-methylquinoline
NASA Astrophysics Data System (ADS)
Arjunan, V.; Saravanan, I.; Ravindran, P.; Mohan, S.
2009-10-01
The Fourier transform infrared (FTIR) and FT-Raman spectra of 4-amino-2-methylquinoline (AMQ) have been recorded in the range 4000-400 and 4000-100 cm -1, respectively. The experimental vibrational frequency was compared with the wavenumbers obtained theoretically by ab initio HF and DFT-B3LYP gradient calculations employing the standard 6-31G** and high level 6-311++G** basis sets for optimised geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the experimental FTIR and FT-Raman data, and quantum mechanical studies. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The potential energy distribution of the fundamental modes was calculated with ab initio force fields utilising Wilson's FG matrix method. The NH -π interactions and the influence of amino and methyl groups on the skeletal modes are investigated.
Structural Analysis of SiGe and SiGeC Alloys by Ab Initio Total-Energy Calculations
NASA Astrophysics Data System (ADS)
Yamada, Akira; Konagai, Nagako
1999-04-01
The structural properties of SiGe and SiGeC alloysare studied byab initio total-energy calculations.It is found from these calculations that the Ge cluster isa stable structure in a SiGe alloy. Furthermore, it is alsodemonstrated that Vegard's law is validin a SiGeC system whose C content is less than 3%.The total-energy calculation of the Si0.72Ge0.25C0.03alloy in which the number of Ge C bonds around a C atom variesshows that the energy increases on increasing the number of Ge C bonds.The mechanism of this increase is considered, taking into account thecohesive energy difference of the SiC and GeC alloys and the atomicconfiguration around the C atom.
NASA Astrophysics Data System (ADS)
Binev, Y. I.; Petrova, R. R.; Tsenov, J. A.; Binev, I. G.
2000-01-01
The structures of (4-nitrophenyl)acetonitrile and of its carbanion were studied on the basis of both quantitative IR spectra and ab initio force field calculations. The spectral and structural changes, which take place in the course of the conversion of the parent molecule into the carbanion, are essential and spread over the whole species. In agreement between theory and experiment, the conversion studied causes strong frequency decreases (down to 136 cm -1) and intensity increases (up to 90-fold) of the cyano and nitro stretching bands. The molecule→carbanion conversion is accompanied by both quinoidization of the phenylene ring and a change in the configuration of the methylenic carbon atom: from tetrahedral in the molecule it becomes planar in the carbanion. The carbanionic charge is delocalized over the carbanionic center (0.40 e -), phenylene (0.24 e -), nitro (0.21 e -) and cyano (0.15 e -) groups.
Ab initio structural and electronic analysis of CH3SH self-assembled on a Cu(110) substrate
NASA Astrophysics Data System (ADS)
D'Agostino, S.; Chiodo, L.; Della Sala, F.; Cingolani, R.; Rinaldi, R.
2007-05-01
Ab initio Density Functional Theory calculations are here reported to characterize the adsorption of methanethiol at the Cu(110) surface. Theoretical results suggest that the binding of the adsorbate to the substrate is rather weak and the molecular geometry is correspondingly almost unaffected by the adsorption. Otherwise, when CH3SH deprotonates producing methanethiolate, a stronger chemical bond is realized between the sulfur atom of CH3S radical and Cu surface atoms. A detailed study of structural and electronic properties of methanethiolate on Cu(110) for a p(2×2) and a c(2×2) overlayer structure has been carried out. We find that, in the most stable configuration, the molecule adsorbs in the shortbridge site. The chemical bond arises due to a strong hybridization among p orbitals of sulfur and d states from the substrate, as it is deduced by an analysis of partial densities of states and charge densities.
NASA Astrophysics Data System (ADS)
Berg, Rolf W.
2007-04-01
The oxide complexation chemistry in molten tetrachloroaluminate salts and ionic liquids is discussed with respect to what possible structures may be formed in addition to [AlCl4]-: [Al2OCl6]2-, [Al3OCl8]-, [Al2O2Cl4]2-, [Al3O2Cl6]- and [Al4O2Cl10]2-. Ab initio molecular orbital calculations are carried out on these various aluminium chloride and oxochloride ions, in assumed isolated gaseous free ionic state, by use of the Gaussian 03W program at the restricted Hartree-Fock (HF) level and with the 6-31+G(d,p) basis set.Without any pre-assumed symmetries and with tight optimization convergence criteria and by using the modified GDIIS algorithm, the model calculations generally converge. The structures and their binding energies are presented. The expected geometries are supported, with one exception perhaps being the [Al2OCl6]2- ion, that gave a linear Al-O-Al bonding system of staggered AlCl3-groups (approximate D3d symmetry), in analogy to the linear Al-O-Al geometry of the analogous [Al2OF6]2- ion, found previously. The calculations include determination of the vibrational harmonic normal modes and the infrared and Raman spectra (vibrational band wavenumbers and intensities), without any empiric adjustments of the harmonic force constants, using constants directly predicted from the Gaussian 03W program. Previously obtained IR absorption and Raman scattering spectra of melts are assigned, by comparing to the ab initio quantum mechanical vibrational analysis results. It is concluded that the small oxide content commonly found in basic and neutral tetrachloroaluminate melts, most probably consists of [Al4O2Cl10]2- ions, and the vibrational spectra are given.
NASA Astrophysics Data System (ADS)
Suleiman, Mohammed S. H.; Joubert, Daniel P.
2015-11-01
In the present work, the atomic and the electronic structures of Au3N, AuN and AuN2 are investigated using first-principles density-functional theory (DFT). We studied cohesive energy vs. volume data for a wide range of possible structures of these nitrides. Obtained data were fitted to a Birch-Murnaghan third-order equation of state (EOS) so as to identify the most likely candidates for the true crystal structure in this subset of the infinite parameter space, and to determine their equilibrium structural parameters. The analysis of the electronic properties was achieved by the calculations of the band structure and the total and partial density of states (DOS). Some possible pressure-induced structural phase transitions have been pointed out. Further, we carried out GW0 calculations within the random-phase approximation (RPA) to the dielectric tensor to investigate the optical spectra of the experimentally suggested modification: Au3N(D09). Obtained results are compared with experiment and with some available previous calculations.
NASA Astrophysics Data System (ADS)
Hemzalová, P.; Friák, M.; Šob, M.; Ma, D.; Udyansky, A.; Raabe, D.; Neugebauer, J.
2013-11-01
We have employed parameter-free density functional theory calculations to study the thermodynamic stability and structural parameters as well as elastic and electronic properties of Ni4N in eight selected crystallographic phases. In agreement with the experimental findings, the cubic structure with Pearson symbol cP5, space group Pm3¯m (221) is found to be the most stable and it is also the only thermodynamically stable structure at T=0 K with respect to decomposition to the elemental Ni crystal and N2 gas phase. We determine structural parameters, bulk moduli, and their pressure derivatives for all eight allotropes. The thermodynamic stability and bulk modulus is shown to be anticorrelated. Comparing ferromagnetic and nonmagnetic states, we find common features between the magnetism of elemental Ni and studied ferromagnetic Ni4N structures. For the ground-state Ni4N structure and other two Ni4N cubic allotropes, we predict a complete set of single-crystalline elastic constants (in the equilibrium and under hydrostatic pressure), the Young and area moduli, as well as homogenized polycrystalline elastic moduli obtained by different homogenization methods. We demonstrate that the elastic anisotropy of the ground-state Ni4N is qualitatively opposite to that in the elemental Ni, i.e., these materials have hard and soft crystallographic directions interchanged. Moreover, one of the studied metastable cubic phases is found auxetic, i.e., exhibiting negative Poisson ratio.
Ab-initio calculations of electronic, transport, and structural properties of boron phosphide
Ejembi, J. I.; Nwigboji, I. H.; Franklin, L.; Malozovsky, Y.; Zhao, G. L.; Bagayoko, D.
2014-09-14
We present results from ab-initio, self-consistent density functional theory calculations of electronic and related properties of zinc blende boron phosphide (zb-BP). We employed a local density approximation potential and implemented the linear combination of atomic orbitals formalism. This technique follows the Bagayoko, Zhao, and Williams method, as enhanced by the work of Ekuma and Franklin. The results include electronic energy bands, densities of states, and effective masses. The calculated band gap of 2.02 eV, for the room temperature lattice constant of a=4.5383 Å, is in excellent agreement with the experimental value of 2.02±0.05 eV. Our result for the bulk modulus, 155.7 GPa, agrees with experiment (152–155 GPa). Our predictions for the equilibrium lattice constant and the corresponding band gap, for very low temperatures, are 4.5269 Å and 2.01 eV, respectively.
Optimized Structures and Proton Affinities of Fluorinated Dimethyl Ethers: An Ab Initio Study
NASA Technical Reports Server (NTRS)
Orgel, Victoria B.; Ball, David W.; Zehe, Michael J.
1996-01-01
Ab initio methods have been used to investigate the proton affinity and the geometry changes upon protonation for the molecules (CH3)2O, (CH2F)2O, (CHF2)2O, and (CF3)2O. Geometry optimizations were performed at the MP2/3-2 I G level, and the resulting geometries were used for single-point energy MP2/6-31G calculations. The proton affinity calculated for (CH3)2O was 7 Kjoule/mole from the experimental value, within the desired variance of +/- 8Kjoule/mole for G2 theory, suggesting that the methodology used in this study is adequate for energy difference considerations. For (CF3)20, the calculated proton affinity of 602 Kjoule/mole suggests that perfluorinated ether molecules do not act as Lewis bases under normal circumstances; e.g. degradation of commercial lubricants in tribological applications.
Lister, C.J.; McCutchan, E.A.
2014-06-15
A new generation of ab-initio calculations, based on realistic two- and three-body forces, is having a profound impact on our view of how nuclei work. To improve the numerical methods, and the parameterization of 3-body forces, new precise data are needed. Electromagnetic transitions are very sensitive to the dynamics which drive mixing between configurations. We have made a series of precise (< 3%) measurements of electromagnetic transitions in the A=10 nuclei {sup 10}C and {sup 10}Be by using the Doppler Shift Attenuation method carefully. Many interesting features can be reproduced including the strong α clustering. New measurements on {sup 8}Be and {sup 12}Be highlight the interplay between the alpha clusters and their valence neutrons.
NASA Astrophysics Data System (ADS)
Liu, X. K.; Tang, B.; Zhang, Y.
2013-10-01
The structural and thermodynamic properties of tetragonal-TiH2 under high temperatures and pressures are investigated by Ab initio calculations based on pseudo-potential plane-wave density functional theory method within using the generalized gradient approximation (GGA) and quasi-harmonic Debye model. Some ground state properties such as lattice constants, bulk modulus and elastic constants are good agreement with the available experimental results and other theoretical data. Through the quasiharmonic Debye model, in which the phononic effects are considered, the thermodynamic properties of tetragonal-TiH2 such as thermal expansion coefficient, Debye temperature, heat capacity and Grüneisen parameters dependence of temperature and pressure in the range of 0-1000 K and 0-10 GPa are also presented, respectively.
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
1988-01-01
Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F+H2 yields HF+H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
1989-01-01
Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.
Pigozzi, Giancarlo; Janczak-Rusch, Jolanta; Passerone, Daniele; Antonio Pignedoli, Carlo; Patscheider, Joerg; Jeurgens, Lars P. H.; Antusek, Andrej; Parlinska-Wojtan, Magdalena; Bissig, Vinzenz
2012-10-29
Nano-sized Ag-Cu{sub 8nm}/AlN{sub 10nm} multilayers were deposited by reactive DC sputtering on {alpha}-Al{sub 2}O{sub 3}(0001) substrates. Investigation of the phase constitution and interface structure of the multilayers evidences a phase separation of the alloy sublayers into nanosized grains of Ag and Cu. The interfaces between the Ag grains and the quasi-single-crystalline AlN sublayers are semi-coherent, whereas the corresponding Cu/AlN interfaces are incoherent. The orientation relationship between Ag and AlN is constant throughout the entire multilayer stack. These observations are consistent with atomistic models of the interfaces as obtained by ab initio calculations.
NASA Astrophysics Data System (ADS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.
NASA Astrophysics Data System (ADS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F+H2 yields HF+H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.
NASA Astrophysics Data System (ADS)
Spassova, Milena; Enchev, Venelin
2004-03-01
An ab initio HF and MP2 study of the static (hyper)polarizabilities of 2,4-substituted imidazoles and thiazoles is presented. The comparison of the two types of five-membered heterocycles suggests, that the exocyclic heteroatoms have much more influence upon the calculated hyperpolarizabilities, than the ring heteroatoms. It has been found, that adding diffuse functions to the 6-31G** basis set and inclusion of the electron correlation result in drastic changes in the second hyperpolarizability. The changes are more pronounced for the structures with larger number of sulfur atoms. A HF/6-31G** investigation of a push-pull system, in which thiorhodanine has been chosen as acceptor fragment shows an enhancement of the molecular polarizabilities with respect to the corresponding typical donor-acceptor NH 2/NO 2 polyene.
Bylaska, Eric J.; Dixon, David A.; Felmy, Andrew R.
2000-01-01
The presence of different anionic species in natural waters can significantly alter the degradation rates of chlorinated methanes and other organic compounds. Favorable reaction energetics is a necessary feature of these nucleophilic substitution reactions that can result in the degradation of the chlorinated methanes. In this study, ab initio electronic structure theory is used to evaluate the free energies of reaction of a series of monovalent anionic species (OH-, SH-, NO3 -, HCO3 -, HSO3 -, HSO4 -, H2PO4 -, and F-) that can occur in natural waters with the chlorinated methanes, CCl4, CCl3H, CCl2H2, and CClH3. The results of this investigation show that nucleophilic substitution reactions of OH-, SH-, HCO3 -, and F- are significantly exothermic for chlorine displacement, NO3 - reactions are slightly exothermic to thermoneutral, HSO3
Lu, Sheng-Jie; Hu, Lian-Rui; Xu, Xi-Ling; Xu, Hong-Guang; Chen, Hui; Zheng, Wei-Jun
2016-07-27
Gold-doped germanium clusters, AuGen(-) (n = 2-12), were investigated by using anion photoelectron spectroscopy in combination with ab initio calculations. Their geometric structures were determined by comparison of the theoretical calculations with the experimental results. The results show that the most stable isomers of AuGen(-) with n = 2-10 are all exohedral structures with the Au atom capping the vertex, edge or face of Gen clusters, while AuGe11(-) is found to be the critical size of the endohedral structure. Interestingly, AuGe12(-) has an Ih symmetric icosahedral structure with the Au atom located at the center. The molecular orbital analysis of the AuGe12(-) cluster suggests that the interactions between the 5d orbitals of the Au atom and the 4s4p hybridized orbitals of the Ge atoms may stabilize the Ih symmetric icosahedral cage and promote the Au atom to be encapsulated in the cage of Ge12. The NICS(0) and NICS(1) values are calculated to be -143.7 ppm and -36.3 ppm, respectively, indicating that the icosahedral AuGe12(-) cluster is significantly aromatic. PMID:27066757
Structure of ZnCl2 Melt. Part I: Raman Spectroscopy Analysis Driven by Ab Initio Methods.
Alsayoud, Abduljabar Q; Venkateswara Rao, Manga; Edwards, Angharad N; Deymier, Pierre A; Muralidharan, Krishna; Potter, B G; Runge, Keith; Lucas, Pierre
2016-05-01
The structure of molten ZnCl2 is investigated using a combination of computer simulation and experimental methods. Ab initio molecular dynamics (AIMD) is used to model the structure of ZnCl2 at 600 K. The structure factors and pair distribution functions derived from AIMD show a good match with those previously measured by neutron diffraction (ND). In addition, Raman spectroscopy is used to investigate the structure of liquid ZnCl2 and identify the relative fractions of constituent structural units. To ascertain the assignment of each Raman mode, a series of ZnCl2 crystalline prototypes are modeled and the corresponding Raman modes are derived by first-principles calculations. Curve fitting of experimental Raman spectra using these mode assignments shows excellent agreement with both AIMD and ND. These results confirm the presence of significant fractions of edge-sharing tetrahedra in liquid ZnCl2. The presence of these structural motifs has significant impact on the fragility of this tetrahedral glass-forming liquid. The assignment of Raman bands present in molten ZnCl2 is revised and discussed in view of these results. PMID:27070739
Rong, Xi; Kolpak, Alexie M
2015-05-01
The design of efficient, stable, and inexpensive catalysts for oxygen evolution and reduction is crucial for the development of electrochemical energy conversion devices such as fuel cells and metal-air batteries. Currently, such design is limited by challenges in atomic-scale experimental characterization and computational modeling of solid-liquid interfaces. Here, we begin to address these issues by developing a general-, first-principles-, and electrochemical-principles-based framework for prediction of catalyst surface structure, stoichiometry, and stability as a function of pH, electrode potential, and aqueous cation concentration. We demonstrate the approach by determining the surface phase diagram of LaMnO3, which has been studied for oxygen evolution and reduction and computing the reaction overpotentials on the relevant surface phases. Our results illustrate the critical role of solvated cation species in governing the catalyst surface structure and stoichiometry, and thereby catalytic activity, in aqueous solution. PMID:26263350
Structure and energetics of graphene oxide isomers: ab initio thermodynamic analysis.
Chaban, Vitaly V; Prezhdo, Oleg V
2015-10-28
Graphene oxide (GO) holds significant promise for electronic devices and nanocomposite materials. A number of models were proposed for the GO structure, combining carboxyl, hydroxyl, carbonyl and epoxide groups at different locations. The complexity and variety of GO isomers, whose thermodynamic stability and formation kinetics depend on the applied conditions, make determination of the GO structure with atomistic precision challenging. We report high level theoretical investigation of multiple molecular configurations, which are anticipated in GO. We conclude that all oxygen containing groups at the GO surface are thermodynamically permitted, whereas the 'edge' positions are systematically more favorable than the 'center' and 'side' positions. We discuss a potentially novel type of chemical bond or bonding reinforcement in GO, which consists of a covalent bond and a strong electrostatic contribution from a polarized graphene plane. We observe and analyze significant modifications of the graphene geometry and electronic structure upon oxidation. The reported thermodynamic data guide experiments aimed at deciphering the GO chemical composition and structure, and form the basis for predicting GO properties required for nano-technological applications. PMID:26420562
Structure and energetics of graphene oxide isomers: ab initio thermodynamic analysis
NASA Astrophysics Data System (ADS)
Chaban, Vitaly V.; Prezhdo, Oleg V.
2015-10-01
Graphene oxide (GO) holds significant promise for electronic devices and nanocomposite materials. A number of models were proposed for the GO structure, combining carboxyl, hydroxyl, carbonyl and epoxide groups at different locations. The complexity and variety of GO isomers, whose thermodynamic stability and formation kinetics depend on the applied conditions, make determination of the GO structure with atomistic precision challenging. We report high level theoretical investigation of multiple molecular configurations, which are anticipated in GO. We conclude that all oxygen containing groups at the GO surface are thermodynamically permitted, whereas the `edge' positions are systematically more favorable than the `center' and `side' positions. We discuss a potentially novel type of chemical bond or bonding reinforcement in GO, which consists of a covalent bond and a strong electrostatic contribution from a polarized graphene plane. We observe and analyze significant modifications of the graphene geometry and electronic structure upon oxidation. The reported thermodynamic data guide experiments aimed at deciphering the GO chemical composition and structure, and form the basis for predicting GO properties required for nano-technological applications.
NASA Astrophysics Data System (ADS)
Canè, E.; di Lonardo, G.; Fusina, L.; Jerzembeck, W.; Bürger, H.; Breidung, J.; Thiel, W.
The high resolution infrared spectrum of 123SbD3 has been recorded in the 20-350 cm-1 range and in the regions of the ν1, ν3 and ν2, ν4 fundamental bands centred at 1350 and 600 cm-1, respectively. Splitting of the K'' = 3, 6 lines have been observed both in the rotation and ro-vibration spectra. A large number of 'perturbation allowed' transitions with selection rules Δ(k -l) = ± 3, ± 6, and ± 9 have been identified in all fundamental bands. Accurate ground state molecular parameters have been determined by means of a simultaneous fit of the rotational transitions and about 12 000 ground state combination differences from the infrared bands. The A and B reductions of the rotational Hamiltonian provided almost equivalent results. The molecular parameters of the νi = 1 (i = 1 - 4) states were obtained as a result of the simultaneous analysis of the ν1 (A1)/ν3 (E) stretching and of the ν2 (A1)/ν4 (E) bending dyads. In fact, the corresponding excited states are affected by strong perturbations due to rovibrational interactions of Coriolis and k-type that have been treated explicitly in the model adopted for the analysis. Improved effective ground state and equilibrium geometries were determined for the molecule and compared to those of 123SbH3. Ab initio calculations at the coupled cluster CCSD(T) level with an energy-consistent large-core pseudopotential and large basis sets were carried out to determine the equilibrium structure, the anharmonic force field, and the associated spectroscopic constants of 123SbH3 and 123SbD3. The theoretical results are in good agreement with the experimental data.
Crystal structure determination of Efavirenz
NASA Astrophysics Data System (ADS)
Popeneciu, Horea; Tripon, Carmen; Borodi, Gheorghe; Pop, Mihaela Maria; Dumitru, Ristoiu
2015-12-01
Needle-shaped single crystals of the title compound, C14H9ClF3NO2, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.
Zhou, Yanzi; Wang, Shenglong; Zhang, Yingkai
2010-01-01
Acetylcholinesterase (AChE) is a remarkably efficient serine hydrolase responsible for the termination of impulse signaling at cholinergic synapses. By employing Born-Oppenheimer molecular dynamics simulations with B3LYP/6-31G(d) QM/MM potential and the umbrella sampling method, we have characterized its complete catalytic reaction mechanism for hydrolyzing neurotransmitter acetylcholine (ACh) and determined its multi-step free energy reaction profiles for the first time. In both acylation and deacylation reaction stages, the first step involves the nucleophilic attack to the carbonyl carbon with the triad His447 serving as the general base, and leads to a tetrahedral covalent intermediate stabilized by the oxyanion hole. From the intermediate to the product, the orientation of His447 ring needs to be adjusted very slightly, and then the proton transfers from His447 to the product and the break of the scissile bond happen spontaneously. For the three-pronged oxyanion hole, it only makes two hydrogen bonds with the carbonyl oxygen at either the initial reactant or the final product state, but the third hydrogen bond is formed and stable at all transition and intermediate states during the catalytic process. At the intermediate state of the acylation reaction, a short and low-barrier hydrogen bond (LBHB) is found to be formed between two catalytic triad residues His447 and Glu334, and the spontaneous proton transfer between two residues has been observed. However, it is only about 1 ~ 2 kcal/mol stronger than the normal hydrogen bond. In comparison with previous theoretical investigations of the AChE catalytic mechanism, our current study clearly demonstrates the power and advantages of employing Born-Oppenheimer ab initio QM/MM MD simulations in characterizing enzyme reaction mechanisms. PMID:20550161
Ma, Xiaoyan; Cai, Kaicong; Wang, Jianping
2011-02-10
Infrared (IR) experiment, ab initio computations, and molecular dynamics (MD) simulations were used to examine the dynamical structures of ethylene glycol (EG) and 1,2-ethanedithiol (EDT) in carbon tetrachloride and deuterated chloroform. Using the O-H and S-H stretching modes as structural probes, EG and EDT were found to exhibit different conformational preferences, even though they share similar molecular formula. Results suggest that the gauche conformation of EG presents and is stabilized by the intramolecular hydrogen bond (IHB), while both the trans and gauche EDT are possible in the two solvents. Exchangeable IHB donor and acceptor pairs were predicted in the case of EG. Anharmonic vibrational frequencies, anharmonicities, and couplings of the O-H and S-H stretching modes were predicted and found to be structurally dependent. Linear IR and two-dimensional IR spectra containing these structural signatures were simulated and discussed. These results demonstrate that a combination of the methods used here is very useful in revealing structural dynamics of small molecules in condensed phases. PMID:21208002
Determinants and Polynomial Root Structure
ERIC Educational Resources Information Center
De Pillis, L. G.
2005-01-01
A little known property of determinants is developed in a manner accessible to beginning undergraduates in linear algebra. Using the language of matrix theory, a classical result by Sylvester that describes when two polynomials have a common root is recaptured. Among results concerning the structure of polynomial roots, polynomials with pairs of…
Ona, Ofelia; Facelli, Julio C.; Bazterra, Victor E.; Caputo, Maria C.; Ferraro, Marta B.
2005-11-15
The results of ab initio global optimizations of the structures of Si{sub n}H, n=4-10, atomic clusters using a parallel genetic algorithm are presented. Driving the global search with the parallel implementation of the genetic algorithm are presented and using the density functional theory as implemented in the Carr-Parinello molecular dynamics code to calculate atomic cluster energies and perform the local optimization of their structures, we have been able to demonstrate that it is possible to perform global optimizations of the structure of atomic clusters using ab initio methods. The results show that this approach is able to find many structures that were not previously reported in the literature. Moreover, in most cases the new structures have considerable lower energies than those previously known. The results clearly demonstrate that these calculations are now possible and in spite of their larger computational demands provide more reliable results.
Structural determinants of limited proteolysis.
Kazanov, Marat D; Igarashi, Yoshinobu; Eroshkin, Alexey M; Cieplak, Piotr; Ratnikov, Boris; Zhang, Ying; Li, Zhanwen; Godzik, Adam; Osterman, Andrei L; Smith, Jeffrey W
2011-08-01
Limited or regulatory proteolysis plays a critical role in many important biological pathways like blood coagulation, cell proliferation, and apoptosis. A better understanding of mechanisms that control this process is required for discovering new proteolytic events and for developing inhibitors with potential therapeutic value. Two features that determine the susceptibility of peptide bonds to proteolysis are the sequence in the vicinity of the scissile bond and the structural context in which the bond is displayed. In this study, we assessed statistical significance and predictive power of individual structural descriptors and combination thereof for the identification of cleavage sites. The analysis was performed on a data set of >200 proteolytic events documented in CutDB for a variety of mammalian regulatory proteases and their physiological substrates with known 3D structures. The results confirmed the significance and provided a ranking within three main categories of structural features: exposure > flexibility > local interactions. Among secondary structure elements, the largest frequency of proteolytic cleavage was confirmed for loops and lower but significant frequency for helices. Limited proteolysis has lower albeit appreciable frequency of occurrence in certain types of β-strands, which is in contrast with some previous reports. Descriptors deduced directly from the amino acid sequence displayed only marginal predictive capabilities. Homology-based structural models showed a predictive performance comparable to protein substrates with experimentally established structures. Overall, this study provided a foundation for accurate automated prediction of segments of protein structure susceptible to proteolytic processing and, potentially, other post-translational modifications. PMID:21682278
Structural determinants of limited proteolysis
Kazanov, Marat D.; Igarashi, Yoshinobu; Eroshkin, Alexey M.; Cieplak, Piotr; Ratnikov, Boris; Zhang, Ying; Li, Zhanwen; Godzik, Adam; Osterman, Andrei L.; Smith1, Jeffrey W.
2011-01-01
Limited or regulatory proteolysis plays a critical role in many important biological pathways like blood coagulation, cell proliferation, and apoptosis. A better understanding of mechanisms that control this process is required for discovering new proteolytic events and for developing inhibitors with potential therapeutic value. Two features that determine the susceptibility of peptide bonds to proteolysis are the sequence in the vicinity of the scissile bond and the structural context in which the bond is displayed. In this study we assessed statistical significance and predictive power of individual structural descriptors and combination thereof for the identification of cleavage sites. The analysis was performed on a dataset of >200 proteolytic events documented in CutDB for a variety of mammalian regulatory proteases and their physiological substrates with known 3D structures. The results confirmed the significance and provided a ranking within three main categories of structural features: exposure > flexibility > local interactions. Among secondary structure elements, the largest frequency of proteolytic cleavage was confirmed for loops and lower but significant frequency for helices. Limited proteolysis has lower albeit appreciable frequency of occurrence in certain types of β-strands, which is in contrast with some previous reports. Descriptors deduced directly from the amino acid sequence displayed only marginal predictive capabilities. Homology-based structural models showed a predictive performance comparable to protein substrates with experimentally established structures. Overall, this study provided a foundation for accurate automated prediction of segments of protein structure susceptible to proteolytic processing and, potentially, other post-translational modifications. PMID:21682278
Castellano, O; Bermúdez, Y; Giffard, M; Mabon, G; Cubillan, N; Sylla, M; Nguyen-Phu, X; Hinchliffe, A; Soscún, H
2005-11-17
The geometries and the static dipole (hyper)polarizabilities (alpha, beta, gamma) of a series of aromatic anions were investigated at the ab initio (HF, MP2, and MP4) and density functional theory DFT (B3LYP) levels of theory. The anions chosen for the present study are the benzenethiolate (Ph-S-), benzenecarboxylate (Ph-CO2-), benzenesulfinate (Ph-SO2-), benzenesulfonate (Ph-SO3-), and 1,3-benzenedicarboxylate (1,3-Ph-(CO2)2(2-)). For benzenethiolate anion, additional alpha, beta, and gamma calculations were performed at the coupled cluster CCSD level with MP2 optimized geometries. The standard diffuse and polarized 6-31+G(d,p) basis set was employed in conjunction to the ab initio and DFT methods. Additional HF calculations were performed with the 6-311++G(3d,3p) basis set for all the anions. The correlated electric properties were evaluated numerically within the formalism of finite field. The optimized geometries were analyzed in terms of the few reports about the phenolate and sulfonate ions. The results show that electron correlation effects on the polarizabilities are very important in all the anion series. Was found that Ph-SO2- is highly polarizable in terms of alpha and beta, and the Ph-S- is the highest second hyperpolarizable in the series. The results of alpha were rationalized in terms of the analysis of the polarization of charge based in Mulliken atomic population and the structural features of the optimized geometries of anions, whereas the large differences in the beta and gamma values in the series were respectively interpreted in terms of the bond length alternation BLA and the separation of charge in the aromatic ring by effects of the substitution. These results allowed us to suggest the benzenesulfinate and benzenethiolate anions as promising candidates that should be incorporated in ionic materials for second and third-order nonlinear optical devices. PMID:16833334
Ab initio calculation and anharmonic force field of hypochlorous acid, HOCl
NASA Astrophysics Data System (ADS)
Halonen, L.; Ha, T.-K.
1988-03-01
Ab initio calculations on HOCl have been performed at the third-order Møller-Plesset perturbation theory level to determine the equilibrium structure and the anharmonic force field. An empirical anharmonic force field based on the ab initio results is obtained using available experimental vibration-rotation data. Four of the six harmonic and six of the ten cubic force constants have been determined experimentally, the remaining values being fixed at the ab initio values. A good fit to the experimental vibration-rotation data of four isotopic species is obtained.
Marqués, Miriam; González, Luis E; González, David J
2016-02-24
The static and dynamic properties of liquid Fe at high pressure and temperature have been studied using an ab initio molecular dynamics method. We have focused on four thermodynamic states at pressures of 27, 42, 50 and 58 GPa for which x-ray scattering data are available. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak which becomes more marked with increasing pressure. The dynamical structure reveals the existence of propagating density fluctuations and the associated dispersion relation has also been determined. The relaxation mechanisms for the density fluctuations have been analyzed in terms of a model with two decay channels (fast and slow, respectively). We found that the thermal relaxation proceeds along the slow decaying channel whereas the fast one is that of the viscoelastic relaxation. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, qp, as suggested by the recently reported appearance of high frequency transverse waves in liquid Li under high pressures; the second region is around qp/2, as suggested by the recent finding of transverse acoustic modes in inelastic x-ray scattering intensities of liquid Fe at ambient pressure. Finally, results are also reported for several transport coefficients. PMID:26811899
NASA Astrophysics Data System (ADS)
Marqués, Miriam; González, Luis E.; González, David J.
2016-02-01
The static and dynamic properties of liquid Fe at high pressure and temperature have been studied using an ab initio molecular dynamics method. We have focused on four thermodynamic states at pressures of 27, 42, 50 and 58 GPa for which x-ray scattering data are available. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak which becomes more marked with increasing pressure. The dynamical structure reveals the existence of propagating density fluctuations and the associated dispersion relation has also been determined. The relaxation mechanisms for the density fluctuations have been analyzed in terms of a model with two decay channels (fast and slow, respectively). We found that the thermal relaxation proceeds along the slow decaying channel whereas the fast one is that of the viscoelastic relaxation. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, q p , as suggested by the recently reported appearance of high frequency transverse waves in liquid Li under high pressures; the second region is around q p /2, as suggested by the recent finding of transverse acoustic modes in inelastic x-ray scattering intensities of liquid Fe at ambient pressure. Finally, results are also reported for several transport coefficients.
NASA Astrophysics Data System (ADS)
Elerman, Y.; Kara, H.; Elmali, A.
2003-06-01
The synthesis and characterization of [Cu2(L1)(3,5 prz)] (L1=1,3-Bis(2-hydroxy-3,5-chlorosalicylideneamino) propan-2-ol) 1 and of [Cu2(L2)(3,5 prz)] (L2=1,3-Bis(2-hydroxy-bromosalicylideneamino) propan-2-ol) 2 are reported. The compounds were studied by elemental analysis, infrared and electronic spectra. The structure of the Cu2(L1)(3,5 prz)] complex was determined by x-ray diffraction. The magnetochemical characteristics of these compounds were determined by temperaturedependent magnetic susceptibility measurements, revealing their antiferromagnetic coupling. The superexchange coupling constants are 210 cm-1 for 1 and 440 cm-1 for 2. The difference in the magnitude of the coupling constants was explained by the metal-ligand orbital overlaps and confirmed by ab-initio restricted Hartree-Fock (RHF) calculations. In order to determine the nature of the frontier orbitals, Extended Hückel Molecular Orbital (EHMO) calculations are also reported.
NASA Astrophysics Data System (ADS)
Yoon, Sangmoon; Jin, Kyoungsuk; Kang, Seoung-Hun; Nam, Ki Tae; Kim, Miyoung; Kwon, Young-Kyun
Manganese oxide nanoparticles have attracted a lot of attentions as a promising candidate for next-generation catalyst. Therefore, understanding the electronic structure of manganese oxide in room temperature is highly required for the rational design of catalysts. We study the effects of paramagnetism and electron correlations on the electronic structure of MnO using ab initio density functional theory. Spin configurations of paramagnetism are postulated as the ensemble average of various spin disorders. Each initial disordered spin configuration is randomly generated with two constraints on magnetic local moments. We first investigate the influence of magnetic ordering on the elctronic structure of MnO using noncollinear spin calculations and find that the magnetic disorders make valence band maximum more delocalized. Moreover, we examine the role of electron correlations in the electronic structure of paramagnetic MnO using DFT +U calculations. Strong electron correlations modify not only the size of band gap but also the magnitude of local moments as in the antiferromagnetic MnO. Besides, the initialized spin disorder remains almost unchanged as electron correlation get stronger. Furthermore, our results obtained by considering both strong electron correlation and paramagnetism confirm experimentally-observed oxygen K edge X-ray emission spectra [1] reflecting the feature of valence bands. [1] E. Z. Kurmaev et al., Phys. Rev. B. 77, 165127 (2008).
Ab initio study of the structures and hydrogen storage capacity of (H2)nCH4 compound
NASA Astrophysics Data System (ADS)
Wang, Minghui; Cheng, Xinlu; Ren, Dahua; Zhang, Hong; Tang, Yongjian
2015-05-01
The hydrogen-rich compound (H2)nCH4 (for n = 1, 2, 3, 4) or for short (H2)nM is one of the most promising hydrogen storage materials. The (H2)4M molecule is the best hydrogen-rich compound among the (H2)nM structures and it can reach the hydrogen storage capacity of 50.2 wt.%. However, the (H2)nM always requires a certain pressure to remain stable. In this work, we first investigated the binding energy of the different structures in (H2)nM and energy barrier of H2 rotation under different pressures at ambient temperature, applying ab initio methods based on van der Waals density functional (vdW-DF). It was found that at 0 GPa, the (H2)nM is not stable, while at 5.8 GPa, the stability of (H2)nM strongly depends on its structure. We further investigate the Raman spectra of (H2)nM structures at 5.8 GPa and found the results were consistent with experiments. Excitingly, we found that boron nitride nanotubes (BNNTs) and graphite and hexagonal boron nitride (h-BN) can be used to store (H2)4M, which give insights into hydrogen storage practical applications.
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.
Ab Initio Study of the Structural, Electronic, and Thermal Properties of Alloy
NASA Astrophysics Data System (ADS)
Benkaddour, I.; Khachai, H.; Chiker, F.; Benosman, N.; Benkaddour, Y.; Murtaza, G.; Omran, S. Bin; Khenata, R.
2015-07-01
The results of a first-principle study of the structural, electronic, and thermal properties of a alloy, using the full-potential linear muffin-tin-orbital (FP-LMTO) method in the framework of density functional theory, within both the local density approximation and the generalized gradient approximation are presented. The composition effect on lattice constants, bulk moduli, band gaps, and effective masses is analyzed. The quasi-harmonic Debye model, using a set of total energy versus volume calculations obtained with the FP-LMTO method, is applied to study the thermal and vibrational effects. The temperature effect on the lattice parameters, thermal expansions, heat capacities, and Debye temperatures is determined from the non-equilibrium Gibbs functions. The microscopic origins of the bowing parameter were explained using the approach of Zunger and coworkers.
NASA Astrophysics Data System (ADS)
Shimizu, Toshihiko; Yoshino, Ruriko; Ishiuchi, Shun-ichi; Hashimoto, Kenro; Miyazaki, Mitsuhiko; Fujii, Masaaki
2013-02-01
IR spectra of trans-1-naphthol-(H2O)n (n = 0-3) clusters in the S1 state were measured by UV-IR fluorescence dip spectroscopy. The observed dip spectra were compared with theoretical ones of various stable conformations predicted by ab initio MO calculations. From the comparison, linear (n = 1) and cyclic hydrogen-bond structures (n = 2 and 3) were concluded. The relation between the structures and photochemical reactivity was discussed.
NASA Astrophysics Data System (ADS)
Mohamed, Tarek A.; Shaltout, I.; Al Yahyaei, K. M.
2006-05-01
Systems of iron tellurite glasses were prepared by melt quenching with compositions of [85%TeO 2 + 5%Fe 2O 3 + 10%TMO], where transition metal oxides (TMO) are TiO 2, V 2O 5, MnO, CoO, NiO and CuO. Furthermore, the main structural units of these samples have been characterized by means of Raman spectra (150-1200 cm -1) as well as wavenumber predictions by means of Gaussian 98 ab initio calculations for the proposed site symmetries of TeO 44- triagonal bipyramid ( C2v) and Te 2O 76- bridged tetrahedra ( Cs and C1). Aided by normal coordinate analysis, calculated vibrational frequencies, Raman scattering activities, force constants in internal coordinates and potential energy distributions (PEDs), revised vibrational assignments for the fundamental modes have been proposed. The main structural features are correlated to the dominant units of triagonal bipyramid (tbp) or bridged tetrahedral (TeO 3+1 binds to TeO 3 through TeOTe bridge; corner sharing). Moreover, the Raman spectra of the investigated tellurites reflect a structural change from tbp (coordination number is four) to triagonal pyramidal (coordination number is three).
Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations
Leung, Kevin; Nenoff, Tina M.
2012-08-21
We apply DFT+U-based ab initio molecular dynamics simulations to study the hydration structures of U(III) and U(IV) ions, pertinent to redox reactions associated with uranium salts in aqueous media. U(III) is predicted to be coordinated to 8 water molecules, while U(IV) has a hydration number between 7 and 8. At least one of the innershell water molecules of the hydrated U(IV) complex becomes spontaneously deprotonated. As a result, the U(IV)-O pair correlation function exhibits a satellite peak at 2.15 A associated with the shorter U(IV)-(OH{sup -}) bond. This feature is not accounted for in analysis of extended x-ray absorption fine structure and x-ray adsorption near edge structure measurements, which yield higher estimates of U(IV) hydration numbers. This suggests that it may be useful to include the effect of possible hydrolysis in future interpretation of experiments, especially when the experimental pH is close to the reported hydrolysis equilibrium constant value.
Crystal structure determination of Efavirenz
Popeneciu, Horea Dumitru, Ristoiu; Tripon, Carmen Borodi, Gheorghe Pop, Mihaela Maria
2015-12-23
Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 2}, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.
NASA Astrophysics Data System (ADS)
Mo, Yuxiang; Gao, Shuming; Dai, Zuyang; Li, Hua
2013-06-01
We report a combined experimental and theoretical study on the vibronic structure of CH_3F^+. The results show that the tunneling splittings of vibrational energy levels occur in CH_3F^+ due to the Jahn-Teller effect. Experimentally, we have measured a high resolution ZEKE spectrum of CH_3F up to 3500 cm^-^1 above the ground state. Theoretically, we performed an ab initio calculation based on the diabatic model. The adiabatic potential energy surfaces (APES) of CH_3F^+ have been calculated at the MRCI/CAS/avq(t)z level and expressed by Taylor expansions with normal coordinates as variables. The energy gradients for the lower and upper APES, the derivative couplings between them and also the energies of the APES have been used to determine the coefficients in the Taylor expansion. The spin-vibronic energy levels have been calculated by accounting all six vibrational modes and their couplings. The experimental ZEKE spectra were assigned based on the theoretical calculations. W. Domcke, D. R. Yarkony, and H. Köpple (Eds.), Conical Intersections: Eletronic Structure, Dynamics and Spectroscopy (World Scientific, Singapore, 2004). M. S. Schuurman, D. E. Weinberg, and D. R. Yarkony, J. Chem. Phys. 127, 104309 (2007).
Piazza, Zachary A.; Li, Wei-Li; Wang, Lai-Sheng E-mail: lai-sheng-wang@brown.edu; Popov, Ivan A.; Boldyrev, Alexander I. E-mail: lai-sheng-wang@brown.edu; Pal, Rhitankar; Cheng Zeng, Xiao
2014-07-21
Photoelectron spectroscopy and ab initio calculations are used to investigate the structures and chemical bonding of the B{sub 25}{sup −} cluster. Global minimum searches reveal a dense potential energy landscape with 13 quasi-planar structures within 10 kcal/mol at the CCSD(T)/6-311+G(d) level of theory. Three quasi-planar isomers (I, II, and III) are lowest in energy and nearly degenerate at the CCSD(T) level of theory, with II and III being 0.8 and 0.9 kcal/mol higher, respectively, whereas at two density functional levels of theory isomer III is the lowest in energy (8.4 kcal/mol more stable than I at PBE0/6-311+G(2df) level). Comparison with experimental photoelectron spectroscopic data shows isomer II to be the major contributor while isomers I and III cannot be ruled out as minor contributors to the observed spectrum. Theoretical analyses reveal similar chemical bonding in I and II, both involving peripheral 2c-2e B−B σ-bonding and delocalized interior σ- and π-bonding. Isomer III has an interesting elongated ribbon-like structure with a π-bonding pattern analogous to those of dibenzopentalene. The high density of low-lying isomers indicates the complexity of the medium-sized boron clusters; the method dependency of predicting relative energies of the low-lying structures for B{sub 25}{sup −} suggests the importance of comparison with experiment in determining the global minima of boron clusters at this size range. The appearance of many low-lying quasi-planar structures containing a hexagonal hole in B{sub 25}{sup −} suggests the importance of this structural feature in maintaining planarity of larger boron clusters.
Homologous series of layered structures in binary and ternary Bi-Sb-Te-Se systems: Ab initio study
NASA Astrophysics Data System (ADS)
Govaerts, K.; Sluiter, M. H. F.; Partoens, B.; Lamoen, D.
2014-02-01
In order to account explicitly for the existence of long-periodic layered structures and the strong structural relaxations in the most common binary and ternary alloys of the Bi-Sb-Te-Se system, we have developed a one-dimensional cluster expansion (CE) based on first-principles electronic structure calculations, which accounts for the Bi and Sb bilayer formation. Excellent interlayer distances are obtained with a van der Waals density functional. It is shown that a CE solely based on pair interactions is sufficient to provide an accurate description of the ground-state energies of Bi-Sb-Te-Se binary and ternary systems without making the data set of ab initio calculated structures unreasonably large. For the binary alloys A1-xQx (A =Sb, Bi; Q =Te, Se), a ternary CE yields an almost continuous series of (meta)stable structures consisting of consecutive A bilayers next to consecutive A2Q3 for 0
Dominance of Low Spin and High Deformation in Ab Initio Approaches to the Structure of Light Nuclei
Dytrych, T.; Draayer, J. P.; Sviratcheva, K. D.; Bahri, C.; Vary, J. P.
2009-08-26
Ab initio no-core shell-model solutions for the structure of light nuclei are shown to be dominated by low-spin and high-deformation configurations. This implies that only a small fraction of the full model space is important for a description of bound-state properties of light nuclei. It further points to the fact that the coupling scheme of choice for carrying out calculations for light nuclear systems is an algebraic-based, no-core shell-model scheme that builds upon an LS coupling [SO(3) x SU(2)] foundation with the spatial part of the model space further organized into its symplectic [SO(3) subset of SU(3) subset of Sp(3, R)] structure. Results for {sup 12}C and {sup 16}O are presented with the cluster nature of the excited 0{sup +} states in {sup 16}O analyzed within this framework. The results of the analysis encourages the development of a no-core shell model code that takes advantage of algebraic methods as well as modern computational techniques. Indeed, although it is often a very challenging task to cast complex algebraic constructs into simple logical ones that execute efficiently on modern computational systems, the construction of such a next-generation code is currently underway.
NASA Astrophysics Data System (ADS)
Bucci, F.; Sanna, A.; Continenza, A.; Katrych, S.; Karpinski, J.; Gross, E. K. U.; Profeta, G.
2016-01-01
As a follow-up to the discovery of a new family of Fe-based superconductors, namely, the RE4Fe2As2Te1 -xO4 (42214) (RE = Pr, Sm, and Gd), we present a detailed ab initio study of these compounds highlighting the role of rare-earth (RE) atoms, external pressure, and Te content on their physical properties. Modifications of the structural, magnetic, and electronic properties of the pure (e.g., x =0.0 ) 42214 compounds and their possible correlations with the observed superconducting properties are calculated and discussed. The careful analysis of the results obtained shows that (i) changing the RE atoms allows one to tune the internal pressure acting on the As height with respect to the Fe planes; (ii) similarly to other Fe pnictides, the 42214 pure compounds show an antiferromagnetic-stripe magnetic ground state phase joined by an orthorhombic distortion (not experimentally found yet); (iii) smaller RE atoms increase the magnetic instability of the compounds possibly favoring the onset of the superconducting state; (iv) external pressure induces the vanishing of the magnetic order with a transition to the tetragonal phase and can be a possible experimental route towards higher superconducting critical temperature (Tc) ; and (v) Te vacancies act on the structural parameters, changing the As height and affecting the stability of the magnetic phase.
NASA Astrophysics Data System (ADS)
Roy, Soumendra K.; Jian, Tian; Lopez, Gary V.; Li, Wei-Li; Su, Jing; Bross, David H.; Peterson, Kirk A.; Wang, Lai-Sheng; Li, Jun
2016-02-01
The observation of the gaseous UFO- anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO- is linear with an O-U-F structure and a 3H4 spectral term derived from a U 7sσ25fφ15fδ1 electron configuration, whereas the ground state of neutral UFO has a 4H7/2 spectral term with a U 7sσ15fφ15fδ1 electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations.
NASA Astrophysics Data System (ADS)
Burresi, E.; Celino, M.
2012-05-01
A single wurtzite phase of cadmium sulfide cluster is investigated by ab-initio molecular dynamics simulations at different temperatures, ranging from 100 K to 600 K. In this study we propose a possible procedure to characterize the CdS quantum dots system by means of molecular dynamics calculations using a standard Car-Parrinello scheme. In order to ensure the accuracy of the numerical approach, preliminary calculations to test pseudopotentials, cutoff and box size on both single atoms systems and Cd-Cd, S-S, Cd-S dimers have been performed. Calculated binding energies and bond lengths are obtained in good agreement with experimental data. Subsequently, an uncapped CdS cluster with size below 2 nm, 48 atoms of cadmium and 48 atoms of sulfur, in a wurtzite geometry was structurally optimized to minimize internal stresses. The CdS cluster has been carefully characterized structurally at several temperatures up to T = 600 K. At the temperature of 340 K atomic diffusion on the surface allows the onset of a new stable atomic configuration.
NASA Astrophysics Data System (ADS)
Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra
2015-10-01
The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity.
Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra
2015-01-01
The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362
NASA Astrophysics Data System (ADS)
Juchnovski, I. N.; Tsenov, J. A.; Binev, I. G.
1996-08-01
The structure of alkane- and cycloalkanecarbonitriles (seven compounds) and of their carbanions has been studied by both infrared spectrometry and ab initio force field calculations. The carbanions (counter ions Li +, Na + and K +) have been found to exist mainly as ionic aggregates in hexamethylphosphoric triamide solutions. The calculations describe well the marked decrease, by 124-214 cm -1, in the nitrile band frequencies and also the strong increase, by 1-2 orders, in the nitrile band integrated intensities which accompany the conversion of the parent neutral molecules into carbanions. Cyclopropanecarbonitrile is remarkable as having the highest nitrile band intensity among all the neutral molecules and the lowest one among all the carbanions studied. This result has also been predicted by the calculations, and it can be explained by certain peculiarities in the structure of the particles. The conjugation of the carbanionic charge with the cyano group in the cyclopropanecarbonitrile carbanion is greatly hindered by the considerable deviation (estimated at 56°) of the cyano group from the ring plane. The carbanionic charges of the carbanions studied are delocalized over the cyano groups (0.30-0.41 e -), carbanionic centres (0.08-0.29 e -) and hydrocarbon moieties (0.34-0.63 e -).
NASA Astrophysics Data System (ADS)
Binev, I. G.; Tsenov, J. A.; Velcheva, E. A.; Radomirska, V. B.; Juchnovski, I. N.
1996-05-01
The structures of o-, m- and p-(cyanophenyl)acetonitrile molecules and their carbanions were studied on the basis of infrared spectroscopic data and ab initio force field calculations. The assignment was given for the 3100-1100 cm -1 bands of the substances studied. The scaled theoretical infrared band frequencies agree well with those measured experimentally. An excellent linear correlation ( R = 0.999) was found between the theoretical and experimental vCN frequencies of both molecules and carbanions. The calculations predict well the strong increase in intensity (1.5- to 70-fold) of the vCN, v8 and v19 bands, which accompanies the conversion of the isomeric (cyanophenyl)acetonitrile molecules into the corresponding carbanions. The structures of the lithium, sodium and potassium derivatives of the nitriles studied in dimethyl sulphoxide are close to those of the kinetically free carbanions. The carbanionic centres are practically planar; the cyano groups carry considerable negative charges, but their influences on the carbanionic centres are mainly inductive. The carbanionic charges are delocalized over the phenylene rings (0.35-0.40 e-), methide (0.22-0.29 e-), α-cyano (0.24-0.27 e-) and ring-cyano (0.08-0.14 e-) groups.
Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; Martínez, Todd J.; Gordon, Mark S.
2014-10-20
This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitationmore » on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.« less
Plašienka, Dušan; Cifra, Peter; Martoňák, Roman
2015-04-21
We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in energy (but not density) as well as in diffusion coefficient and electronic properties—semiconductor-metal transition. We also describe the analogy of the investigated process to similar phenomena that take place in two other chalcogens selenium and tellurium. Finally, we remark that the behavior of heated liquid sulfur at ambient pressure might indicate a possible existence of a critical point in the low-pressure region of sulfur phase diagram. PMID:25903892
Plašienka, Dušan Martoňák, Roman; Cifra, Peter
2015-04-21
We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in energy (but not density) as well as in diffusion coefficient and electronic properties—semiconductor-metal transition. We also describe the analogy of the investigated process to similar phenomena that take place in two other chalcogens selenium and tellurium. Finally, we remark that the behavior of heated liquid sulfur at ambient pressure might indicate a possible existence of a critical point in the low-pressure region of sulfur phase diagram.
Bylaska, E.J.; Dixon, D.A.; Felmy, A.R.
2000-01-27
The presence of different anionic species in natural waters can significantly alter the degradation rates of chlorinated methanes and other organic compounds. favorable reaction energetics is a necessary feature of these nucleophilic substitution reactions that can result in the degradation of the chlorinated methanes. In this study, ab initio electronic structure theory is used to evaluate the free energies of reaction of a series of monovalent anionic species (OH{sup {minus}}, SH{sup {minus}}, NO{sub 3}{sup {minus}}, HCO{sub 3}{sup {minus}}, HSO{sub 3}{sup {minus}}, HSO{sub 4}{sup {minus}}, H{sub 2}PO{sub 4}{sup {minus}}, and F{sup {minus}}) that can occur in natural waters with the chlorinated methanes, CCk{sub 4}, CCl{sub 3}H, CCl{sub 2}H{sub 2}, and CClH{sub 3}. The results of this investigation show that nucleophilic substitution reactions of OH{sup {minus}}, SH{sup {minus}}, HCO{sub 3}{sup {minus}}, and F{sup {minus}} are significantly exothermic for chlorine displacement, NO{sub 3}{sup {minus}} reactions are slightly exothermic to the thermoneutral, HSO{sub 3}{sup {minus}} reactions are slightly endothermic to thermoneutral and HSO{sub 4}{sup {minus}}, and H{sub 2}PO{sub 4}{sup {minus}} reactions are significantly endothermic. In the case of OH{sup {minus}}, SH{sup {minus}}, and F{sup {minus}} where there are limited experimental data, these results agree well with experiment. The results for HCO{sub 3}{sup {minus}} are potentially important given the near ubiquitous occurrence of carbonate species in natural waters. The calculations reveal that the degree of chlorination, with the exception of substitution of OH{sup {minus}}, does not have a large effect on the Gibbs free energies of the substitution reactions. These results demonstrate that ab initio electronic structure methods can be used to calculate the reaction energetics of a potentially large number of organic compounds with other aqueous species in natural waters and can be used to help identify
NASA Astrophysics Data System (ADS)
Harchaoui, N.; Hellal, S.; Grosdidier, B.; Gasser, J. G.
2008-02-01
The physical properties of disordered matter depend on the 'atomic structure' i.e. the arrangement of the atoms. This arrangement is described by the structure factor S (q) in reciprocal space and by the pair correlation function g(r) in real space. The structure factor is obtained experimentally while the numerical simulation enables us to obtain the pair correlation function. Liquid sodium is one of the elements the most studied and one can wonder about new scientific contribution appropriateness. The majority of theoretical calculations are compared with the experiment of Waseda. However two other posterior measurements have been published and give different results, in particular with regard to the height of the first peak of the structure factor. Three models of pseudopotential are considered to describe the electron-ion interaction. The first is a local pseudopotential with the alternative known as 'individual' of the model suggested by Fiolhais et al. The second model considered is that of Bachelet et al. This one, ab-initio and 'norm conserving', is non local. The last model is that proposed by Shaw known as 'first principles' and 'energy dependent'. Various static dielectric functions characteristic of the effects of exchange and correlation have been used and developed by Hellal et al. We calculated the form factors (pseudopotential in reciprocal space) and deduce the normalized energy-wave-number characteristic FN (q), the interatomic pair potential Veff (r), then the pair correlation function g(r) by molecular dynamics. The structure factor S(q) is obtained by Fourier transform and is compared with the experiment. Our calculations with the Bachelet and Shaw pseudopotentials are close to the last experiments of Greenfield et al. and of Huijben et al. Our results are discussed.
Structure determination of enterovirus 71
Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G.
2013-02-20
Enterovirus 71 is a picornavirus that causes hand, foot and mouth disease but may induce fatal neurological illness in infants and young children. Enterovirus 71 crystallized in a body-centered orthorhombic space group with two particles in general orientations in the crystallographic asymmetric unit. Determination of the particle orientations required that the locked rotation function excluded the twofold symmetry axes from the set of icosahedral symmetry operators. This avoided the occurrence of misleading high rotation-function values produced by the alignment of icosahedral and crystallographic twofold axes. Once the orientations and positions of the particles had been established, the structure was solved by molecular replacement and phase extension.
Ab initio investigations of the electronic structure and chemical bonding of Li{sub 2}ZrN{sub 2}
Matar, S.F.; Poettgen, R.; Al Alam, A.F.; Ouaini, N.
2012-06-15
The electronic structure of the ternary nitride Li{sub 2}ZrN{sub 2} is examined from ab initio with DFT computations for an assessment of the properties of chemical bonding. The compound is found insulating with 1.8 eV band gap; it becomes metallic and less ionic upon removal of one equivalent of Li. The chemical interaction is found mainly between Zr and N on one hand and Li and N on the other hand. While all pair interactions are bonding, antibonding N-N interactions are found dominant at the top of the valence band of Li{sub 2}ZrN{sub 2} and they become less intense upon removal of Li. From energy differences the partial delithiation leading to Li{sub 2-x}ZrN{sub 2} (x={approx}1) is favored. - Graphical abstract: Trigonal structure of Li{sub 2}ZrN{sub 2} showing the Zr-N-Li layers along the c-axis. Highlights: Black-Right-Pointing-Pointer Li{sub 2}ZrN{sub 2} calculated insulating with a 1.8 eV gap in agreement with its light green color. Black-Right-Pointing-Pointer Lithium de-intercalation is energetically favored for one out of two Li equivalents. Black-Right-Pointing-Pointer Li plays little role in the change of the structure, ensured by Zr and N binding. Black-Right-Pointing-Pointer Similar changes in the electronic structure as for various intercalated phases of ZrN.
NASA Astrophysics Data System (ADS)
Keith, J. Brandon; Fennick, Jacob R.; Junkermeier, Chad E.; Nelson, Daniel R.; Lewis, James P.
2009-03-01
FIREBALL is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access FIREBALL's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation. Program summaryProgram title: FireballUI Catalogue identifier: AECF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 279 784 No. of bytes in distributed program, including test data, etc.: 12 836 145 Distribution format: tar.gz Programming language: Java Computer: PC and workstation Operating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package. RAM: 512 MB Word size: 32 or 64 bits Classification: 4.14 Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations. Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are
Noell, J.O.; Hay, P.J.
1982-01-01
The structures and relative energies of Pt(PH/sub 3/)XY isomers are investigated with use of ab initio molecular orbital theory and effective potentials. In particular, the cis and trans isomers of the dihydride, dichloride, and hydrochloride are studied. In all cases, the trans isomer is the more stable. Available experimental information is in good agreement with calculated bond lengths, bond angles, and vibrational frequencies.
Putungan, Darwin Barayang; Lin, Shi-Hsin; Wei, Ching-Ming; Kuo, Jer-Lai
2015-05-01
Utilizing ab initio random structure searching, we investigated Li adsorption on MoS2 and hydrogen molecules on Li-decorated MoS2. In contrast to graphene, Li can be adsorbed on both sides of MoS2, with even stronger binding than on the single side. We found that high coverages of Li can be attained without Li clustering, which is essential for hydrogen storage and Li ion batteries. Moreover, regarding battery applications, Li diffusion was also found to be easy. The fully-lithiated MoS2 can then adsorb H2 with 4.4 wt%. Interestingly, our calculations revealed that hydrogen molecules can be dissociated at high Li coverage with a minimal energy barrier. We further showed that the dissociated hydrogen atom can readily diffuse on the surface, thus keeping the reaction site active. We therefore propose that Li-MoS2 could be an inexpensive alternative catalyst to noble metals in hydrogen dissociation reactions. PMID:25849099
NASA Astrophysics Data System (ADS)
Ramya, T.; Gunasekaran, S.; Ramkumaar, G. R.
2015-10-01
The experimental and theoretical spectra of (S)-2-Oxopyrrolidin-1-yl Butanamide (S2OPB) were studied. FT-IR and FT-Raman spectra of S2OPB in the solid phase were recorded and analyzed in the range 4000-450 and 5000-50 cm-1 respectively. The structural and spectroscopic analyses of S2OPB were calculated using ab initio Hartree Fock (HF) and density functional theory calculations (B3PW91, B3LYP) with 6-31G(d,p) basis set. A complete vibrational interpretation has been made on the basis of the calculated Potential Energy Distribution (PED). The HF, B3LYP and B3PW91 methods based NMR calculation has been used to assign the 1H NMR and 13C NMR chemical shift of S2OPB. Comparative study on UV-Vis spectral analysis between the experimental and theoretical (B3PW91, B3LYP) methods and the global chemical parameters and local descriptor of reactivity through the Fukui function were performed. Finally the thermodynamic properties of S2OPB were calculated at different temperatures and the corresponding relations between the properties and temperature were also studied.
Ramya, T; Gunasekaran, S; Ramkumaar, G R
2015-10-01
The experimental and theoretical spectra of (S)-2-Oxopyrrolidin-1-yl Butanamide (S2OPB) were studied. FT-IR and FT-Raman spectra of S2OPB in the solid phase were recorded and analyzed in the range 4000-450 and 5000-50 cm(-1) respectively. The structural and spectroscopic analyses of S2OPB were calculated using ab initio Hartree Fock (HF) and density functional theory calculations (B3PW91, B3LYP) with 6-31G(d,p) basis set. A complete vibrational interpretation has been made on the basis of the calculated Potential Energy Distribution (PED). The HF, B3LYP and B3PW91 methods based NMR calculation has been used to assign the (1)H NMR and (13)C NMR chemical shift of S2OPB. Comparative study on UV-Vis spectral analysis between the experimental and theoretical (B3PW91, B3LYP) methods and the global chemical parameters and local descriptor of reactivity through the Fukui function were performed. Finally the thermodynamic properties of S2OPB were calculated at different temperatures and the corresponding relations between the properties and temperature were also studied. PMID:25956325
Tohme, Samir N.; Korek, Mahmoud E-mail: fkorek@yahoo.com; Awad, Ramadan
2015-03-21
Ab initio techniques have been applied to investigate the electronic structure of the LiYb molecule. The potential energy curves have been computed in the Born–Oppenheimer approximation for the ground and 29 low-lying doublet and quartet excited electronic states. Complete active space self-consistent field, multi-reference configuration interaction, and Rayleigh Schrödinger perturbation theory to second order calculations have been utilized to investigate these states. The spectroscopic constants, ω{sub e}, R{sub e}, B{sub e}, …, and the static dipole moment, μ, have been investigated by using the two different techniques of calculation with five different types of basis. The eigenvalues, E{sub v}, the rotational constant, B{sub v}, the centrifugal distortion constant, D{sub v}, and the abscissas of the turning points, R{sub min} and R{sub max}, have been calculated by using the canonical functions approach. The comparison between the values of the present work, calculated by different techniques, and those available in the literature for several electronic states shows a very good agreement. Twenty-one new electronic states have been studied here for the first time.
NASA Astrophysics Data System (ADS)
Velcheva, Evelina A.; Binev, Yuri I.; Petrova, Milena J.
1999-01-01
The structures of 4-hydroxybenzylidenemalononitrile (HO-C 6H 4-CHC(CN) 2, I), its oxyanion ( -O-C 6H 4-CHC(CN) 2, II), cyanide adduct (HO-C 6H 4-CH(CN)-C¯(CN) 2, III) and adduct-oxyanion ( -O-C 6H 4-CH(CN)-C¯(CN) 2, IV) have been studied by means of both quantitative IR spectra and ab initio force field calculations. The conversion of ( I) into the anionic species causes strong changes in the IR spectra: decreases in the ν CN frequency down to 110 cm -1, up to 7-fold increases in the ACN intensity, up to 58 cm -1 ν CN splitting, etc. The charge analysis shows that the intramolecular charge transfer between the electronegative [C(CN) 2] and electropositive fragments of ( I) is 0.34 e -. Nearly 0.6 e - of the oxyanionic charge of ( II) remains within the oxyphenylene fragment and nearly 0.5 e - of the carbanionic charge of ( III) delocalizes within the dicyanomethide fragment. The two charges in ( IV) are spread over the whole species.
Uranus and Neptune structure models with ab initio EOS data for CH4, NH3, and H2O
NASA Astrophysics Data System (ADS)
Nettelmann, Nadine; Fortney, Jonathan; Hamel, Sebastien; Bethkenhagen, Mandy; Redmer, Ronald
2014-05-01
Uranus and Neptune are supposed to be rich in ices in their deep interiors as their mean density closely resembles that of liquid water. Moreover, highly super-solar abundances of CH4 and CO, indicative of internal water, have been observed in their atmospheres. We here compare ab initio equations of state for CH4, NH3, and H2O and apply them to compute ice-rich, adiabatic internal structure models of Uranus and Neptune. The explicit consideration of the light ices CH4 and NH3 allows us to put tighter constraints on the minimum H/He abundance in their deep interior, which was found to be non-zero in all previous Uranus and in most of the Neptune models that were based on water as a proxy for ices. In particular, we investigate if hydrogen in the deep interior can solely be a result of assumed Carbon sedimentation (diamond rain), as an alternative scenario to the early accretion of H/He containing material during the formation of the planets. We conclude by discussing the deep internal H/He abundance in light of rock-rich and warmer-than-adiabatic interiors, which has been suggested to explain Uranus' low intrinsic luminosity. Our models serve to better understand the formation and bulk composition of Neptune-sized planets.
Tohme, Samir N; Korek, Mahmoud; Awad, Ramadan
2015-03-21
Ab initio techniques have been applied to investigate the electronic structure of the LiYb molecule. The potential energy curves have been computed in the Born-Oppenheimer approximation for the ground and 29 low-lying doublet and quartet excited electronic states. Complete active space self-consistent field, multi-reference configuration interaction, and Rayleigh Schrödinger perturbation theory to second order calculations have been utilized to investigate these states. The spectroscopic constants, ωe, Re, Be, …, and the static dipole moment, μ, have been investigated by using the two different techniques of calculation with five different types of basis. The eigenvalues, Ev, the rotational constant, Bv, the centrifugal distortion constant, Dv, and the abscissas of the turning points, Rmin and Rmax, have been calculated by using the canonical functions approach. The comparison between the values of the present work, calculated by different techniques, and those available in the literature for several electronic states shows a very good agreement. Twenty-one new electronic states have been studied here for the first time. PMID:25796254
NASA Astrophysics Data System (ADS)
Tohme, Samir N.; Korek, Mahmoud; Awad, Ramadan
2015-03-01
Ab initio techniques have been applied to investigate the electronic structure of the LiYb molecule. The potential energy curves have been computed in the Born-Oppenheimer approximation for the ground and 29 low-lying doublet and quartet excited electronic states. Complete active space self-consistent field, multi-reference configuration interaction, and Rayleigh Schrödinger perturbation theory to second order calculations have been utilized to investigate these states. The spectroscopic constants, ωe, Re, Be, …, and the static dipole moment, μ, have been investigated by using the two different techniques of calculation with five different types of basis. The eigenvalues, Ev, the rotational constant, Bv, the centrifugal distortion constant, Dv, and the abscissas of the turning points, Rmin and Rmax, have been calculated by using the canonical functions approach. The comparison between the values of the present work, calculated by different techniques, and those available in the literature for several electronic states shows a very good agreement. Twenty-one new electronic states have been studied here for the first time.
NASA Astrophysics Data System (ADS)
Pask, J. E.; Sterne, P. A.
2004-03-01
The finite-element (FE) method is a general approach for the solution of partial differential equations. Like the planewave (PW) method, the FE method is a systematically improvable expansion approach. Unlike the PW method, however, its basis functions are strictly local in real space, which allows for variable resolution in real space and facilitates massively parallel implementation. We discuss the application of the FE method to ab initio electronic-structure calculations.(J.E. Pask, B.M. Klein, C.Y. Fong, and P.A. Sterne, Phys. Rev. B 59), 12352 (1999). In particular, we discuss the use of nonlocal pseudopotentials in bulk calculations, and the handling of long-range interactions in the construction of the Kohn-Sham effective potential and total energy. We show that the total energy converges variationally, and at the optimal theoretical rate consistent with the cubic completeness of the basis. This work was performed under the auspices of the U.S. Department of Energy by University of California, Lawrence Livermore National Laboratory under Contract W-7405-Eng-48.
NASA Astrophysics Data System (ADS)
Binev, Ivan G.; Vassileva-Boyadjieva, Pavlina; Binev, Yuri I.
1998-06-01
The spectral and structural changes taking place during the course of the conversion of 4-hydroxyacetanilide (paracetamol), HOC 6H 4NHCOCH 3, into the corresponding oxyanion, -OC 6H 4NHCOCH 3, and dianion, -OC 6H 4N¯COCH 3, have been followed by both quantitative infrared spectra and ab initio HF/6-31G force-field calculations. The changes accompanying the first deprotonation concern mainly the oxyphenylene fragment; those resulting from the second one are spread over the whole dianion. Analysis of the atomic charge changes shows that over 90% of the first (oxyanionic) charge remains localized within the oxyphenylene fragment. The second (nitranionic) charge delocalizes over the acetyl (0.51 e-) and phenylene (0.26 e-) groups, nitranionic (0.14 e-) and oxyanionic (0.09 e-) centres. The trans conformers (with respect to phenylene and methyl groups) have been calculated to be more stable than the cis ones in all cases studied.
Structural Determinants of Arrestin Functions
Gurevich, Vsevolod V.; Gurevich, Eugenia V.
2015-01-01
Arrestins are a small protein family with only four members in mammals. Arrestins demonstrate an amazing versatility, interacting with hundreds of different G protein-coupled receptor (GPCR) subtypes, numerous nonreceptor signaling proteins, and components of the internalization machinery, as well as cytoskeletal elements, including regular microtubules and centrosomes. Here, we focus on the structural determinants that mediate various arrestin functions. The receptor-binding elements in arrestins were mapped fairly comprehensively, which set the stage for the construction of mutants targeting particular GPCRs. The elements engaged by other binding partners are only now being elucidated and in most cases we have more questions than answers. Interestingly, even very limited and imprecise identification of structural requirements for the interaction with very few other proteins has enabled the development of signaling-biased arrestin mutants. More comprehensive understanding of the structural underpinning of different arrestin functions will pave the way for the construction of arrestins that can link the receptor we want to the signaling pathway of our choosing. PMID:23764050
Pressure Induced Structural Phase Transition in Actinide Monophospides: Ab Initio Calculations
NASA Astrophysics Data System (ADS)
Makode, Chandrabhan; Sanyal, Sankar P.
2011-07-01
The structural and electronic properties of monophospides of Thorium, Uranium and Neptunium have been investigated using tight binding linear muffin-in-orbital (TB-LMTO) method within the local density approximation (LDA). From present study with the help of total energy calculations it is found that ThP, UP and NpP are stable in NaCl- type structure under ambient pressure. The structure stability of ThP, UP and NpP changes under the application of pressure. We predict a structural phase transition from NaCl-type (B1-phase) structure to CsCl-type (B2-phase) structure for these phospides in the pressure range of 37.0-24.0 GPa (ThP to NpP). The calculated equilibrium lattice parameters and bulk modulus are in good agreement with experimental and theoretical work.
Pressure induced structural phase transition in actinide mono-bismuthides: Ab initio calculations
NASA Astrophysics Data System (ADS)
Pataiya, J.; Makode, C.; Aynyas, M.; Sanyal, Sankar P.
2013-06-01
The structural and electronic properties of mono-bismuthides of Plutonium and Americium have been investigated using tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). From present study with the help of total energy calculations it is found that PuBi and AmBi are stable in NaCl - type structure under ambient pressure. The structure stability of PuBi and AmBi changes under the application of pressure. We predict a structural phase transition from NaCl-type (B1-phase) structure to CsCl-type (B2-phase) structure for these phospides in the pressure range of 45 - 4.5 GPa for PuBi and AmBi respectively. The calculated equilibrium lattice parameters and bulk modulus are in good agreement with experimental and theoretical work.
Strajbl, M; Florian, J
1996-02-01
Conformational flexibility of the methyl methoxymethyl phosphonate anion (CH3-O-PO2-CH2-O-CH3)-, a nuclease resistant alternative to the phosphodiester linkage in DNA, have been investigated by ab initio quantum mechanical calculations. The potential of backbone torsional degrees of freedom of methyl methoxymethyl phosphonate anion (MMP) was determined at the Hartree-Fock (HF) 3-21G* level using the adiabatic mapping technique. Energies, geometries, and effective atomic charges of different conformers were calculated at HF/6-31G* and MP2/6-31G* levels of theory. These were compared to the results obtained for dimethyl phosphate calculated at the same level. The impact on DNA structure from inserting a methylene group between phosphorus and oxygen of the nucleoside sugar moiety was examined via distance and angle-constrained geometry optimizations. Due to its high flexibility, MMP has been shown to be compatible with both A and B forms of DNA. PMID:8906889
NASA Astrophysics Data System (ADS)
Aryal, Sita Ram
The alumino-silicate solid solution series (Al 4+2xSi2-2 xO10-x) is an important class of ceramics. Except for the end member (x=0), Al2 SiO5 the crystal structures of the other phases, called mullite, have partially occupied sites. Stoichiometric supercell models for the four mullite phases 3Al2O 3 · 2SiO2 · 2Al 2O3 · SiO2, 4 Al2O3· SiO 2, 9Al2O3 · SiO2, and iota-Al2 O3 (iota-alumina) are constructed starting from experimentally reported crystal structures. A large number of models were built for each phase and relaxed using the Vienna ab initio simulation package (VASP) program. The model with the lowest total energy for a given x was chosen as the representative structure for that phase. Electronic structure and mechanical properties of mullite phases were studied via first-principles calculations. Of the various phases of transition alumina, iota-Al 2O3 is the least well known. In addition structural details have not, until now, been available. It is the end member of the aluminosilicate solid solution series with x=1. Based on a high alumina content mullite phase, a structural model for iota- Al2O3 is constructed. The simulated x-ray diffraction (XRD) pattern of this model agrees well with a measured XRD pattern. The iota-Al2 O3 is a highly disordered ultra-low-density phase of alumina with a theoretical density of 2854kg/m3. Using this theoretically constructed model, elastic, thermodynamic, electronic, and spectroscopic properties of iota-Al2 O3 have been calculated and compared it with those of alpha- Al2O3 and gamma- Al2O3. Boron carbide (B4C) undergoes an amorphization under high velocity impacts. The mechanism of amorphization is not clear. Ab initio methods are used to carry out large-scale uniaxial compression simulations on two polytypes of stoichiometric boron carbide (B4C), B 11C-CBC, and B12- CCC where B11C or B12 is the 12-atom icosahedron and CBC or CCC is the three-atom chain. The simulations were performed on large supercells of 180 atoms
AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS
Turchi, P A
2004-04-14
Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.
DiStasio, Robert A.; Santra, Biswajit; Li, Zhaofeng; Wu, Xifan; Car, Roberto
2014-08-28
In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H{sub 2}O){sub 128} significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, S{sub OO}(Q), and corresponding oxygen-oxygen radial distribution function, g{sub OO}(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, P{sub OOO}(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.
High-pressure stability, structure and compressibility of Cmcm -MgAl2O4: an ab initio study
NASA Astrophysics Data System (ADS)
Catti, M.
Quantum-mechanical solid-state calculations have been performed on the highest-pressure polymorph of magnesium aluminate (CaTi2O4-type structure, Cmcm space group), as well as on the low-pressure (Fd3m) spinel phase and on MgO and Al2O3. An ab initio all-electron periodic scheme with localized basis functions (Gaussian-type atomic orbitals) has been used, employing density-functional-theory Hamiltonians based on LDA and B3LYP functionals. Least-enthalpy structure optimizations in the pressure range 0 to 60 GPa have allowed us to predict: (1) the full crystal structure, the pV equation of state and the compressibility of Cmcm-MgAl2O4 as a function of pressure; (2) the phase diagram of the MgO-Al2O3-MgAl2O4 system (with exclusion of CaFe2O4-type Pmcn-MgAl2O4), and the equilibrium pressures for the reactions of formation/decomposition of the Fd3m and Cmcm polymorphs of MgAl2O4 from the MgO + Al2O3 assemblage. Cmcm-MgAl2O4 is predicted to form at 39 and 57 GPa by LDA and B3LYP calculations, with K0=248 (K'=3.3) and 222 GPa (K'=3.8), respectively. Results are compared to experimental data, where available, and the performance of different DFT functionals is discussed.
DiStasio, Robert A; Santra, Biswajit; Li, Zhaofeng; Wu, Xifan; Car, Roberto
2014-08-28
In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H2O)128 significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, SOO(Q), and corresponding oxygen-oxygen radial distribution function, gOO(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, POOO(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment. PMID:25173016
Kobayashi, Takanori; Hayakawa, Daichi; Khishigjargal, Tegshjargal; Ueda, Kazuyoshi
2014-03-31
The crystal structure of cellulose triacetate I (CTA I) was investigated using first-principles density functional theory (DFT) calculations. The results are in good agreement with the experimental structure obtained by Sikorski et al. when performing the calculation with inclusion of the dispersion correction. However, the cell parameters calculated with inclusion of the dispersion correction are slightly smaller than those experimentally obtained, especially along the a-axis. This smaller cell parameter could be reasonably explained by considering thermal expansion effects, since optimization with the density functional calculation gives the structure without inclusion of thermal effects. The atoms-in-molecules (AIM) theory is also employed to identify and characterize interatomic interactions in the CTA I crystal. CH/O interactions sites are shown to exist in the crystal structure of CTA I. Moreover, CH/O interactions are considered the main interactions in operation to maintain the crystal structure of CTA I. PMID:24614690
NASA Astrophysics Data System (ADS)
Makode, Chandrabhan; Sanyal, Sankar P.
2011-09-01
We have investigated the structural and electronic properties of monophospides of thorium, uranium and neptunium. The total energy as a function of volume is obtained by means of the self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). From the present study with the help of total energy calculations it is found that ThP, UP and NpP are stable in NaCl-type structure at ambient pressure. The structural stability of ThP, UP and NpP changes under the application of pressure. We predict a structural phase transition from NaCl-type (B 1-phase) structure to CsCl-type (B 2-phase) structure for these phospides in the pressure range of 37.0-24.0 GPa (ThP-NpP). We also calculate lattice parameter ( a0), bulk modulus ( B0), band structure and density of states. From energy band diagram it is observed that ThP, UP and NpP exhibit metallic behavior. The calculated equilibrium lattice parameters and bulk modulus are in good agreement with experimental and theoretical work.
Ab initio study of pressure induced structural and electronic properties in uranium monobismuthide
NASA Astrophysics Data System (ADS)
Pataiya, Jagdish; Aynyas, Mahendra; Makode, C.; Singh, A.; Sanyal, Sankar P.
2014-04-01
We have investigated the pressure induced structural and electronic properties of uranium monobismuthide. The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). We predict structural phase transition from NaCl to CsCl-type structure at a pressure of 4.6 GPa. From energy band diagram it is observed that UBi exhibits metallic behavior. The calculated equilibrium lattice parameter is in good agreement with the experimental and other theoretical work.
Ab initio study of pressure induced structural and electronic properties in uranium monobismuthide
Pataiya, Jagdish Makode, C.; Aynyas, Mahendra; Singh, A.; Sanyal, Sankar P.
2014-04-24
We have investigated the pressure induced structural and electronic properties of uranium monobismuthide. The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). We predict structural phase transition from NaCl to CsCl-type structure at a pressure of 4.6 GPa. From energy band diagram it is observed that UBi exhibits metallic behavior. The calculated equilibrium lattice parameter is in good agreement with the experimental and other theoretical work.
Milowska, Karolina Z.; Birowska, Magdalena; Majewski, Jacek A.
2013-12-04
We present exemplary results of extensive studies of structural, mechanical and electronic properties of covalent functionalization of carbon nanotubes (CNTs). We report new results for metallic (9,0), and semiconducting (10,0) single-wall carbon nanotubes (CNT) functionalized with -COOH, -OH, and both groups with concentration up to 12.5%. Our studies are performed in the framework of the density functional theory (DFT). We discuss here the stability, local and global changes in structure, elastic moduli (Young's, Shear, and Bulk), electronic structure and resulting band gaps, as a function of the density of the adsorbed molecules.
Structure electronique de nanorubans de graphene avec des contacts metalliques: Une etude ab initio
NASA Astrophysics Data System (ADS)
Archambault, Chloe
Graphene, a graphite monolayer presenting novel exciting properties, has attracted much attention recently in the scientific community as well as in the high-technology industry. In electronics, nanoribbons -- narrow strips of graphene which happen to be semiconducting-- could possibly allow further miniaturization of electronic devices such as transistors because of their atomic thickness. On the other hand, once making devices, the problem of metallic contacts, which can have critical impact at the nanoscopic scale, cannot be evaded. For example, metal induced gap states may short-circuit very short devices. With this in mind, the interaction of gold, palladium and titanium contacts with finite size graphene nanoribbons has been studied using ab initio density functional theory calculations. This theoretical approach made it possible to study separately and then conjugate four important aspects of the metal-ribbon interaction: bonding, charge transfer, electrostatics and metal induced gap states. Another goal of this project was to study size effects related to the ribbons' dimensions and to estimate the minimal channel length necessary for a device to operate as expected without the unwanted effect of induced gap states. Aside from the high precision achieved, these calculations stand out from earlier studies because they take into account finite size effects which often prevail in small ribbons. Using this model for the metal-nanoribbon junction, it was shown that, as for two-dimensional graphene, the bonding between a ribbon and a metal can be of two types depending on the electronic configuration of the metal. In the first case, physisorption, weak bonding resulting in a large separation distance between ribbon and electrode, is illustrated by the gold contact. On the other hand, titanium, because of its high density of states at the Fermi level, binds more strongly with graphene nanoribbons. This chemisorption is characterized by strong hybridization between
Ab initio investigation of the electronic structure and the magnetic trends within equiatomic FeN
NASA Astrophysics Data System (ADS)
Houari, A.; Matar, S. F.; Belkhir, M. A.
2007-05-01
The magnetic properties of equiatomic FeN nitride have been investigated within the density functional theory (DFT) using the augmented spherical wave method (ASW). Calculation of the energy versus volume in hypothetic rocksalt (RS), zinc-blende (ZB) and wurtzite (W) types structures show that the RS-type structure is preferred. At equilibrium, energy/volume spin polarized calculations indicate that the ground state of RS-FeN is ferromagnetic with a high moment, while ZB-FeN and W-FeN are non magnetic. The magnetovolume effects with respect to the Slater-Pauling-Friedel model are discussed. Analyses of the electronic structure (density of states and chemical bonding) are reported. A discussion of the structural and magnetic properties of FeN compound is given with respect to N local environment of Fe.
Structures and optical absorptions of PbSe clusters from ab initio calculations
NASA Astrophysics Data System (ADS)
Zeng, Qun; Shi, Jing; Jiang, Gang; Yang, Mingli; Wang, Fan; Chen, Jun
2013-09-01
Based on the low-lying structures of (PbSe)n (n = 1-10) clusters identified with a first-principles molecular dynamics approach, two growth patterns with distinct structure and energy evolutions were predicted for the even-n and odd-n clusters, respectively. Moreover, the clusters favor a simple cubic and bulk-like growth pattern, unlike the extensively studied II-VI clusters whose structural diversity has been well established. The overlap between 6p of Pb and 4p of Se makes not only the ordered and bulk-like structures but also a stable building block of (PbSe)4. The high stability of (PbSe)4 is recognized in terms of its binding energy, HOMO-LUMO gap, appearance in the structures of larger-size clusters, as well as its appearance in the fragmentation products of PbSe clusters. The geometrical and electronic structures of the PbSe clusters were further studied within the density functional theory framework including spin-orbital (SO) coupling. We found that SO coupling does not change the relative stability of the clusters but reduces their binding energy significantly. Particularly, the SO effect has a great impact on the UV-vis spectra of the clusters, which were simulated with time-dependent density functional theory at SO level of zeroth-order regular approximation.
NASA Astrophysics Data System (ADS)
Suwardi; Pranowo, Harno Dwi; Armunanto, Ria
2015-09-01
The structure and dynamics of Hf4+ ion in liquid ammonia have been investigated by an ab initio quantum mechanics molecular mechanics (QM/MM) molecular dynamics simulation. The structural data was obtained in terms of radial distribution, coordination number and angular distribution, and then the dynamics in mean ligand residence time. The Hf4+ ion is coordinated by five ammonia molecules in the first solvation shell showing a distorted square pyramidal structure with an average Hf4+-N distance of 2.38 Å. No ammonia ligand was observed for exchange processes between the first and second shells.
Roy, Soumendra K; Jian, Tian; Lopez, Gary V; Li, Wei-Li; Su, Jing; Bross, David H; Peterson, Kirk A; Wang, Lai-Sheng; Li, Jun
2016-02-28
The observation of the gaseous UFO(-) anion is reported, which is investigated using photoelectron spectroscopy and relativisitic ab initio calculations. Two strong photoelectron bands are observed at low binding energies due to electron detachment from the U-7sσ orbital. Numerous weak detachment bands are also observed due to the strongly correlated U-5f electrons. The electron affinity of UFO is measured to be 1.27(3) eV. High-level relativistic quantum chemical calculations have been carried out on the ground state and many low-lying excited states of UFO to help interpret the photoelectron spectra and understand the electronic structure of UFO. The ground state of UFO(-) is linear with an O-U-F structure and a (3)H4 spectral term derived from a U 7sσ(2)5fφ(1)5fδ(1) electron configuration, whereas the ground state of neutral UFO has a (4)H(7/2) spectral term with a U 7sσ(1)5fφ(1)5fδ(1) electron configuration. Strong electron correlation effects are found in both the anionic and neutral electronic configurations. In the UFO neutral, a high density of electronic states with strong configuration mixing is observed in most of the scalar relativistic and spin-orbit coupled states. The strong electron correlation, state mixing, and spin-orbit coupling of the electronic states make the excited states of UFO very challenging for accurate quantum chemical calculations. PMID:26931704
Bylaska, Eric J.; Glaesemann, Kurt R.; Felmy, Andrew R.; Vasiliu, Monica; Dixon, David A.; Tratnyek, P. G.
2010-11-25
Electronic structure methods were used to calculate the gas-phase and aqueous phase reaction energies for reductive dechlorination (i.e. hydrogenolysis), reductive Beta-elimination, dehydrochlorination, and nucleophilic substitution by OH- of 1,2,3-trichloropropane. The thermochemical properties Delta Hof(298.15K), So(298.15K,1 bar), and Delta GS(298.15K, 1 bar) were calculated by using ab initio electronic structure calculations, isodesmic reactions schemes, gas-phase entropy estimates, and continuum solvation models for 1,2,3-trichloropropane and several likely metabolites. On the basis of these thermochemical estimates, together with a Fe(II)/Fe(III) chemical equilibrium model for natural reducing environments, all of the reactions studied were predicted to be very favorable in the standard state and under a wide range of pH conditions. The most favorable reaction was reductive Beta-elimination (Delta Gorxn ≈ -32 kcal/mol), followed closely by reductive dechlorination (Delta Gorxn ≈ -27 kcal/mol), dehydrochlorination (Delta Gorxn ≈ -27kcal/mol), and nucleophilic substitution by OH- (Delta Gorxn ≈ -25 kcal/mol). For both reduction reactions studied, it was found that the first electron-transfer step, yielding the intermediate CH2-CHCl-CH2Cl , and CH2Cl-CH-CH2Cl species, was not favorable in the standard state (Delta Gorxn ≈ +15 kcal/mol) and was predicted to occur only at relatively high pH values. This result suggests that reduction by natural attenuation is unlikely.
NASA Astrophysics Data System (ADS)
Marqués, M.; González, D. J.; González, L. E.
2016-07-01
The melting curve of sodium for a pressure range up to 100 GPa has been evaluated by the orbital free ab initio molecular dynamics method. This method uses the electronic density as the basic variable combined with an approximate electronic kinetic energy functional and a local ionic pseudopotential and makes it possible to perform simulations with a large number of particles and for long simulation times. The calculated melting curve shows a maximum melting temperature at a pressure around 30 GPa followed by a steep decrease up to 100 GPa. For various pressures and temperatures we have evaluated several static properties, including average and local structure, electronic properties, like the electron localization function (ELF), and dynamic properties, both single-particle and collective ones, from which some transport coefficients are deduced. Despite the accurate reproduction of the available experimental data, we do not observe any indication of an early transition from a bcc-like to an fcc-like liquid, as suggested previously by other authors, but rather pressure-induced change in the variation of icosahedral-like order and bcc-like order, with no sign of fcc-like structures in the whole liquid range studied. We also consider the evolution of the ELF within this type of local arrangement upon pressurization. In the dynamic realm, we find an enlarged wave-vector region where atomic collisions play an important role in the dynamic properties of the system as pressure is increased and temperature decreased along the melting line, leading to a peculiar behavior of the dynamic properties.
Electronic structure and anisotropic chemical bonding in TiNF from ab initio study
Matar, Samir F.
2012-01-15
Accounting for disorder in anatase titanium nitride fluoride TiNF is done through atoms re-distributions based on geometry optimizations using ultra soft pseudo potentials within density functional theory DFT. The fully geometry relaxed structures are found to keep the body centering of anatase (I4{sub 1}/amd No. 141). The new structural setups are identified with space groups I-4m2 No. 119 and Imm2 No. 44 which obey the 'group to subgroup' relationships with respect to anatase. In the ground state Imm2 structure identified from energy differences, TiNF is found semi-conducting with similar density of states features to anatase TiO{sub 2} and a chemical bonding differentiated between covalent like Ti-N versus ionic like Ti-F. Inter-anion N-F bonding is also identified. - Graphical Abstract: The geometry optimized ground state anatase derived TiNF structure with arrangement of open faceted TiN3F3 distorted octahedra. The insert shows the arrangement of octahedra in anatase TiO{sub 2}. Highlights: Black-Right-Pointing-Pointer Original approach of TiNF structure for addressing the electronic band structure. Black-Right-Pointing-Pointer Based on anatase, two different ordering scheme models with geometry optimization. Black-Right-Pointing-Pointer New structures obeying the group{yields}subgroup relationships with Imm2 ground state from energy. Black-Right-Pointing-Pointer In the ground state TiNF is found semi-conducting with similar density of states to anatase TiO{sub 2}. Black-Right-Pointing-Pointer Chemical bonding differentiated between covalent like Ti-N and ionic Ti-F.
Low-temperature structure of ξ'-Al-Pd-Mn optimized by ab initio methods
NASA Astrophysics Data System (ADS)
Frigan, Benjamin; Santana, Alejandro; Engel, Michael; Schopf, Daniel; Trebin, Hans-Rainer; Mihalkovič, Marek
2011-11-01
We have studied and resolved occupancy correlations in the existing average structure model of the complex metallic alloy ξ'-Al-Pd-Mn [Boudard , Philos. Mag. APMAADG0141-861010.1080/01418619608242169 74, 939 (1996)], which has approximately 320 atoms in the unit cell and many fractionally occupied sites. Model variants were constructed systematically in a tiling-decoration approach and subjected to simulated annealing by use of both density functional theory and molecular dynamics with empirical potentials. To obtain a measure for thermodynamic stability, we reproduce the Al-Pd-Mn phase diagram at T=0 K, and derive an enthalpy of formation for each structure. Our optimal structure resolves a cloud of fractionally occupied sites in pseudo-Mackay clusters. In particular, we demonstrate the presence of rotational degrees of freedom of an Al9 inner shell, which is caged within two icosahedrally symmetric outer shells Al30 and Pd12. Outside these clusters, the chemical ordering on a chain of three nearby sites surprisingly breaks the inversion symmetry of the surrounding structure, and couples to an Al/vacancy site nearby. Our refined tiling-decoration model applies to any structure within the ɛ-phases family, including the metastable decagonal quasicrystalline phase.
Ab initio study of structural, electronic, magnetic alloys: XTiSb (X = Co, Ni and Fe)
Ibrir, M. Berri, S.; Lakel, S.; Alleg, S.; Bensalem, R.
2015-03-30
Structural, electronic and magnetic properties of three semi-Heusler compounds of CoTiSb, NiTiSb and FeTiSb were calculated by the method (FP-LAPW) which is based on the DFT code WIEN2k. We used the generalized gradient approximation (GGA (06)) for the term of the potential exchange and correlation (XC) to calculate structural properties, electronic properties and magnetic properties. Structural properties obtained as the lattice parameter are in good agreement with the experimental results available for the electronic and magnetic properties was that: CoTiSb is a semiconductor NiTiSb is a metal and FeTiSb is a half-metal ferromagnetic.
NASA Astrophysics Data System (ADS)
Debbichi, L.; Eriksson, O.; Lebègue, S.
2014-05-01
By means of first-principles GW calculations, we have studied the electronic structure properties of MX2 (M =Mo, W; X =S, Se, Te) bilayers, including hybrid structures of MX2 building blocks. The effect of spin-orbit coupling on the electronic structure and the effect of van der Waals interaction on the geometry were taken into account. All the homogeneous bilayers are identified as indirect band-gap materials, with an increase of the band gap when Mo is changed to W, and a decrease of the band gap when the atomic number of X is increased. The same behavior is also observed for hybrid bilayers with common chalcogen atoms, while bilayers with common metal atoms have a direct band gap. Finally, it is shown that due to their particular band alignment, some heterobilayers enable electron-hole separation, which is of interest for solar cell applications.
Molecular structure and vibrational spectra of dithionite ion by ab initio calculations
NASA Astrophysics Data System (ADS)
Leszczynski, Jerzy; Zerner, Michael C.
1989-07-01
The structure of the dithionite ion, S 2O 42-, is examined using quantum chemical calculations. These studies strongly suggest that only the C 2h (trans) isomer is stable in solution. The C 2v (cis) form reported in Na 2S 2O 4·2H 2O is stabilized by crystal forces. The calculated vibrational spectrum of the C 2h form is in excellent agreement with that observed in aqueous solution. Taking into account the negative frequency calculated for the C 2v structure yields a calculated spectrum in good agreement with that observed for the crystal.
Ab initio investigation of the structural and electronic properties of amorphous HgTe.
Zhao, Huxian; Chen, Xiaoshuang; Lu, Jianping; Shu, Haibo; Lu, Wei
2014-01-29
We present the structure and electronic properties of amorphous mercury telluride obtained from first-principle calculations. The initial configuration of amorphous mercury telluride is created by computation alchemy. According to different exchange–correlation functions in our calculations, we establish two 256-atom models. The topology of both models is analyzed in terms of radial and bond angle distributions. It is found that both the Te and the Hg atoms tend to be fourfold, but with a wrong bond rate of about 10%. The fraction of threefold and fivefold atoms also shows that there are a significant number of dangling and floating bonds in our models. The electronic properties are also obtained. It is indicated that there is a bandgap in amorphous HgTe, in contrast to the zero bandgap for crystalline HgTe. The structures of the band tail and defect states are also discussed. PMID:24592480
Ab-initio study of electronic structure and elastic properties of ZrC
NASA Astrophysics Data System (ADS)
Mund, H. S.; Ahuja, B. L.
2016-05-01
The electronic and elastic properties of ZrC have been investigated using the linear combination of atomic orbitals method within the framework of density functional theory. Different exchange-correlation functionals are taken into account within generalized gradient approximation. We have computed energy bands, density of states, elastic constants, bulk modulus, shear modulus, Young's modulus, Poisson's ratio, lattice parameters and pressure derivative of the bulk modulus by calculating ground state energy of the rock salt structure type ZrC.
Ground state structures of tantalum tetraboride and triboride: an ab initio study.
Wei, Shuli; Li, Da; Lv, Yunzhou; Liu, Zhao; Xu, Chunhong; Tian, Fubo; Duan, Defang; Liu, Bingbing; Cui, Tian
2016-07-21
Tantalum-boron compounds, which are potential candidates for superhard multifunctional materials, may possess multiple stoichiometries and structures under pressure. Using first-principle methods, ground-state TaB3 with the monoclinic C2/m space group and high-pressure TaB4 with the orthorhombic Amm2 space group have been found. They are more stable than the previously proposed structures. High-pressure boron-rich Amm2-TaB4 can be quenched to ambient pressure. The ground-state C2/m-TaB3 and high-pressure Amm2-TaB4 are two potential ultra-incompressible and hard materials with a calculated hardness of 17.02 GPa and 30.02 GPa at ambient pressure, respectively. Detailed electronic structure and chemical bonding analysis proved that the high hardness value of Amm2-TaB4 mainly stems from the strong covalent boron-boron bonds in graphene-like B layers as well as B-B bonds between layers. PMID:27327210
Jungen, Ch; Jungen, M; Pratt, S T
2012-11-13
The dissociative recombination (DR) of H(3)(+) ions with electrons, producing neutral atomic and molecular fragments, is driven primarily by the vibronic Jahn-Teller (JT) interaction between the electronic components of the pe' e(-)-H(3)(+) collision (Rydberg) channel. The JT parameters characterizing this interaction are therefore of great interest as they are required for the theoretical predictions of the DR cross section. In this contribution, we review various determinations of these quantities that have been made previously, based both on spectroscopic studies of 3pe' Rydberg-excited H(3) states, and on the analysis of the corresponding ab initio H(3) Rydberg potential surfaces near the conical intersection (D(3h) symmetry) for n=3-5. The highly correlated theoretical 3pe' potential surfaces of Mistrík et al. are used for a new determination of both the linear and quadratic JT terms. PMID:23028155
Structure and energy of point defects in TiC: An ab initio study
NASA Astrophysics Data System (ADS)
Sun, Weiwei; Ehteshami, Hossein; Korzhavyi, Pavel A.
2015-04-01
We employ first-principles calculations to study the atomic and electronic structure of various point defects such as vacancies, interstitials, and antisites in the stoichiometric as well as slightly off-stoichiometric Ti1 -cCc (including both C-poor and C-rich compositions, 0.49 ≤c ≤0.51 ). The atomic structure analysis has revealed that both interstitial and antisite defects can exist in split conformations involving dumbbells. To characterize the electronic structure changes caused by a defect, we introduce differential density of states (dDOS) defined as a local perturbation of the density of states (DOS) on the defect site and its surrounding relative to the perfect TiC. This definition allows us to identify the DOS peaks characteristic of the studied defects in several conformations. So far, characteristic defect states have been discussed only in connection with carbon vacancies. Here, in particular, we have identified dDOS peaks of carbon interstitials and dumbbells, which can be used for experimental detection of such defects in TiC. The formation energies of point defects in TiC are derived in the framework of a grand-canonical formalism. Among the considered defects, carbon vacancies and interstitials are shown to have, respectively, the lowest and the second-lowest formation energies. Their formation energetics are consistent with the thermodynamic data on the phase stability of nonstoichiometric TiC. A cluster type of point defect is found to be next in energy, a titanium [100] dumbbell terminated by two carbon vacancies.
Ab initio study of the structural, electronic and optical properties of ZnTe compound
Bahloul, B.; Deghfel, B.; Amirouche, L.; Bounab, S.; Bentabet, A.; Bouhadda, Y.; Fenineche, N.
2015-03-30
Structural, electronic and optical properties of ZnTe compound were calculated using Density Functional Theory (DFT) based on the pseudopotentials and planewaves (PP-PW) method as implemented in the ABINIT computer code, where the exchange–correlation functional is approximated using the local density approximation (LDA) and the generalized gradient approximation (GGA). The obtained results from either LDA or GGa calculation for lattice parameter, energy band gap and optical parameters, such as the fundamental absorption edge, the peaks observed in the imaginary part of the dielectric function, the macroscopic dielectric constants and the optical dielectric constant, are compared with the available theoretical results and experimental data.
Parkes, Marie V; Greathouse, Jeffery A; Hart, David B; Gallis, Dorina F Sava; Nenoff, Tina M
2016-04-28
The separation of oxygen from nitrogen using metal-organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O2 on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O2 and N2 in the M2(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. This unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize the process of multiple guests competitively binding to coordinatively unsaturated metal sites of a MOF. PMID:27063148
NASA Astrophysics Data System (ADS)
Smeyers, Y. G.; Senent, M. L.; Botella, V.; Moule, D. C.
1993-02-01
The far infrared torsional spectra of acetone (CH3)2CO and (CD3)2CO have been determined from ab initio calculations, and the main features of the experimental data assigned. For this purpose, the potential energy surface for the double methyl rotation was determined with fully relaxed geometry into the RHF and RHF+MP2 approximations using a 6-31G(p,d) basis set. The energy values, as well as the kinetic parameters obtained from the optimized geometry, were fitted to double Fourier expansions as functions of the rotational angles in seven terms. The torsional solutions were developed on the basis of the symmetry eigenvectors of the G36 nonrigid group, which factorize the Hamiltonian matrix into 16 boxes. The energy levels and torsional wave functions for each symmetry specie were then obtained diagonalizing each blocks separately. Intensities were obtained from the calculated electric dipole moment variations and the nuclear statistical weights, and were combined with the torsional frequencies to predict the spectra. The calculated band patterns show a multi- plet structure and reproduce the main features of the experimental data. The torsional bands of the infrared active ν17 mode were found to be clustered into quartets, (A1→A2, G→G, E1→E1, E3→E4), for the v=0→v=1 fundamental, and (A2→A1, G→G, E1→E1, E4→E3) for the v=1→v=2 first sequence transitions. The G→G transitions were found to be the more intense. The correlation between the calculated and observed spectra allows for an assignment of the major bands.
Aguirrechu-Comerón, Amagoia; Hernández-Molina, Rita; Rodríguez-Hernández, Plácida; Muñoz, Alfonso; Rodríguez-Mendoza, Ulises R; Lavín, Vı́ctor; Angel, Ross J; Gonzalez-Platas, Javier
2016-08-01
Copper(I) iodine compounds can exhibit interesting mechanochromic and thermochromic luminescent properties with important technological applications. We report the synthesis and structure determination by X-ray diffraction of a new polymeric staircase copper(I) iodine compound catena(bis(μ2-iodo)-6-methylquinoline-copper(I), [C10H9CuIN]. The structure is composed of isolated polymeric staircase chains of copper-iodine coordinated to organic ligands through Cu-N bonds. High pressure X-ray diffraction to 6.45 GPa shows that the material is soft, with a bulk modulus K0 = 10.2(2)GPa and a first derivative K'0 = 8.1(3), typical for organometallic compounds. The unit-cell compression is very anisotropic with the stiffest direction [302] arising from a combination of the stiff CuI ladders and the shear of the planar quinolone ligands over one another. Full structure refinements at elevated pressures show that pressures reduce the Cu···Cu distances in the compound. This effect is detected in luminescence spectra with the appearance of four sub-bands at 515, 600, 647, and 712 nm above 3.5 GPa. Red-shifts are observed, and they are tentatively associated with interactions between copper(I) ions due to the shortening of the Cu···Cu distances induced by pressure, below twice the van der Waals limit (2.8 Å). Additionally, ab initio simulations were performed, and they confirmed the structure and the results obtained experimentally for the equation of state. The simulation allowed the band structure and the electronic density of states of this copper(I) iodine complex to be determined. In particular, the band gap decreases slowly with pressure in a quadratic way with dEg/dP = -0.011 eV/GPa and d(2)Eg/dP(2) = 0.001 eV/GPa(2). PMID:27429246
Grenier, Romain; To, Quy-Dong; de Lara-Castells, María Pilar; Léonard, Céline
2015-07-01
Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588
Ab initio structural and vibrational properties of GaAs diamondoids and nanocrystals
Abdulsattar, Mudar Ahmed; Hussein, Mohammed T.; Hameed, Hadeel Ali
2014-12-15
Gallium arsenide diamondoids structural and vibrational properties are investigated using density functional theory at the PBE/6-31(d) level and basis including polarization functions. Variation of energy gap as these diamondoids increase in size is seen to follow confinement theory for diamondoids having nearly equiaxed dimensions. Density of energy states transforms from nearly single levels to band structure as we reach larger diamondoids. Bonds of surface hydrogen with As atoms are relatively localized and shorter than that bonded to Ga atoms. Ga-As bonds have a distribution range of values due to surface reconstruction and effect of bonding to hydrogen atoms. Experimental bulk Ga-As bond length (2.45 Å) is within this distribution range. Tetrahedral and dihedral angles approach values of bulk as we go to higher diamondoids. Optical-phonon energy of larger diamondoids stabilizes at 0.037 eV (297 cm{sup -1}) compared to experimental 0.035 eV (285.2 cm{sup -1}). Ga-As force constant reaches 1.7 mDyne/Å which is comparable to Ga-Ge force constant (1.74 mDyne/Å). Hydrogen related vibrations are nearly constant and serve as a fingerprint of GaAs diamondoids while Ga-As vibrations vary with size of diamondoids.
Ab initio calculations on the defect structure of β-Ga2O3
NASA Astrophysics Data System (ADS)
Zacherle, T.; Schmidt, P. C.; Martin, M.
2013-06-01
The intrinsic point defects of β-Ga2O3 are investigated using density functional theory. We have chosen two different exchange-correlation potentials: the generalized gradient approximation (GGA) and a hybrid potential (HSE06). Defect formation energies were determined taking into account finite-size effects. Schottky, anti-Frenkel, and Frenkel energies have been extracted for T=0 K. We calculate formation entropies for an oxygen and a gallium vacancy and determine the Gibbs energy of Schottky disorder. Furthermore, we investigate the defect concentrations as a function of the oxygen partial pressure. The obtained purely intrinsic defect concentrations for charged defects are very small and result in a pO2 dependence of the electron concentration of [e']˜ pO2-1/6, whereas experimentally [e']˜ pO2-1/4 is found. So we assume that, experimentally, a small unintentional donor doping is unavoidable. A small extrinsic donor concentration [D·] = 1018 cm-3 (10 ppm) changes the electron concentration to [e']˜ pO2-1/4 and gives an activation energy of the conductivity σ of 1.7 eV in good agreement to experimental values. So we propose as majority disorder 3[VGa'''] = [D·] with electrons being minority defects.
Miller, J.; Miaskiewicz, K.; Osman, R.
1993-12-01
Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.
NASA Astrophysics Data System (ADS)
Schiffmann, Florian; VandeVondele, Joost
2015-06-01
We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.
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.
Furmanchuk, Al'ona; Shishkin, Oleg V; Isayev, Olexandr; Gorb, Leonid; Leszczynski, Jerzy
2010-09-01
The correlation between hydration of Nucleic Acid Bases (NABs) and their conformational flexibility was analyzed based on the results of Car-Parrinello Molecular Dynamics (CPMD) simulations of NABs in bulk water environment. Correlations with quantum chemical results were drawn whenever it was possible. Statistical analysis confirmed that hydration causes bond length alteration in NABs and formation of zwitter-ionic resonance structures. In contrast to the gas phase, bulk hydration results in restricted mobility of amino group and increase in population of its planar-like conformations. At the same time, rings of all NABs become almost equally flexible in the dynamic aqueous environment. Therefore, each NAB possesses a non-planar effective conformation of pyrimidine ring despite the fact that planar geometry corresponds to minimum on the potential energy surface. PMID:20532343
Schiffmann, Florian; VandeVondele, Joost
2015-06-28
We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step. PMID:26133420
Gas-phase acidities of tetrahedral oxyacids from ab initio electronic structure theory
Rustad, J.R.; Dixon, D.A.; Kubicki, J.D.; Felmy, A.R.
2000-05-04
Density functional calculations have been performed on several protonation states of the oxyacids of Si, P, V, As, Cr, and S. Structures and vibrational frequencies are in good agreement with experimental values where these are available. A reasonably well-defined correlation between the calculated gas-phase acidities and the measured pK{sub a} in aqueous solution has been found. The pK{sub a}/gas-phase acidity slopes are consistent with those derived from previous molecular mechanics calculations on ferric hydrolysis and the first two acidity constants for orthosilicic acid. The successive deprotonation of other H{sub n}TO{sub 4} species, for a given tetrahedral anion T are roughly consistent with this slope, but not to the extent that there is a universal correlation among all species.
Schiffmann, Florian; VandeVondele, Joost
2015-06-28
We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.
NASA Astrophysics Data System (ADS)
Kong, Bo; Zhang, Yachao
2016-07-01
The electronic structures of the cubic GdH3 are extensively investigated using the ab initio many-body GW calculations treating the Gd 4f electrons either in the core (4f-core) or in the valence states (4f-val). Different degrees of quasiparticle (QP) self-consistent calculations with the different starting points are used to correct the failures of the GGA/GGA + U/HSE03 calculations. In the 4f-core case, GGA + G0W0 calculations give a fundamental band gap of 1.72 eV, while GGA+ GW0 or GGA + GW calculations present a larger band gap. In the 4f-val case, the nonlocal exchange-correlation (xc) functional HSE03 can account much better for the strong localization of the 4f states than the semilocal or Hubbard U corrected xc functional in the Kohn-Sham equation. We show that the fundamental gap of the antiferromagnetic (AFM) or ferromagnetic (FM) GdH3 can be opened up by solving the QP equation with improved starting point of eigenvalues and wave functions given by HSE03. The HSE03 + G0W0 calculations present a fundamental band gap of 2.73 eV in the AFM configuration, and the results of the corresponding GW0 and GW calculations are 2.89 and 3.03 eV, respectively. In general, for the cubic structure, the fundamental gap from G0W0 calculations in the 4f-core case is the closest to the real result. By G0W0 calculations in the 4f-core case, we find that H or Gd defects can strongly affect the band structure, especially the H defects. We explain the mechanism in terms of the possible electron correlation on the hydrogen site. Under compression, the insulator-to-metal transition in the cubic GdH3 occurs around 40 GPa, which might be a satisfied prediction.
NASA Astrophysics Data System (ADS)
Xue, X.; Kanzaki, M.
In order to gain insight into the correlations between 29Si, 17O and 1H NMR properties (chemical shift and quadrupolar coupling parameters) and local structures in silicates, ab initio self-consistent field Hartree-Fock molecular orbital calculations have been carried out on silicate clusters of various polymerizations and intertetrahedral (Si-O-Si) angles. These include Si(OH)4 monomers (isolated as well as interacting), Si2O(OH)6 dimers (C2 symmetry) with the Si-O-Si angle fixed at 5° intervals from 120° to 180°, Si3O2(OH)8 linear trimers (C2 symmetry) with varying Si-O-Si angles, Si3O3(OH)6 three-membered rings (D3 and C1 symmetries), Si4O4(OH)8 four-membered ring (C4 symmetry) and Si8O12(OH)8 octamer (D4 symmetry). The calculated 29Si, 17O and 1H isotropic chemical shifts (δiSi, δiO and δiH) for these clusters are all close to experimental NMR data for similar local structures in crystalline silicates. The calculated 17O quadrupolar coupling constants (QCC) of the bridging oxygens (Si-O-Si) are also in good agreement with experimental data. The calculated 17O QCC of silanols (Si-O-H) are much larger than those of the bridging oxygens, but unfortunately there are no experimental data for similar groups in well-characterized crystalline phases for comparison. There is a good correlation between δiSi and the mean Si-O-Si angle for both Q1 and Q2, where Qn denotes Si with n other tetrahedral Si next-nearest neighbors. Both the δiO and the 17O electric field gradient asymmetry parameter, η of the bridging oxygens have been found to depend strongly on the O site symmetry, in addition to the Si-O-Si angle. On the other hand, the 17O QCC seems to be influenced little by structural parameters other than the Si-O-Si angle, and is thus expected to be the most reliable 17O NMR parameter that can be used to decipher Si-O-Si angle distribution information. Both the 17O QCC and the 2H QCC of silanols decrease with decreasing length of hydrogen bond to a second O atom
NASA Astrophysics Data System (ADS)
Zhu, Xiaolei; Zeng, X. C.
2003-02-01
Ab initio all-electron molecular-orbital calculations have been carried out to study the structure and relative stability of small silicon clusters (Sin, n=7-11). A number of low-energy geometric isomers are optimized at the second-order Møller-Plesset (MP2) MP2/6-31G(d) level. Harmonic vibrational analysis has been performed to assure that the optimized geometries are stable. The total energies of stable isomers are computed at the coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] CCSD(T)/6-31G(d) level. The calculated binding energies per atom at both the MP2/6-31G(d) and CCSD(T)/6-31G(d) levels agree with the experiments. For Si7, Si8, and Si10, the lowest-energy structures are the same as those predicted previously from the all-electron optimization at the Hartree-Fock (HF) HF/6-31G(d) level [Raghavachari and Rohlfing, J. Chem. Phys. 89, 2219 (1988)]. For Si9, the lowest-energy isomer is same as that predicted based on density-functional plane-wave pseudopotential method [Vasiliev, Ogut, and Chelikowsky, Phys. Rev. Lett. 78, 4805 (1997)]. Particular attention has been given to Si11 because several low-energy geometric isomers were found nearly isoenergetic. On the basis of MP2/6-311G(2d)//CCSD(T)/6-311G(2d) calculation, we identified that the C2v isomer, a tricapped trigonal prism with two additional caps on side trigonal faces, is most likely the global-minimum structure. However, another competitive geometric isomer for the global minimum is also found on basis of the MP2/6-311G(2d)//CCSD(T)/6-311G(2d) calculation. Additionally, calculations of the binding energy and the cluster polarizability offer more insights into relatively strong stability of two magic-number clusters Si6 and Si10.
Structure determination of transient transcription complexes.
Cramer, Patrick
2016-08-15
The determination of detailed 3D structures of large and transient multicomponent complexes remains challenging. Here I describe the approaches that were used and developed by our laboratory to achieve structure solution of eukaryotic transcription complexes. I hope this collection serves as a resource for structural biologists seeking solutions for difficult structure determination projects. PMID:27528766
Ab initio approach to structural, electronic, and ferroelectric properties of antimony sulphoiodide
NASA Astrophysics Data System (ADS)
Amoroso, Danila; Picozzi, Silvia
2016-06-01
By means of first-principles calculations for the SbSI semiconductor, we show that bare density functional theory fails to reproduce the experimentally observed ferroelectric phase, whereas a more advanced approach, based on hybrid functionals, correctly works. When comparing the paraelectric and ferroelectric phases, our results show polar displacements along the c direction of the Sb and S sublattices with respect to the iodine framework, leading to a predicted spontaneous polarization of P ≃20 μ C/cm2 , in good agreement with experiments. In the ferroelectric phase, the semiconducting behavior of SbSI is confirmed by relatively large values for the indirect and direct gaps (≃2.15 eV and 2.3 eV , respectively). An analysis of the electronic structure, in terms of density of states, charge density distribution, and anomalies in the Born effective charges, reveals (i) the clear presence of a Sb(III) lone pair and (ii) a large covalency in the SbSI bonding, based on the hybridization between Sb and S ions, in turn more ionically bonded to iodine anions. Finally, the interplay between ferroelectricity and spin-orbit coupling reveals a coexistence of Dresselhaus and Rashba relativistic effects and a spin texture that can be reversed by switching the polarization, of potential appeal in electrically controlled spintronics.
Ab initio electronic structure study of a model water splitting dimer complex.
Fernando, Amendra; Aikens, Christine M
2015-12-28
A model manganese dimer electrocatalyst bridged by μ-OH ligands is used to investigate changes in spin states that may occur during water oxidation. We have employed restricted open-shell Hartree-Fock (ROHF), second-order Møller-Plesset perturbation theory (MP2), complete active space self-consistent field (CASSCF), and multireference second-order Møller-Plesset perturbation theory (MRMP2) calculations to investigate this system. Multiconfigurational methods like CASSCF and MRMP2 are appropriate methods to study these systems with antiferromagnetically-coupled electrons. Orbital occupations and distributions have been closely analyzed to understand the electronic details and contributions to the water splitting from manganese and oxygen atoms. The presence of Mn(IV)O˙ radical moieties has been observed in this catalytic pathway. Multiple nearly degenerate excited states were found close to the ground state in all structures. This suggests competing potential energy landscapes near the ground state may influence the reactivity of manganese complexes such as the dimers studied in this work. PMID:26593689
An ab-initio study of adsorption of gaseous molecules on doped graphene structures
NASA Astrophysics Data System (ADS)
Balangi, H. R.; Shokri, A. A.
2015-11-01
In this work, electronic properties of bare and doped graphene layers in the presence of N, B and a type of defective impurities are investigated under adsorption of CO, NO, NH3 and NO2 molecules on it's external surface. We use a fully self-consistent density function theory (DFT) based calculations as implemented in SIESTA package. The local-density approximation (LDA) is considered for the exchange-correlation function. Total density of state (TDOS), partial density of state (PDOS) and charge density calculations are also considered to elucidate the difference in the CO, NO, NH3 and NO2 gases detection mechanism of pristine and doped graphene structures. With regard to that the charge transfer is occurring between the graphene sheet and gaseous molecules, the NO2 and NH3 molecules are considered as the recipient and donor of electrons, respectively. We show that the states contributed by the adsorbed CO and NO molecules are quite localized near the center of original band gap and they suggest that the charge transport in such systems cannot be enhanced considerably, while NO2 and NH3 molecules adsorption acts as the acceptor and donor, respectively. Our results can serve as a base for developments in designing nano-electronic devices.
NASA Astrophysics Data System (ADS)
Wu, Hai-Ying; Chen, Ya-Hong; Zhou, Ping; Han, Xiang-Yu; Liu, Zi-Jiang
2014-09-01
The structural, electronic, and mechanical stability properties of magnesium sulfide in different phases are presented using the plane wave pseudopotential method within the generalized gradient approximation. Eight different phases such as rocksalt (B1), zincblende (B3), wurtzite (B4), nickel arsenide (B8), cesium chloride (B2), PH4I-type (B11), FeSi-type (B28), and MnP-type (B31) are considered in great detail. The calculated ground-state properties of these phases are consistent with available experimental and theoretical data. It is found that MgS in the B1 and B8 phases are indirect band gap materials, the B3, B4, B11, B28, and B31 phases are all direct gap materials, while the B2 phase displays the metallic character. The B1, B3, B4, B8, B28, and B31 phases are mechanically stable at ambient conditions, but the B2 and B11 phases are mechanically unstable under zero pressure and zero temperature
An efficient ab-initio approach for the anharmonic properties of structurally complex ceramics
NASA Astrophysics Data System (ADS)
Huang, Liang-Feng; Rondinelli, James M.
In the conventional quasiharmonic method for the simulation of crystal anharmonic properties (e.g., thermal expansion and thermomechanics), the phonon spectra of about ten (or more) volumes have to be calculated, which is often computationally prohibitive for complex ceramics with large unit cells. In this work, we describe an efficient alternative method, i.e., a self-consistent quasiharmonic approximation (SC-QHA) method, where the phonon modes of only two or three volumes are necessary. At the same time, it provides a convenient framework to analyze the microscopic origins underlying the anharmonic properties. We successfully apply the SC-QHA method to the hybrid improper ferroelectric Ca3Ti2O7 to explain the recent experimentally measured thermal expansion data [Senn, Phys. Rev. Lett., 114, 0 (2015)], and related lattice dynamical properties in an efficient manner. Supported by the ONR MURI Understanding Atomic Scale Structure in Four Dimensions to Design and Control Corrosion Resistant Alloys under Grant No. N00014-14-1-0675.
Electronic structure of Sc C[sub 60]. An ab initio theoretical study
Guo, T.; Odom, G.K.; Scuseria, G.E. )
1994-08-11
We have studied the electronic structure of Sc C[sub 60] at the self-consistent-field Hartree-Fock (SCF-HF) level of theory employing a double-zeta (DZ) basis set. Binding energies have also been calculated employing a hybrid of HF and density functional theory (herein denoted as HF-BLYP). Several electronic states in C[sub 50] and C[sub 30] symmetry were considered. A double-minimum configuration is found for the open-shell [sup 4]A[sub 2] electronic ground state in C[sub 50] symmetry. The lowest energy minimum has Sc located 1.175 [angstrom] away from the center of the cage, approaching a C[sub 60] pentagon along a C[sub 5] axis. Bonding between the Sc atom and the cage occurs by donation of the 4s electrons to the lowest unoccupied orbital of C[sub 60] and by 3d electron interaction with the antibonding orbital associated with the five double bonds radiating from the pentagon closest to Sc ([approximately] 2.5 [angstrom]). The other local minimum has Sc located at the center of the cage and is predicted to be 1.2 eV higher in energy at the highest level of theory employed in this work (DZ/HF-BLYP). The energy barrier for moving Sc from the center of the cage to the lowest energy position is predicted to be 0.1 eV at the same level of theory. 33 refs., 2 figs., 2 tabs.
Synthesis, bioassay, crystal structure and ab initio studies of Erlenmeyer azlactones
NASA Astrophysics Data System (ADS)
Parveen, Mehtab; Ali, Akhtar; Ahmed, Sarfaraz; Malla, Ali Mohammed; Alam, Mahboob; Pereira Silva, P. S.; Silva, Manuela Ramos; Lee, Dong-Ung
2013-03-01
Several 4-arylidene-2-phenyl-5(4H)-azlactones have been synthesized via Erlenmeyer method. The synthesized compounds have been characterized on the basis of systematic spectral studies (IR, 1H NMR, 13C NMR, and MS). The compound (4Z)-4-(3,5-dimethoxybenzylidene)-2-phenyl-1,3-oxazol-5(4H)-one, C18H15NO4, (5), crystallizes in the orthorhombic system, space group P212121, with a = 5.6793(3) Å, b = 15.2038(7) Å, c = 17.6919(10) Å, Mr = 309.31, V = 1527.64(14) Å3, Z = 4 and R = 0.0547. The compound (4Z)-2-phenyl-4-(3,4,5-trimethoxybenzylidene)-1,3-oxazol-5(4H)-one, C19H17NO5, (6) crystallizes in triclinic geometry with space group P-1, having unit cell parameters a = 7.3814(3) Å, b = 8.1446(3) Å, c = 13.9845(5) Å, α = 86.918(3), β = 83.314(2), γ = 82.462(3), Mr = 339.34, V = 827.16(5) Å3, Z = 2 and R = 0.0433. The DFT calculations of compounds (5) and (6) have been carried out to ascertain the stability of Z-conformer. The in vitro antimicrobial activity of all the compounds (1-6) was evaluated by the disk diffusion method against gram +ve and gram -ve microorganism and fungal strains. The MIC of the synthesized compounds was determined by agar well diffusion method in 96-well microtiter plate. All the synthesized compounds were also screened for their free radical scavenging activity by DPPH method.
Bylaska, Eric J; Glaesemann, Kurt R; Felmy, Andrew R; Vasiliu, Monica; Dixon, David A; Tratnyek, Paul G
2010-11-25
Electronic structure methods were used to calculate the gas and aqueous phase reaction energies for reductive dechlorination (i.e., hydrogenolysis), reductive β-elimination, dehydrochlorination, and nucleophilic substitution by OH− of 1,2,3-trichloropropane. The thermochemical properties ΔH(f)°(298.15 K), S°(298.15 K, 1 bar), and ΔG(S)(298.15 K, 1 bar) were calculated by using ab initio electronic structure calculations, isodesmic reactions schemes, gas-phase entropy estimates, and continuum solvation models for 1,2,3-trichloropropane and several likely degradation products: CH3−CHCl−CH2Cl, CH2Cl−CH2−CH2Cl, C•H2−CHCl−CH2Cl, CH2Cl−C•H−CH2Cl, CH2═CCl−CH2Cl, cis-CHCl═CH−CH2Cl, trans-CHCl═CH−CH2Cl, CH2═CH−CH2Cl, CH2Cl−CHCl−CH2OH, CH2Cl−CHOH−CH2Cl, CH2═CCl−CH2OH, CH2═COH−CH2Cl, cis-CHOH═CH−CH2Cl, trans-CHOH═CH−CH2Cl, CH(═O)−CH2−CH2Cl, and CH3−C(═O)−CH2Cl. On the basis of these thermochemical estimates, together with a Fe(II)/Fe(III) chemical equilibrium model for natural reducing environments, all of the reactions studied were predicted to be very favorable in the standard state and under a wide range of pH conditions. The most favorable reaction was reductive β-elimination (ΔG(rxn)° ≈ −32 kcal/mol), followed closely by reductive dechlorination (ΔG(rxn)° ≈ −27 kcal/mol), dehydrochlorination (ΔG(rxn)° ≈ −27 kcal/mol), and nucleophilic substitution by OH− (ΔG(rxn)° ≈ −25 kcal/mol). For both reduction reactions studied, it was found that the first electron-transfer step, yielding the intermediate C•H2−CHCl−CH2Cl and the CH2Cl−C•H−CH2Cl species, was not favorable in the standard state (ΔG(rxn)° ≈ +15 kcal/mol) and was predicted to occur only at relatively high pH values. This result suggests that reduction by natural attenuation is unlikely. PMID:21038905
NASA Astrophysics Data System (ADS)
Riedl, Kira; Guterding, Daniel; Jeschke, Harald O.; Gingras, Michel J. P.; Valentí, Roser
2016-07-01
We present a general framework for deriving effective spin Hamiltonians of correlated magnetic systems based on a combination of relativistic ab initio density functional theory calculations, exact diagonalization of a generalized Hubbard Hamiltonian on finite clusters, and spin projections onto the low-energy subspace. A key motivation is to determine anisotropic bilinear exchange couplings in materials of interest. As an example, we apply this method to the pyrochlore Lu2V2O7 where the vanadium ions form a lattice of corner-sharing spin-1/2 tetrahedra. In this compound, anisotropic Dzyaloshinskii-Moriya interactions (DMIs) play an essential role in inducing a magnon Hall effect. We obtain quantitative estimates of the nearest-neighbor Heisenberg exchange, the DMI, and the symmetric part of the anisotropic exchange tensor. Finally, we compare our results with experimental ones on the Lu2V2O7 compound.
NASA Astrophysics Data System (ADS)
Dąbrowska, Aleksandra; Makowski, Mariusz; Jacewicz, Dagmara; Chylewska, Agnieszka; Chmurzyński, Lech
2008-12-01
UV absorption spectra of methyl 3-azido-6-iodo-2,3,6-trideoxy-α- D- arabino-hexopyranoside were recorded over a wide pH range. On this basis, a relationship between absorbance and pH was plotted, from which deprotonation equilibrium constants of this compound were determined. Further, quantum-mechanical calculations were performed at the ab initio level both in the gas phase by using the Restricted Hartree Fock (RHF), Møller-Plesset (MP2) methods and under consideration of solvation effects within the Polarizable Continuum Model (PCM), which enabled location of preferred protonation and deprotonation centers of this compound. The results provided the basis for discussion of the influence of substituents in the sugar ring on protolytic equilibria occurring in aqueous solutions of 3-azido-2,3-dideoxy sugars.
NASA Astrophysics Data System (ADS)
Datta, Debasis
Systematic inclusion of many-body effects in open d and f subshell atoms has long been known as a formidable challenge in atomic structure theory. Due to the presence of competing relativistic effects in such systems, an appropriate theoretical approach needs to incorporate electron correlation within the framework of the Special Theory of Relativity. To this aim, the Relativistic Configuration Interaction methodology as developed by Beck and others has been extended and applied to multi-reference situations in ((n - 1)d + ns) ^{rm N} type valence configurations. Specific focus has been on the hyperfine structure and electron affinity studies of the transition metal ions and the rare earths respectively. Energies and magnetic dipole and electric quadrupole hyperfine structure constants of all the fifteen Zr II (4d + 5s)^3 J = 0.5, 1.5 levels and the twenty one Nb II (4d + 5s)^4 J = 2 levels have been determined with unprecedented accuracies. The average errors in energy are 0.087 eV and 0.050 eV for Zr II J = 3/2 & 1/2 respectively while that for the ten bottom levels of Nb II J = 2 is 0.055 eV. For the levels known experimentally, the corresponding errors in magnetic dipole hyperfine structure constants are 9.2%, 31.8% and 3.8%. Quite a few of the many-body hyperfine constant values exhibit striking improvements over the Multi-Configurational Dirac Fock values. A new value of nuclear quadrupole moment has also been predicted for Zr II. In all cases certain previous level assignments have been corrected and five previously unknown levels have been identified in Nb II. The rigorous systematics of the many-body effects important for the energy level and hyperfine structure of these systems has been presented including core-valence and core-core effects. Contrary to the conventional wisdom and theoretical predictions of the last decade, the attachment of an f electron has been discarded as the most likely mechanism for the formation of Lanthanide and Actinide negative
Fakhraee, Mostafa; Zandkarimi, Borna; Salari, Hadi; Gholami, Mohammad Reza
2014-12-11
The influences of hydroxyl functional group (-OH) on the thermodynamic and structural properties of ionic liquids (ILs) composed of 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C2OHmim](+)) cation and the six different conventional anions, including [Cl](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) have been extensively investigated using classical molecular dynamics (MD) simulations combined with ab initio calculations over a wide range of temperature (298-550 K). The volumetric thermodynamic properties, enthalpy of vaporization, cohesive energy density, Hildebrand solubility parameter, and heat capacity at constant pressure were estimated at desired temperature. The simulated densities were in good agreement with the experimental data with a slight overestimation. The interionic interaction of selected ILs was also computed using both the MD simulations and ab initio calculations. It was found that the highest association of cation and anion is attributed to [C2OHmim][Cl] followed by [C2OHmim][NO3], and [C2OHmim][Tf2N] with the bulkiest anion has the weakest interionic interaction among chosen ILs. The similar trend of interactions energies was nearly observed from cohesive energy density results. Additional structural details were comprehensively yielded by calculating radial distribution functions (RDFs) and spatial distribution function (SDFs) at 358 K. The most stable configurations of isolated and dimer ion pairs of these ILs were in excellent consistency with RDFs and SDFs results. Significant changes in arrangement of anions around the [C2OHmim](+) cation in comparison with conventional imidazolium-based ILs can be inferred from the MD simulations and ab initio results. Also, microscopic structural properties disclosed that the most strong cation-cation interaction is ascribed to the hydroxyl-functionalized ILs composed of bulkier anions, whereas ILs incorporating [Cl](-) and [NO3](-) anions are mainly involved in cation-anion interactions. The
Glaz, W.; Bancewicz, T.; Godet, J.-L.; Maroulis, G.; Haskopoulos, A.
2006-04-15
The collision-induced (CI) first hyperpolarizability tensor for the He-Ne pair composed of the lightest noble gas elements has been obtained on the grounds of an ab initio method as a function of the interatomic distance R. Collision-induced hyper-Rayleigh (CIHR) spectra scattered in mixtures of such atoms at temperatures of 95 and 295 K are computed in absolute units both quantum mechanically and classically for the frequency shifts up to 1000 cm{sup -1}. The spectral features of the CIHR profiles due to the vector b{sub 1} and septor b{sub 3} parts of the hyperpolarizability tensor are discussed. The quantum character of computed spectra, especially significant at lower temperatures, has been found out. The integrated intensities of the spectra have been evaluated and used as a criterion of the reliability of the computed profiles. The frequency-dependent depolarization ratio of the CIHR spectra was evaluated and discussed. The properties of the resulting HR profiles have been compared with the depolarized CI Rayleigh spectrum of the He-Ne pair.
NASA Astrophysics Data System (ADS)
Sangiovanni, D. G.; Hellman, O.; Alling, B.; Abrikosov, I. A.
2016-03-01
We revisit the color-diffusion algorithm [Aeberhard et al., Phys. Rev. Lett. 108, 095901 (2012), 10.1103/PhysRevLett.108.095901] in non equilibrium ab initio molecular dynamics (NE-AIMD) and propose a simple efficient approach for the estimation of monovacancy jump rates in crystalline solids at temperatures well below melting. Color-diffusion applied to monovacancy migration entails that one lattice atom (colored atom) is accelerated toward the neighboring defect site by an external constant force F. Considering bcc molybdenum between 1000 and 2800 K as a model system, NE-AIMD results show that the colored-atom jump rate kNE increases exponentially with the force intensity F , up to F values far beyond the linear-fitting regime employed previously. Using a simple model, we derive an analytical expression which reproduces the observed kNE(F ) dependence on F . Equilibrium rates extrapolated by NE-AIMD results are in excellent agreement with those of unconstrained dynamics. The gain in computational efficiency achieved with our approach increases rapidly with decreasing temperatures and reaches a factor of 4 orders of magnitude at the lowest temperature considered in the present study.
Kessler, Jan; Elgabarty, Hossam; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D
2015-08-01
The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab initio molecular dynamics simulations in conjunction with an instantaneous surface definition [Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface. PMID:26174102
NASA Astrophysics Data System (ADS)
Powers, Nathan Lee
2008-10-01
The [Fe2S2]2+/[Fe2S 2]+ electronic structure of seven Rieske protein active sites (bovine mitochondrial cytochrome bc1 complex, spinach chloroplast cytochrome b6f complex, Rieske-type ferredoxin associated with biphenyl dioxygenase from Burkholderia cepacia, yeast cytochrome bcl complex from Saccharomyces cerevisiae, Rieske subunit of arsenite oxidase from Alcaligenes faecalis, respiratory-type Rieske protein from Thermus thermophilus, and Rieske protein II (soxF) from Sulfolobus acidocaldarius), which lie in a reduction potential range from -150 mV to 375 mV, have been studied by both single and multi-determinant quantum mechanical methods. Calculated reduction potentials and magnetic properties are found comparable to experimental values.
NASA Astrophysics Data System (ADS)
Naumov, Panče; Jovanovski, Gligor; Ohashi, Yuji
2002-02-01
Ground-state ab initio molecular geometries and vibrational spectra of 24 N-substituted isolated saccharins with small-size B, Br, C, Cl, F, N, O, P or S-groups and the parent molecule are predicted at RHF/6-31G level to examine the molecular structural changes stemming from N-substitution of saccharin (o-sulfobenzimide). Trends in the molecular geometrical parameters of the sulfimide ring and the carbonyl stretching frequency are discussed in relation to the electronic properties of the substituent and the solid state effects. The results are compared with the crystallographic data for N-substituted saccharins and metal saccharinato salts/complexes retrieved from the Cambridge Structural Database. The ability of several theoretical methods to describe the substitution/deprotonation of the conjugated CONHSO 2 structure is summarized. Electronic properties of the substituent affect significantly only the immediate CN and SN bonds by as much as ±0.014 Å, while other bonds are relatively less influenced (±0.004 Å). Combined with the effects of the crystal packing and thermal vibrations, they impose flexibility on the intramolecular lengths up to ±0.02 Å. High correlation ( R=0.966) between the theoretical ν(CO) frequencies and CO distances is predictable for both of these parameters, but is lowered notably in the crystal by both vibrational and solid-state circumstances. From the structural viewpoint, the N sac-X bonds (X = B, Br, C, Cl, F, N, O, P, S; sac denotes saccharin) behave similarly to the purely covalent N sac-metal bonds.
NASA Astrophysics Data System (ADS)
Bedjaoui, A.; Bouhemadou, A.; Bin-Omran, S.
2016-04-01
The structural, elastic and thermodynamic properties of the α (tetragonal) and β (orthorhombic) polymorphs of the Sr2GeN2 compound have been examined in detail using ab initio density functional theory pseudopotential plane-wave calculations. Apart the structural properties at the ambient conditions, all present reported results are predicted for the first time. The calculated equilibrium lattice parameters and inter-atomic bond-lengths of the considered polymorphs are in good agreement with the available experimental data. It is found that α-Sr2GeN2 is energetically more stable than β-Sr2GeN2. The two examined polymorphs are very similar in their crystal structures and have almost identical local environments. The single-crystal and polycrystalline elastic parameters and related properties - including elastic constants, bulk, shear and Young's moduli, Poisson's ratio, anisotropy indexes, Pugh's criterion, elastic wave velocities and Debye temperature - have been predicted. Temperature and pressure dependence of some macroscopic properties - including the unit-cell volume, bulk modulus, volume thermal expansion coefficient, heat capacity and Debye temperature - have been evaluated using ab initio calculations combined with the quasi-harmonic Debye model.
M Kondo; T Mates; D Fischer; F Wudl; E Kramer
2011-12-31
Interfaces between phenylacetylene (PA) monolayers and two silicon surfaces, Si(111) and Si(100), are probed by X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and the results are analyzed using ab initio molecular orbital calculations. The monolayer systems are prepared via the surface hydrosilylation reaction between PA and hydrogen-terminated silicon surfaces. The following spectral features are obtained for both of the PA-Si(111) and PA-Si(100) systems: a broad {pi}-{pi}* shakeup peak at 292 eV (XPS), a broad first ionization peak at 3.8 eV (UPS), and a low-energy C 1s {yields} {pi}* resonance peak at 284.3 eV (NEXAFS). These findings are ascribed to a styrene-like {pi}-conjugated molecular structure at the PA-Si interface by comparing the experimental data with theoretical analysis results. A conclusion is drawn that the vinyl group can keep its {pi}-conjugation character on the hydrogen-terminated Si(100) [H:Si(100)] surface composed of the dihydride (SiH{sub 2}) groups as well as on hydrogen-terminated Si(111) having the monohydride (SiH) group. The formation mechanism of the PA-Si(100) interface is investigated within cluster ab initio calculations, and the possible structure of the H:Si(100) surface is discussed based on available data.
NASA Astrophysics Data System (ADS)
Jaiganesh, G.; Jaya, S. Mathi
2015-06-01
The magnetism, structure and spin polarized electronic structure of Ti substituted MO (M = Mg, Ca, Sr) are studied using the ab-initio techniques within the framework of the density functional theory. Appropriately constructed supercell along with the full structural optimization of these cells is used for studying the influence of Ti substitution on the magnetism and electronic structure of these compounds. We find from our calculations that the Ti substituted MO compounds energetically favor magnetically ordered state. The Ti concentration is found to be important in deciding the magnetic order and we have observed antiferromagnetic order for the Ti concentration of 0.25. The Ti substituted MO compounds are thus an interesting class of materials that deserve further studies.
Jaiganesh, G. Jaya, S. Mathi
2015-06-24
The magnetism, structure and spin polarized electronic structure of Ti substituted MO (M = Mg, Ca, Sr) are studied using the ab-initio techniques within the framework of the density functional theory. Appropriately constructed supercell along with the full structural optimization of these cells is used for studying the influence of Ti substitution on the magnetism and electronic structure of these compounds. We find from our calculations that the Ti substituted MO compounds energetically favor magnetically ordered state. The Ti concentration is found to be important in deciding the magnetic order and we have observed antiferromagnetic order for the Ti concentration of 0.25. The Ti substituted MO compounds are thus an interesting class of materials that deserve further studies.
NASA Astrophysics Data System (ADS)
Goodrow, Anthony; Bell, Alexis T.; Head-Gordon, Martin
2008-11-01
Transition state search algorithms, such as the nudged elastic band can fail, if a good initial guess of the transition state structure cannot be provided. The growing string method (GSM) [J. Chem. Phys. 120, 7877 (2004)] eliminates the need for an initial guess of the transition state. While this method only requires knowledge of the reactant and product geometries, it is computationally intensive. To alleviate the bottlenecks in the GSM, several modifications were implemented: Cartesian coordinates were replaced by internal coordinates, the steepest descent method for minimization of orthogonal forces to locate the reaction path was replaced by the conjugate gradient method, and an interpolation scheme was used to estimate the energy and gradient, thereby reducing the calls to the quantum mechanical (QM) code. These modifications were tested to measure the reduction in computational time for four cases of increasing complexity: the Müller-Brown potential energy surface, alanine dipeptide isomerization, H abstraction in methanol oxidation, and C-H bond activation in oxidative carbonylation of toluene to p-toluic acid. These examples show that the modified GSM can achieve two- to threefold speedups (measured in terms of the reduction in actual QM gradients computed) over the original version of the method without compromising accuracy of the geometry and energy of the final transition state. Additional savings in computational effort can be achieved by carrying out the initial search for the minimum energy pathway (MEP) using a lower level of theory (e.g., HF/STO-3G) and then refining the MEP using density functional theory at the B3LYP level with larger basis sets (e.g., 6-31G∗, LANL2DZ). Thus, a general strategy for determining transition state structures is to initiate the modified GSM using a low level of theory with minimal basis sets and then refining the calculation at a higher level of theory with larger basis sets.
Goodrow, Anthony; Bell, Alexis T; Head-Gordon, Martin
2008-11-01
Transition state search algorithms, such as the nudged elastic band can fail, if a good initial guess of the transition state structure cannot be provided. The growing string method (GSM) [J. Chem. Phys. 120, 7877 (2004)] eliminates the need for an initial guess of the transition state. While this method only requires knowledge of the reactant and product geometries, it is computationally intensive. To alleviate the bottlenecks in the GSM, several modifications were implemented: Cartesian coordinates were replaced by internal coordinates, the steepest descent method for minimization of orthogonal forces to locate the reaction path was replaced by the conjugate gradient method, and an interpolation scheme was used to estimate the energy and gradient, thereby reducing the calls to the quantum mechanical (QM) code. These modifications were tested to measure the reduction in computational time for four cases of increasing complexity: the Muller-Brown potential energy surface, alanine dipeptide isomerization, H abstraction in methanol oxidation, and C-H bond activation in oxidative carbonylation of toluene to p-toluic acid. These examples show that the modified GSM can achieve two- to threefold speedups (measured in terms of the reduction in actual QM gradients computed) over the original version of the method without compromising accuracy of the geometry and energy of the final transition state. Additional savings in computational effort can be achieved by carrying out the initial search for the minimum energy pathway (MEP) using a lower level of theory (e.g., HF/STO-3G) and then refining the MEP using density functional theory at the B3LYP level with larger basis sets (e.g., 6-31G( *), LANL2DZ). Thus, a general strategy for determining transition state structures is to initiate the modified GSM using a low level of theory with minimal basis sets and then refining the calculation at a higher level of theory with larger basis sets. PMID:19045335
NASA Astrophysics Data System (ADS)
Campetella, M.; Bovi, D.; Caminiti, R.; Guidoni, L.; Bencivenni, L.; Gontrani, L.
2016-07-01
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-1), where the vibrational motions involve the NH3+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm-1 where the antisymmetric stretching mode (ν3) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D3h 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.
Campetella, M; Bovi, D; Caminiti, R; Guidoni, L; Bencivenni, L; Gontrani, 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(-1)), where the vibrational motions involve the NH3+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm(-1) where the antisymmetric stretching mode (ν3) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D3h 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. PMID:27421420
NASA Astrophysics Data System (ADS)
Bentouaf, Ali; Hassan, Fouad El Haj
2015-05-01
Density functional theory based on full-potential linearized augmented plane wave (FP LAPW) method is used to investigate the structural, electronic and magnetic properties of Co2VSi Heusler alloys, with L21 structure. It is shown that calculated lattice constants and spin magnetic moments using the general gradient approximation method are in good agreement with experimental values. We also presented the thermal effects using the quasi-harmonic Debye model, in which the lattice vibrations are taken into account. Temperature and pressure effects on the structural parameters, heat capacities, thermal expansion coefficient, and Debye temperatures are determined from the non-equilibrium Gibbs functions.
Surface structure determines dynamic wetting
Wang, Jiayu; Do-Quang, Minh; Cannon, James J.; Yue, Feng; Suzuki, Yuji; Amberg, Gustav; Shiomi, Junichiro
2015-01-01
Liquid wetting of a surface is omnipresent in nature and the advance of micro-fabrication and assembly techniques in recent years offers increasing ability to control this phenomenon. Here, we identify how surface roughness influences the initial dynamic spreading of a partially wetting droplet by studying the spreading on a solid substrate patterned with microstructures just a few micrometers in size. We reveal that the roughness influence can be quantified in terms of a line friction coefficient for the energy dissipation rate at the contact line, and that this can be described in a simple formula in terms of the geometrical parameters of the roughness and the line-friction coefficient of the planar surface. We further identify a criterion to predict if the spreading will be controlled by this surface roughness or by liquid inertia. Our results point to the possibility of selectively controlling the wetting behavior by engineering the surface structure. PMID:25683872
Pi, Xiaodong; Ni, Zhenyi; Yang, Deren E-mail: christophe.delerue@isen.fr; Delerue, Christophe E-mail: christophe.delerue@isen.fr
2014-11-21
In contrast to the conventional doping of bulk silicon (Si), the doping of Si nanocrystals (NCs) that are often smaller than 5 nm in diameter may lead to serious structural changes. Since the electronic and optical properties of Si NCs are intimately associated with their structures, it is critical to understand how doping impacts the structures of Si NCs. By means of ab initio calculation we now compare 1.4 nm phosphorus (P)-doped Si NCs without structural relaxation and those with structural relaxation. Structural changes induced by structural relaxation are manifested by the stretching and compressing of bonds and apparent variations in bond angles. With the increase of the concentration of P structural changes induced by structural relaxation become more serious. It is found that structural relaxation makes differences in the energy-level schemes of P-doped Si NCs. Structural relaxation also causes the binding energy of an electron in a P-doped Si NC to more significantly increase as the concentration of P increases. With the increase of the concentration of P structural relaxation leads to more pronounced changes in the optical absorption of P-doped Si NCs.
Appalakondaiah, S.; Vaitheeswaran, G.; Lebègue, S.
2014-01-07
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 increment 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.
Haskins, Justin B; Bauschlicher, Charles W; Lawson, John W
2015-11-19
Density functional theory (DFT), density functional theory molecular dynamics (DFT-MD), and classical molecular dynamics using polarizable force fields (PFF-MD) are employed to evaluate the influence of Li(+) on the structure, transport, and electrochemical stability of three potential ionic liquid electrolytes: N-methyl-N-butylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([pyr14][TFSI]), N-methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide ([pyr13][FSI]), and 1-ethyl-3-methylimidazolium boron tetrafluoride ([EMIM][BF4]). We characterize the Li(+) solvation shell through DFT computations of [Li(Anion)n]((n-1)-) clusters, DFT-MD simulations of isolated Li(+) in small ionic liquid systems, and PFF-MD simulations with high Li-doping levels in large ionic liquid systems. At low levels of Li-salt doping, highly stable solvation shells having two to three anions are seen in both [pyr14][TFSI] and [pyr13][FSI], whereas solvation shells with four anions dominate in [EMIM][BF4]. At higher levels of doping, we find the formation of complex Li-network structures that increase the frequency of four anion-coordinated solvation shells. A comparison of computational and experimental Raman spectra for a wide range of [Li(Anion)n]((n-1)-) clusters shows that our proposed structures are consistent with experiment. We then compute the ion diffusion coefficients and find measures from small-cell DFT-MD simulations to be the correct order of magnitude, but influenced by small system size and short simulation length. Correcting for these errors with complementary PFF-MD simulations, we find DFT-MD measures to be in close agreement with experiment. Finally, we compute electrochemical windows from DFT computations on isolated ions, interacting cation/anion pairs, and liquid-phase systems with Li-doping. For the molecular-level computations, we generally find the difference between ionization energy and electron affinity from isolated ions and interacting cation/anion pairs to
NASA Astrophysics Data System (ADS)
Zhu, Xiaolei; Yarkony, David R.
2016-01-01
In this work, we demonstrate that for moderate sized systems, here a system with 13 atoms, global coupled potential energy surfaces defined for several electronic states over a wide energy range and for distinct regions of nuclear coordinate space characterized by distinct electron configurations, can be constructed with precise energetics and an excellent description of non-adiabatic interactions in all regions. This is accomplished using a recently reported algorithm for constructing quasi-diabatic representations, Hd, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an Hd to describe the photodissociation of phenol from its first and second excited electronic states. The representation treats all 33 internal degrees of freedom in an even handed manner. The ab initio adiabatic electronic structure data used to construct the fit are obtained exclusively from multireference configuration interaction with single and double excitation wave functions comprised of 88 × 106 configuration state functions, at geometries determined by quasi-classical trajectories. Since the algorithm uses energy gradients and derivative couplings in addition to electronic energies to construct Hd, data at only 7379 nuclear configurations are required to construct a representation, which describes all nuclear configurations involved in H atom photodissociation to produce the phenoxyl radical in its ground or first excited electronic state, with a mean unsigned energy error of 202.9 cm-1 for electronic energies <60 000 cm-1.
Bryk, Taras; Wax, J-F
2016-05-21
Using a combination of ab initio molecular dynamics and several fit models for dynamic structure of liquid metals, we explore an issue of possible manifestation of non-acoustic collective excitations in longitudinal dynamics having liquid Na as a case study. A model with two damped harmonic oscillators (DHOs) in time domain is used for analysis of the density-density time correlation functions. Another similar model with two propagating contributions and three lowest exact sum rules is considered, as well as an extended hydrodynamic model known as thermo-viscoelastic one which permits two types of propagating modes outside the hydrodynamic region to be used for comparison with ab initio obtained time correlation functions and calculations of dispersions of collective excitations. Our results do not support recent suggestions that, even in simple liquid metals, non-hydrodynamics transverse excitations contribute to the longitudinal collective dynamics and can be detected as a DHO-like spectral shape at their transverse frequency. We found that the thermo-viscoelastic dynamic model permits perfect description of the density-density and current-current time correlation functions of the liquid Na in a wide range of wave numbers, which implies that the origin of the non-hydrodynamic collective excitations contributing to longitudinal dynamics can be short-wavelength heat waves. PMID:27208952
NASA Astrophysics Data System (ADS)
Bryk, Taras; Wax, J.-F.
2016-05-01
Using a combination of ab initio molecular dynamics and several fit models for dynamic structure of liquid metals, we explore an issue of possible manifestation of non-acoustic collective excitations in longitudinal dynamics having liquid Na as a case study. A model with two damped harmonic oscillators (DHOs) in time domain is used for analysis of the density-density time correlation functions. Another similar model with two propagating contributions and three lowest exact sum rules is considered, as well as an extended hydrodynamic model known as thermo-viscoelastic one which permits two types of propagating modes outside the hydrodynamic region to be used for comparison with ab initio obtained time correlation functions and calculations of dispersions of collective excitations. Our results do not support recent suggestions that, even in simple liquid metals, non-hydrodynamics transverse excitations contribute to the longitudinal collective dynamics and can be detected as a DHO-like spectral shape at their transverse frequency. We found that the thermo-viscoelastic dynamic model permits perfect description of the density-density and current-current time correlation functions of the liquid Na in a wide range of wave numbers, which implies that the origin of the non-hydrodynamic collective excitations contributing to longitudinal dynamics can be short-wavelength heat waves.
NASA Astrophysics Data System (ADS)
Durig, J. R.; Zhao, Wenyun; Little, T. S.; Dakkouri, M.
1988-12-01
The infrared (3500 to 50 cm -1) and Raman (3500 to 20 cm -1) spectra of solid 1,1-dicyanocyclobutane have been recorded. Additionally, the Raman spectrum of the liquid has been recorded and qualitative depolarization values have been obtained. The spectral features observed at room temperature for the solid phase (m.p. 37 °C) are very similar to those obtained for the neat liquid at ≈ 60 °C but the spectral features observed at -120 °C were clearly those of an annealed solid. These spectra have been interpreted on the basis of C s molecular symmetry for 1,1-dicyanocyclobutane where the ring is puckered and the two cyano groups are "quasi-linear". The vibrational assignment is based on depolarization values, group frequencies, and in some cases the relative intensities of the observed bands. The potential function governing the ring puckering motion has been determined from optimized geometries obtained by ab initio Hartree-Fock gradient calculations at both the 3-21G and 4-31G basis set levels. The assignments of the fundamental vibrational frequencies are compared to those obtained from a force field obtained by ab initio calculations employing the 3-21G basis set. These results are discussed and compared to those obtained for some similar molecules.
NASA Astrophysics Data System (ADS)
Ikeda, Tohru; Nagayoshi, Kanade; Kitaura, Kazuo
2003-03-01
A computational procedure is proposed for calculating the lattice energy of molecular crystals using the ab initio MO method. Our method does not require any adjustable parameters and provides a general description for various molecular crystals including electron donor-acceptor (EDA) complexes. Using the method, the packing structure of H 3N-BF 3 crystal was optimized at the HF/3-21 + G level and the lattice energy was calculated at the MP2/6-311 + G * level. The calculation reproduced the experimental lattice constants with reasonable accuracy. Moreover, the structural feature of the H 3N-BF 3 crystal was discussed based on the molecular interactions in the crystal.
Collective rotation from ab initio theory
NASA Astrophysics Data System (ADS)
Caprio, M. A.; Maris, P.; Vary, J. P.; Smith, R.
2015-08-01
Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments and electromagnetic transitions. In this review, NCCI calculations of 7-9Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction.
Finding the stable structures of N1-xWx with an ab initio high-throughput approach
NASA Astrophysics Data System (ADS)
Mehl, Michael J.; Finkenstadt, Daniel; Dane, Christian; Hart, Gus L. W.; Curtarolo, Stefano
2015-05-01
Using density functional theory calculations, many researchers have predicted that various tungsten nitride compounds N1-xWx (x <1/2 ) will be "ultraincompressible" or "superhard," i.e., as hard as or harder than diamond. Necessary conditions for such compounds are that they have large bulk and shear moduli, greater than approximately 200 GPa, and are elastically and vibrationally stable. Compounds with such desirable properties also must be energetically stable against decomposition into other compounds. This test for stability can only be found after the determination of the convex hull for N1-xWx , which connects the lowest enthalpy structures as a function of composition. Unfortunately, the experimental phase diagram of the N-W structure is uncertain, as it is difficult to break the N2 bond to form compounds with tungsten. Experiment also indicates that there are a large number of partially filled sites in most N-W structures. This introduces computational difficulties since we cannot easily model randomly placed vacancies. In addition, van der Waals forces play a significant role in determining the structure of solid N2 and the nitrogen-rich compounds. This makes it difficult to determine the relative energies of these compounds, as there is no universally accepted density functional incorporating van der Waals interactions. The exact shape and even composition of the convex hull is dependent upon the choice of density functional, even if we only chose between the local density approximation and a generalized gradient functional. Despite these difficulties, computations can determine much about the ground-state form of the convex hull. Here, we use high-throughput calculations to map out the hull and other low-energy structures for the N-W system. The lowest-energy structures all have vacancies, on the tungsten sites in hexagonal-based compounds, and on both the nitrogen and tungsten sites in cubic compounds. We find that most of the N-W structures proposed in
Bylaska, Eric J.; Dixon, David A.; Felmy, Andrew R.; Apra, Edoardo; Windus, Theresa L.; Zhan, Chang-Guo; Tratnyek, Paul G.
2004-07-08
Electronic structure methods were used to calculate the aqueous reaction energies for hydrogenolysis, dehydrochlorination, and nucleophilic substitution by OH- of 4,4¢-DDT. Thermochemical properties ¢Hf° (298.15 K), S° (298.15 K, 1 bar), ¢GS (298.15 K, 1 bar) were calculated by using ab initio electronic structure calculations, isodesmic reactions schemes, gas-phase entropy estimates, and continuum solvation models for a series of DDT type structures (p-C6H4Cl)2-CH-CCl3, (p-C6H4Cl)2-CH-CCl2¥, (p-C6H4Cl)2-CHCHCl2, (p-C6H4Cl)2-CdCCl2, (p-C6H4Cl)2-CH-CCl2OH, (p-C6H4Cl)2-CH-CCl(dO), and (p-C6H4-Cl)2-CH-COOH. On the basis of these thermochemical estimates, the overall aqueous reaction energetics of hydrogenolysis, dehydrochlorination, and hydrolysis of 4,4¢-DDT were estimated. The results of this investigation showed that the dehydrochlorination and hydrolysis reactions have strongly favorable thermodynamics in the standard state, as well as under a wide range of pH conditions. For hydrogenolysis with the reductant aqueous Fe(II), the thermodynamics are strongly dependent on pH, and the stability region of the (p-C6H4Cl)2-CH-CCl2¥(aq) species is a key to controlling the reactivity in hydrogenolysis. These results illustrate the use of ab initio electronic structure methods to identify the potentially important environmental degradation reactions by calculation of the reaction energetics of a potentially large number of organic compounds with aqueous species in natural waters.
NASA Astrophysics Data System (ADS)
Pan, Zhifang
The six normal mode vibration frequencies and infrared intensities for H_4^+ and three tetra-atomic lithium-hydrogen ion clusters have been calculated using ab initio SCF, MP2 and CISD methods. Vibrational frequencies are also reported for all possible deuterated analogs of the four ions. The normal mode vibrational characteristics and structures of the ions are discussed and compared to each other. The H_4^+ ion can reasonably be regarded as a strongly bonded, triangle H_3^+ core with an additional H atom ligand less strongly bound to the ring. The calculated normal mode vibration frequencies for H_4^+ and its deuterated analogs confirm this picture. The hydrogen-lithium clusters, LiH_3^+, Li_2 H_2^+ and Li _4^+, have structures and normal mode frequencies which did not yield the same strong-ring, weak -ligand picture as in H_4^+. Instead, they behaved more like two interacting diatomic molecule fragments (e.g., H_2 and LiH ^+ subunits in LiH_3^+ ) oriented perpendicular to each other. This resulted in a locally flat potential surface for the hydrogen-lithium cluster ions, with two extremely low frequency modes not seen in H_4^+. The potential surface and decomposition reaction path of H_4 cluster are studied by ab initio SCF calculations. H _4 decomposition is considered to proceed from the Franck-Condon geometry dictated by charge neutralization of H_4^+ ion: H_4^+ +e^ - to H_4^ * to H_2 + H_2, where H_4 ^* refers to the Franck-Condon geometry. The minimum energy decomposition path (MEP) of H_4 ^* is calculated in two, four and six dimensional potential surface of H_4 is calculated as a grid of ab initio energy points in the vicinity of the H_4^*>=ometry, and a decomposition path is found graphically which agrees well with the MEP calculations. Structures and vibrational frequencies of CF_4^- and CF_3Cl^- are calculated at ab initio SCF and UMP2 level using 6 -31g and D95 basis sets with and without polarization functions added.
Suturina, Elizaveta A; Maganas, Dimitrios; Bill, Eckhard; Atanasov, Mihail; Neese, Frank
2015-10-19
Over the past several decades, tremendous efforts have been invested in finding molecules that display slow relaxation of magnetization and hence act as single-molecule magnets (SMMs). While initial research was strongly focused on polynuclear transition metal complexes, it has become increasingly evident that SMM behavior can also be displayed in relatively simple mononuclear transition metal complexes. One of the first examples of a mononuclear SMM that shows a slow relaxation of the magnetization in the absence of an external magnetic field is the cobalt(II) tetra-thiolate [Co(SPh)4](2-). Fascinatingly, substitution of the donor ligand atom by oxygen or selenium dramatically changes zero-field splitting (ZFS) and relaxation time. Clearly, these large variations call for an in-depth electronic structure investigation in order to develop a qualitative understanding of the observed phenomena. In this work, we present a systematic theoretical study of a whole series of complexes (PPh4)2[Co(XPh)4] (X = O, S, Se) using multireference ab initio methods. To this end, we employ the recently proposed ab initio ligand field theory, which allows us to translate the ab initio results into the framework of ligand field theory. Magneto-structural correlations are then developed that take into account the nature of metal-ligand covalent bonding, ligand spin-orbit coupling, and geometric distortions away from pure tetrahedral symmetry. The absolute value of zero-field splitting increases when the ligand field strength decreases across the series from O to Te. The zero-field splitting of the ground state of the hypothetical [Co(TePh)4](2-) complex is computed to be about twice as large as for the well-known (PPh4)2[Co(SPh)4] compound. It is shown that due to the π-anisotropy of the ligand donor atoms (S, Se) magneto-structural correlations in [Co(OPh)4](2-) complex differ from [Co(S/SePh)4](2-). In the case of almost isotropic OPh ligand, only variations in the first
NASA Astrophysics Data System (ADS)
Huczyński, Adam; Janczak, Jan; Brzezinski, Bogumil
2012-12-01
A new crystalline complex formed between 1-naphthylmethyl ester of the naturally occurring antibiotic - monensin A (MON8) with sodium perchlorate has been obtained and studied using X-ray crystallography and FT-IR spectroscopy. The X-ray data of the complex show that MON8 forms a pseudo-cyclic structure stabilised by one weak intramolecular hydrogen bond and the sodium cation co-ordinated by two oxygen atoms of hydroxyl groups and four etheric oxygen atoms in the hydrophilic sphere. Within this structure the oxygen atoms of the ester groups are not involved in the coordination of sodium cation. In contrast to the solid state structure of the complex, in acetonitrile solution an equilibrium between two structures, in which the oxygen atom of the carbonyl ester group is either involved or not involved in the complexation of the sodium cation, is found. In acetonitrile this equilibrium is shifted towards the latter structure i.e. the structure existing in the solid state. The gas-phase structure of [MON8sbnd Na]+ cation as shown the ab initio MO calculations is comparable with the crystal one. Three-dimensional molecular electrostatic potential calculated for the neutral MON8 and [MON8sbnd Na]+ molecules is helpful for understanding the structural aspects of the sodium complex formation.
Kellö, Vladimir
2015-01-22
Highly correlated scalar relativistic calculations of electric field gradients at nuclei in diatomic molecules in combination with accurate nuclear quadrupole coupling constants obtained from microwave spectroscopy are used for determination of nuclear quadrupole moments.
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.
Koukaras, Emmanuel N; Zdetsis, Aristides D; Sigalas, Michael M
2012-09-26
On the basis of the attractive possibility of efficient hydrogen storage in light metal hydrides, we have examined a large variety of Mg(n)H(m) nanoclusters and (MgH(2))(n) nanocrystals (n = 2-216, m = 2-436) using high level coupled cluster, CCSD(T), ab initio methods, and judicially chosen density functional calculations of comparable quality and (near chemical) accuracy. Our calculated desorption energies as a function of size and percentage of hydrogen have pinpointed optimal regions of sizes and concentrations of hydrogen which are in full agreement with recent experimental findings. Furthermore, our results reproduce the experimental desorption energy of 75.5 kJ/mol for the infinite system with remarkable accuracy (76.5 ± 1.5 kJ/mol). PMID:22920498
NASA Astrophysics Data System (ADS)
Ohsawa, Takeo; Ueda, Shigenori; Suzuki, Motohiro; Tateyama, Yoshitaka; Williams, Jesse R.; Ohashi, Naoki
2015-10-01
Crystalline-polarity-dependent electronic structures of gallium nitride (GaN) were studied by photoemission spectroscopy (PES) using soft and hard x-rays with different linear polarizations. A peak located near the valence band (VB) maximum was enhanced for a (0001) surface compared with that for a ( 000 1 ¯ ) surface regardless of photon energy. Comparison of the VB density of states obtained by ab-initio calculations with the observed VB-PES spectra indicates that the crystalline-polarity dependence is associated with the Ga 4p and N 2p states. The most plausible origin of the crystalline-polarity-dependent VB feature is based on the photoemission phenomena of electrons in the pz-orbitals due to spontaneous electric polarization along the c-axis of GaN.
NASA Astrophysics Data System (ADS)
Choi, Heechae; Lee, Eung-Kwan; Cho, Sung Beom; Chung, Yong-Chae
2012-04-01
Using ab initio calculations, we investigated the changes of the magnetic moment and electronic structures of Fe adatoms on strained graphene sheets. By the uniaxial tensile strains in armchair and zig-zag directions on graphene sheets, the amounts of charge transfers from graphene 2pz orbital to Fe adatom 3d orbitals were linearly increased. The magnetic moments of Fe, however, show the tendency of linear decrements with the uniaxial tensile strains. The increased Fe magnetic moments by uniaxialy graphene compressions resulted from the shifting of spin-minority states of electrons while the decreased Fe magnetic moments were due to the reduction in the spin-majority states of 3dxy-orbitals of the Fe adatom.
NASA Astrophysics Data System (ADS)
Binev, Ivan G.; Binev, Yuri I.
1997-12-01
The structure of 2-cyano-3,3-bis(dimethylamino)acrylonitrile and 2-methoxycarbonyl-3,3-bis(dimethylamino)acrylonitrile has been studied on the basis of both infrared spectra and ab initio force field calculations. The 3012-376 cm -1 region bands have been assigned; a good agreement has been found between the theoretical and experimental spectroscopic characteristics. According to both infrared data and bond parameters, the CC bond in the molecules studied is strongly polarized. The ground-state charge transfer between the electropositive and electronegative fragments of the molecules is more than 0.5 e -, so the species studied have a dual character, both molecular and zwitterionic.
NASA Astrophysics Data System (ADS)
Childs, W. J.; Nielsen, U.
1988-01-01
The atomic-beam laser-rf double-resonance method has been used to measure precisely the dipole and quadrupole hyperfine structure (hfs) of 11 levels of the 5d26s configuration and four levels of the 5d3 configuration of 139La i. The results, together with earlier results for lower-lying levels, are compared in detail with new multiconfiguration Dirac-Fock (MCDF) ab initio calculations. The agreement is good to fair overall, but is poor in some areas. The comparison yields new insights and suggests areas in which the theoretical approach must be improved. In particular, the theory underestimates the importance of contact hfs in the 5d26s configuration by 25-40 %. In addition, there is at present no self-consistent way in the MCDF approach to take account of the large core polarization observed in the 5d3 4F term.
An ab initio study of the structures and energetics of CH{sub 3}OCl and CH{sub 3}ClO
Francisco, J.S.
1999-05-15
The high concentrations of Cl and ClO over Antarctica during the austral spring is now well known to be due to the catalytic cycle for the destruction of ozone for which these species are participants. The equilibrium structures, vibrational spectra, and heats of formation for CH{sub 3}OCl and CH{sub 3}ClO have been estimated using high levels of ab initio molecular orbital theory. The lowest energy isomer is found to be CH{sub 3}OCl, and its heat of formation is estimated to be {minus}13.5 {+-} 2 kcal mol{sup {minus}1}, in good agreement with bond additivity estimates. Results for the CH{sub 3}ClO isomer are presented for the first time, and it is found to be 40.5 kcal mol{sup {minus}1} higher in energy relative to CH{sub 3}OCl.
ERIC Educational Resources Information Center
Lord, Richard L.; Davis, Lisa; Millam, Evan L.; Brown, Eric; Offerman, Chad; Wray, Paul; Green, Susan M. E.
2008-01-01
We present a first-principles determination of the photoelectron spectra of water and hypochlorous acid as a laboratory exercise accessible to students in an undergraduate physical chemistry course. This paper demonstrates the robustness and user-friendliness of software developed for the Franck-Condon factor calculation. While the calculator is…
Ab initio calculations on the structure and nature of the hydrogen bonded complex H2S ṡṡṡ HF
NASA Astrophysics Data System (ADS)
Singh, U. Chandra; Kollman, Peter A.
1984-01-01
Ab initio calculations employing an extended basis set and correlation energy estimates at the MP2 (second order Möller-Plesset) level have been used to estimate the binding energy, minimum energy S ...F distance, and minimum energy bisector angle θ (angle between the twofold axis of H2S and the S ...F line) for the hydrogen bonded complex H2S ... HF. The calculated distance and bisector angle θ are in reasonable agreement with experiment; the calculated binding energy can be used to provide a good estimate of the (as yet unknown) experimental value. Morokuma component analyses and simple electrostatic (molecular mechanics) calculations have been carried out on the complex as a function of bisector angle and they demonstrated that, despite suggestions to the contrary, the H2S ... HF bisector angle is predominantly determined by the electrostatic energy.
NASA Astrophysics Data System (ADS)
Haddadi, K.; Bouhemadou, A.; Bin-Omran, S.; Maabed, S.; Khenata, R.
2015-01-01
The structural parameters, elastic constants, electronic structure and optical properties of the recently reported monoclinic quaternary nitridoaluminate LiCaAlN2 are investigated in detail using the ab initio plane-wave pseudopotential method within the generalized gradient approximation. The calculated equilibrium structural parameters are in excellent agreement with the experimental data, which validate the reliability of the applied theoretical method. The chemical and structural stabilities of LiCaAlN2 are confirmed by calculating the cohesion energy and enthalpy of formation. Chemical band stiffness is calculated to explain the pressure dependence of the lattice parameters. Through the band structure calculation, LiCaAlN2 is predicted to be an indirect band gap of 2.725 eV. The charge-carrier effective masses are estimated from the band structure dispersions. The frequency-dependent dielectric function, absorption coefficient, refractive index, extinction coefficient, reflectivity coefficient and electron energy loss function spectra are calculated for polarized incident light in a wide energy range. Optical spectra exhibit a noticeable anisotropy. Single-crystal and polycrystalline elastic constants and related properties, including isotropic sound velocities and Debye temperatures, are numerically estimated. The calculated elastic constants and elastic compliances are used to analyse and visualize the elastic anisotropy of LiCaAlN2. The calculated elastic constants demonstrate the mechanical stability and brittle behaviour of the considered material.
Nový, Jakub; Böhm, Stanislav; Králová, Jarmila; Král, Vladimír; Urbanová, Marie
2008-02-01
Variations in the structure of d(GGGA)(5) oligonucleotide in the presence of Li(+), Na(+), and K(+) ions and its temperature stability were studied using electronic and vibrational circular dichroism, IR absorption, and ab initio calculations with the Becke 3-Lee-Yang-Parr functional at the 6-31G** level. The samples were characterized by nondenaturing gel electrophoresis. Oligonucleotide d(GGGA)(5) in the presence of Li(+) forms a nonplanar single tetramer, with angles of 102 degrees and 171 degrees between neighboring guanine bases. This tetramer changes its geometry at temperatures >50 degrees C, but does not form a quadruplex structure. In the presence of Na(+), the d(GGGA)(5) structure was optimized to almost planar tetramers with an angle of 177 degrees between neighboring guanines. The spectral results suggest that it stacks into a quadruplex helical structure. This quadruplex structure decayed to a single tetramer at temperatures >60 degrees C. The Hartree-Fock energies imply that d(GGGA)(5) prefers to form complexes with Na(+) rather than Li(+). The d(GGGA)(5) structure in the presence of monovalent ions is stabilized against thermal denaturation in the order Li(+) < Na(+) < K(+). PMID:17960602
Mishra, Karuna Kara; Achary, S Nagabhusan; Chandra, Sharat; Ravindran, T R; Sinha, Anil K; Singh, Manavendra N; Tyagi, Avesh K
2016-09-01
Variable-temperature Raman spectroscopic and synchrotron X-ray diffraction studies were performed on BaTe2O6 (orthorhombic, space group: Cmcm), a mixed-valence tellurium compound with a layered structure, to understand structural stability and anharmonicity of phonons. The structural and vibrational studies indicate no phase transition in it over a wider range of temperature (20 to 853 K). The structure shows anisotropic expansion with coefficients of thermal expansion in the order αb ≫ αa > αc, which was attributed to the anisotropy in bonding and structure of BaTe2O6. Temperature evolution of Raman modes of BaTe2O6 indicated a smooth decreasing trend in mode frequencies with increasing temperature, while the full width at half-maximum (fwhm) of all modes systematically increases due to a rise in phonon scattering processes. With the use of our earlier reported isothermal mode Grüneisen parameters, thermal properties such as thermal expansion coefficient and molar specific heat are calculated. The pure anharmonic (explicit) and quasiharmonic (implicit) contribution to the total anharmonicity is delineated and compared. The temperature dependence of phonon mode frequencies and their fwhm values are analyzed by anharmonicity models, and the dominating anharmonic phonon scattering mechanism is concluded in BaTe2O6. In addition to the lattice modes, several external modes of TeOn (n = 5, 6) are found to be strongly anharmonic. The ab initio electronic structure calculations indicated BaTe2O6 is a direct band gap semiconductor with gap energy of ∼2.1 eV. Oxygen orbitals, namely, O-2p states in the valence band maximum and the sp-hybridized states in the conduction band minimum, are mainly involved in the electronic transitions. In addition a number of electronic transitions are predicted by the electronic structure calculations. Experimental photoluminescence results are adequately explained by the ab initio calculations. Further details of the structural and
Yang, Jun; Hu, Weifeng; Usvyat, Denis; Matthews, Devin; Schütz, Martin; Chan, Garnet Kin-Lic
2014-08-01
Computation of lattice energies to an accuracy sufficient to distinguish polymorphs is a fundamental bottleneck in crystal structure prediction. For the lattice energy of the prototypical benzene crystal, we combined the quantum chemical advances of the last decade to attain sub-kilojoule per mole accuracy, an order-of-magnitude improvement in certainty over prior calculations that necessitates revision of the experimental extrapolation to 0 kelvin. Our computations reveal the nature of binding by improving on previously inaccessible or inaccurate multibody and many-electron contributions and provide revised estimates of the effects of temperature, vibrations, and relaxation. Our demonstration raises prospects for definitive first-principles resolution of competing polymorphs in molecular crystal structure prediction. PMID:25104379
Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.
2008-05-20
Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.
Simple approach for ranking structure determining residues
Luna-Martínez, Oscar D.; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I.; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N.
2016-01-01
Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology. PMID:27366642
Simple approach for ranking structure determining residues.
Luna-Martínez, Oscar D; Vidal-Limón, Abraham; Villalba-Velázquez, Miryam I; Sánchez-Alcalá, Rosalba; Garduño-Juárez, Ramón; Uversky, Vladimir N; Becerril, Baltazar
2016-01-01
Mutating residues has been a common task in order to study structural properties of the protein of interest. Here, we propose and validate a simple method that allows the identification of structural determinants; i.e., residues essential for preservation of the stability of global structure, regardless of the protein topology. This method evaluates all of the residues in a 3D structure of a given globular protein by ranking them according to their connectivity and movement restrictions without topology constraints. Our results matched up with sequence-based predictors that look up for intrinsically disordered segments, suggesting that protein disorder can also be described with the proposed methodology. PMID:27366642
NASA Astrophysics Data System (ADS)
Richard, D.; Muñoz, E. L.; Butz, T.; Errico, L. A.; Rentería, M.
2010-07-01
The time-differential γ-γ perturbed-angular-correlation (TDPAC) technique using T44i→S44c tracers was applied to study the nuclear quadrupole interaction of the first excited I=1 state of S44c in the cubic bixbyite structure of scandium sesquioxide (Sc2O3) . In addition, ab initio calculations of electronic and structural properties and hyperfine parameters at the cationic sites of the Sc2O3 structure were performed using the full-potential augmented plane wave plus local-orbital (APW+lo) method. The accuracy of the calculations and the excellent agreement of the predicted electric-field-gradient (EFG) tensors and the structural properties (lattice parameters, internal positions) with the experimental results enable us to identify the observed hyperfine interactions and to infer the EFG sign that cannot be measured in conventional TDPAC experiments. Additionally, the APW+lo calculations show that the EFG at Sc sites is originated in the population of Sc3p states and give an explanation for the preferential occupation of the asymmetric cationic site C of the structure by the T44i doping impurities. Finally, the validity of the ionic model, usually used to describe the EFG at native cation sites, is discussed.
Distributed structure determination at the JCSG
Bedem, Henry van den Wolf, Guenter; Xu, Qingping; Deacon, Ashley M.
2011-04-01
The software suite Xsolve semi-exhaustively explores key parameters of the X-ray structure-determination process to compute multiple three-dimensional protein structures independently and in parallel from a set of diffraction images. An optimal consensus model for subsequent manual refinement is computed from these structures. The Joint Center for Structural Genomics (JCSG), one of four large-scale structure-determination centers funded by the US Protein Structure Initiative (PSI) through the National Institute for General Medical Sciences, has been operating an automated distributed structure-solution pipeline, Xsolve, for well over half a decade. During PSI-2, Xsolve solved, traced and partially refined 90% of the JCSG’s nearly 770 MAD/SAD structures at an average resolution of about 2 Å without human intervention. Xsolve executes many well established publicly available crystallography software programs in parallel on a commodity Linux cluster, resulting in multiple traces for any given target. Additional software programs have been developed and integrated into Xsolve to further minimize human effort in structure refinement. ConsensusModeler exploits complementarities in traces from Xsolve to compute a single optimal model for manual refinement. Xpleo is a powerful robotics-inspired algorithm to build missing fragments and qFit automatically identifies and fits alternate conformations.
NASA Astrophysics Data System (ADS)
Lasave, J.; Koval, S.; Migoni, R. L.; Dalal, N. S.
2011-08-01
A study of differently polarized structures relevant to the H-bonded antiferroelectric (AFE) compound NH4H2PO4 (ADP) is performed by first-principles calculations in the framework of the density functional theory. The calculated structures for the AFE and paraelectric (PE) phases are found in general good agreement with the available experimental data. We study the energetics and relative stability of different polarized clusters embedded in a PE matrix of ADP. We find that local ferroelectric and AFE clusters are stable and may coexist in the PE phase, which explains the coexistence of both type of microregions determined by electron spin probe measurements above the AFE-PE transition temperature. The dependency with the O-HṡṡṡO bridge length of the energy barrier heights for proton transfer is studied for coordinated proton displacements along the bridges within clusters of different sizes. This dependency may have implications for the geometric isotopic effects on Tc. We analyze Mulliken orbital and bond populations which confirm the existence of a charge flow within the NH_4^+ ion, an essential fact for the stabilization of the AFE phase over other possible polarized structures. This charge transfer is correlated with the optimization of the N-HṡṡṡO bridges and with distortions of the NH_4^+ group.
NASA Astrophysics Data System (ADS)
Kianfar, Ali Hossein; Ramazani, Shapour; Fath, Roghaye Hashemi; Roushani, Mahmoud
2013-03-01
Attempts to spectroscopic and structural study of copper complexes, some Cu(II) Schiff base complexes were synthesized and characterized by means of electronic, IR, 1HNMR spectra and elemental analysis. The thermal analyses of the complexes were investigated and the first order kinetic parameters were derived for them. The cyclic voltammetric studies in acetonitrile were proposed a monomeric structure for complexes. The structures of compounds were determined by ab initio calculations. In the solid state, the ligands exist as keto-amine/enol-imine tautomeric forms with an intramolecular hydrogen bond (Nsbnd H⋯O) between amine and carbonyl group. The kinetic studies of the tautomerism and equilibrium constant of the reactions were calculated using transition state theory. The optimized molecular geometry and atomic charges were calculated using MP2 method with 6-31G(d) basis set for H, C, N and O atoms and LANL2DZ for the Cu atom. The results suggested that, in the complexes, Cu(II) ion is in pseudo square-planar NO3 coordination geometry. Also the bond lengths and angles were studied and compared.
Ab-initio calculations on melting of thorium
NASA Astrophysics Data System (ADS)
Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.
2016-05-01
Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a0)3 and (1.02a0)3 and (1.04a0)3 increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a0 = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures as melting point. The melting point of 2100 K is close to the experimental value of 2023K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.
Ab initio no core full configuration approach for light nuclei
NASA Astrophysics Data System (ADS)
Kim, Youngman; Shin, Ik Jae; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy
2014-07-01
Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.
Ab initio no core full configuration approach for light nuclei
NASA Astrophysics Data System (ADS)
Kim, Youngman; Shin, Ik Jae; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy
2015-10-01
Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.
A structural determinant required for RNA editing
Tian, Nan; Yang, Yun; Sachsenmaier, Nora; Muggenhumer, Dominik; Bi, Jingpei; Waldsich, Christina; Jantsch, Michael F.; Jin, Yongfeng
2011-01-01
RNA editing by adenosine deaminases acting on RNAs (ADARs) can be both specific and non-specific, depending on the substrate. Specific editing of particular adenosines may depend on the overall sequence and structural context. However, the detailed mechanisms underlying these preferences are not fully understood. Here, we show that duplex structures mimicking an editing site in the Gabra3 pre-mRNA unexpectedly fail to support RNA editing at the Gabra3 I/M site, although phylogenetic analysis suggest an evolutionarily conserved duplex structure essential for efficient RNA editing. These unusual results led us to revisit the structural requirement for this editing by mutagenesis analysis. In vivo nuclear injection experiments of mutated editing substrates demonstrate that a non-conserved structure is a determinant for editing. This structure contains bulges either on the same or the strand opposing the edited adenosine. The position of these bulges and the distance to the edited base regulate editing. Moreover, elevated folding temperature can lead to a switch in RNA editing suggesting an RNA structural change. Our results indicate the importance of RNA tertiary structure in determining RNA editing. PMID:21427087
NASA Astrophysics Data System (ADS)
Subotnik, Joseph
In this talk, I will give a broad overview of our work in nonadiabatic dynamics, i.e. the dynamics of strongly coupled nuclear-electronic motion whereby the relaxation of a photo-excited electron leads to the heating up of phonons. I will briefly discuss how to model such nuclear motion beyond mean field theory. Armed with the proper framework, I will then focus on how to calculate one flavor of electron-phonon couplings, known as derivative couplings in the chemical literature. Derivative couplings are the matrix elements that couple adiabatic electronic states within the Born-Oppenheimer treatment, and I will show that these matrix elements show spurious poles using formal (frequency-independent) time-dependent density functional theory. To correct this TD-DFT failure, a simple approximation will be proposed and evaluated. Finally, time permitting, I will show some ab initio calculations whereby one can use TD-DFT derivative couplings to study electronic relaxation through a conical intersection.
What Are the Ground State Structures of C20 and C24? An Explicitly Correlated Ab Initio Approach.
Manna, Debashree; Martin, Jan M L
2016-01-14
A new benchmark study has been performed for six isomers of C20 and four isomers of C24 using explicitly correlated methods, together with coupled cluster theory with large basis sets and DFT with advanced functionals. The relative energy trends obtained are extremely sensitive to the methods used. Combining our best CCSD(T)-MP2 difference with our best MP2 basis set limit, the dehydrocorannulene bowl is found to be the most stable for C20, followed by the cage at about 8 kcal/mol, and the ring at about 46 kcal/mol. For C24, the D3d cage is found to be the most stable isomer, followed at only a few kilocalories per mole by dehydrocoronene, and at larger separations by then octahedral cage and the ring, respectively. This makes C24 the smallest classical fullerene. The estimated residual basis set error of the estimated CCSD(T) basis set limit is conservatively expected to be ±1 kcal/mol. In general, DFT exhibits large errors for relative energies with RMSD values in the 8-34 kcal/mol range. However, among the DFT functionals, the DSD-PBEP86-D3BJ double hybrid comes close to our best ab initio results, while the ωB97X-V range-separated hybrid is in semiquantitative agreement. PMID:26654916
High-pressure structural behaviour of HoVO4: combined XRD experiments and ab initio calculations.
Garg, Alka B; Errandonea, D; Rodríguez-Hernández, P; López-Moreno, S; Muñoz, A; Popescu, C
2014-07-01
We report a high-pressure experimental and theoretical investigation of the structural properties of zircon-type HoVO4. Angle-dispersive x-ray diffraction measurements were carried out under quasi-hydrostatic and partial non-hydrostatic conditions up to 28 and 23.7 GPa, respectively. In the first case, an irreversible phase transition is found at 8.2 GPa. In the second case, the onset of the transition is detected at 4.5 GPa, a second (reversible) transition is found at 20.4 GPa, and a partial decomposition of HoVO4 was observed. The structures of the different phases have been assigned and their equations of state (EOS) determined. Experimental results have also been compared to theoretical calculations which fully agree with quasi-hydrostatic experiments. Theory also suggests the possibility of another phase transition at 32 GPa; i.e. beyond the pressure limit covered by present experiments. Furthermore, calculations show that deviatoric stresses could trigger the transition found at 20.4 GPa under non-hydrostatic conditions. The reliability of the present experimental and theoretical results is supported by the consistency between the values yielded for transition pressures and EOS parameters by the two methods. PMID:24912596
NASA Astrophysics Data System (ADS)
Liu, Lei; Bi, Yan; Xu, Jian; Chen, Xiangrong
2013-03-01
Tungsten monocarbide (WC) exhibits unique physical and chemical properties. It is an indispensable industrial material used as cutting tools and has many potential applications in catalyst, energy storage, and so on. We performed calculations of the electronic structure in the framework of the density functional theory (DFT) with generalized gradient approximation (GGA) to investigate structural and elastic properties of WC. Bulk WC is very incompressible, but its bulk modulus is still smaller than diamond though Lin et al. reported that nano-crystalline WC was as incompressible as diamond. WC undergoes different compressibilities along a and c directions: the a-axis is more compressible than the c-axis. The ratio of shear modulus to bulk modulus (G/B) was studied and it was found that WC translated from the brittle to ductile state at ∼63 GPa. In order to compare with the EOS determined at finite temperature, the vibration effects of the crystal lattice are taken into account based on quasi-harmonic Debye model. The temperature effect on bulk modulus is discussed and the thermodynamic properties of WC, such as heat capacity CV, Debye temperature θD, and thermal expansion α, are calculated simultaneously.
Representing Personal Determinants in Causal Structures.
ERIC Educational Resources Information Center
Bandura, Albert
1984-01-01
Responds to Staddon's critique of the author's earlier article and addresses issues raised by Staddon's (1984) alternative models of causality. The author argues that it is not the formalizability of causal processes that is the issue but whether cognitive determinants of behavior are reducible to past stimulus inputs in causal structures.…
NASA Astrophysics Data System (ADS)
Jezierski, Andrzej; Szytuła, Andrzej
2016-02-01
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 a 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
Ab initio investigations of A-site doping on the structure and electric polarization of HoMnO{sub 3}
S, Sathya Sheela; C, Kanagaraj; Natesan, Baskaran
2015-06-24
We have investigated the effect of A-site doping on the structure and electric polarization of orthorhombic HoMnO{sub 3} using ab initio density functional theory calculations. We find that the substitution of rare earth ions, such as Lu, Y and La in place of Ho in orthorhombic HoMnO{sub 3} modifies the local structure around Mn ions drastically, and leads to the formation of two distinct Mn sites Mn(0) and Mn(1). As a result, large variance between Mn(0)O{sub 6} and Mn(1)O{sub 6} octahedral distortions arises. This variance in the octahedral distortions drives the disparate hopping of electrons between the e{sub g} orbitals enhancing the electronic polarization with increasing rare earth ion radius. The largest polarization of 7 µC/cm{sup 2} is obtained for La doped HoMnO{sub 3}. This increase in polarization has been explained on the basis of radius mismatch induced local structural effects.
Method of fan sound mode structure determination
NASA Technical Reports Server (NTRS)
Pickett, G. F.; Sofrin, T. G.; Wells, R. W.
1977-01-01
A method for the determination of fan sound mode structure in the Inlet of turbofan engines using in-duct acoustic pressure measurements is presented. The method is based on the simultaneous solution of a set of equations whose unknowns are modal amplitude and phase. A computer program for the solution of the equation set was developed. An additional computer program was developed which calculates microphone locations the use of which results in an equation set that does not give rise to numerical instabilities. In addition to the development of a method for determination of coherent modal structure, experimental and analytical approaches are developed for the determination of the amplitude frequency spectrum of randomly generated sound models for use in narrow annulus ducts. Two approaches are defined: one based on the use of cross-spectral techniques and the other based on the use of an array of microphones.
NASA Astrophysics Data System (ADS)
Abadias, G.; Kanoun, M. B.; Goumri-Said, S.; Koutsokeras, L.; Dub, S. N.; Djemia, Ph.
2014-10-01
The structure, phase stability, and mechanical properties of ternary alloys of the Zr-Ta-N system are investigated by combining thin-film growth and ab initio calculations. Zr1-xTaxN films with 0≤x≤1 were deposited by reactive magnetron cosputtering in Ar +N2 plasma discharge and their structural properties characterized by x-ray diffraction. We considered both ordered and disordered alloys, using supercells and special quasirandom structure approaches, to account for different possible metal atom distributions on the cation sublattice. Density functional theory within the generalized gradient approximation was employed to calculate the electronic structure as well as predict the evolution of the lattice parameter and key mechanical properties, including single-crystal elastic constants and polycrystalline elastic moduli, of ternary Zr1-xTaxN compounds with cubic rocksalt structure. These calculated values are compared with experimental data from thin-film measurements using Brillouin light scattering and nanoindentation tests. We also study the validity of Vegard's empirical rule and the effect of growth-dependent stresses on the lattice parameter. The thermal stability of these Zr1-xTaxN films is also studied, based on their structural and mechanical response upon vacuum annealing at 850 °C for 3 h. Our findings demonstrate that Zr1-xTaxN alloys with Ta fraction 0.51⩽x⩽0.78 exhibit enhanced toughness, while retaining high hardness ˜30 GPa, as a result of increased valence electron concentration and phase stability tuning. Calculations performed for disordered or ordered structures both lead to the same conclusion regarding the mechanical behavior of these nitride alloys, in agreement with recent literature findings [H. Kindlund, D. G. Sangiovanni, L. Martinez-de-Olcoz, J. Lu, J. Jensen, J. Birch, I. Petrov, J. E. Greene, V. Chirita, and L. Hultman, APL Materials 1, 042104 (2013), 10.1063/1.4822440].
Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S
2014-06-10
We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good
NASA Astrophysics Data System (ADS)
Kotmool, K.; Bovornratanaraks, T.; Yoodee, K.
2015-10-01
An ab initio study of structural phase transformations and band structure under high pressure was performed on a ternary semiconductor, AgInTe2. Based on DFT within both LDA and GGA exchange-correlation, US-PP, and plane wave basis set, were employed for this work. Transition pressures and calculated parameters with transformation pathway was identified to be; chalcopyrite→cd-B1→cd-Cmcm, were in good agreement with experiments. We also predicted a higher pressure phase based on supercell with size 2×2×2 of B2 structure in which all the configuration of cation structures were accounted to compare and clarify its'cations-disordered state. The predicted structure probably appeared at around 40 GPa from cd-Cmcm to cd-B2. In the case of band structure calculation, NC-PP in which 4p10 electrons of In were not treated, was also employed in chalcopyrite at a pressure range of 0-4 GPa to improve a very narrow band gap of US-PP, and this failure will be discussed. Partial density of state (PDOS), and electronic population analysis were also calculated to finely investigate the electronic transition around the Fermi level. Our calculated results were in good agreement with experiments. The direct energy gap (Eg) was linearly proportional to pressure with increasing rate of 46.4 and 44.6 meV/GPa. In addition, at ambient conditions, Eg was equal to 1.02 eV and 0.95 eV for GGA and LDA, respectively. Band structure from all the calculations have shown a higher second band gap (Eg‧) which could occur due to crystal-field splitting.
Mesbah, Adel; Carton, Anne; Aranda, Lionel; Mazet, Thomas; Porcher, Florence; Francois, Michel
2008-12-15
Organic-inorganic hybrid compounds Ni(II){sub 5}(OH){sub 6}(C{sub 6}H{sub 8}O{sub 4}){sub 2}(1), Ni(II){sub 5}(OH){sub 6}(C{sub 8}H{sub 12}O{sub 4}){sub 2}(2) and Co(II){sub 5}(OH){sub 6}(C{sub 8}H{sub 12}O{sub 4}){sub 2}(3) have a similar layered structure as determined ab initio from synchrotron powder diffraction analysis. The metal sites are octahedrally coordinated by O atoms. The slabs are built from edge-sharing octahedra in such a way that channels with an average size of 4 A are formed. Bis-bidentate and bridging dicarboxylate anions lead to a 3D framework. The compounds (1) and (2) order antiferromagnetically below T{sub N}=26.5 and 19.3 K, respectively, while (3) is ferrimagnetic with T{sub C}=16.2 K. Crystal data for compounds are as follows: (1)a=11.6504(1) A, b=6.8021(3) A, c=6.3603(1) A, {alpha}=73.52(1){sup o}, {beta}=99.69(1){sup o}, {gamma}=96.16(1){sup o}, R{sub B}=0.070, 668 reflections; (2)a=13.9325(1) A, b=6.7893(1) A, c=6.3534(4) A, {alpha}=73.63(1){sup o}, {beta}=95.14(1){sup o}, {gamma}=91.80(1){sup o}, R{sub B}=0.052, 804 reflections; (3)a=13.9806(1) A, b=6.9588(1) A, c=6.3967(1) A, {alpha}=73.05(1){sup o}, {beta}=94.51(1){sup o}, {gamma}=92.19(1){sup o}, R{sub B}=0.048, 410 reflections. The space group is P-1 for the three compounds. - Graphical abstract: The hybrid metal-organic compounds Ni(II){sub 5}(OH){sub 6}(C{sub 6}H{sub 8}O{sub 4}){sub 2}(1), Ni(II){sub 5}(OH){sub 6}(C{sub 8}H{sub 12}O{sub 4}){sub 2}(2) and Co(II){sub 5}(OH){sub 6}(C{sub 8}H{sub 12}O{sub 4}){sub 2}(3) have been synthesized by the hydrothermal route. The microporous metal hydroxide layers are bridged by dicarboxylates anions. (1) and (2) are antiferromagnetic with T{sub N}=26.5 and 19.3 K, respectively, while (3) is ferrimagnetic with T{sub C}=16.2 K.
Structure of mutant human oncogene protein determined
Baum, R.
1989-01-16
The protein encoded by a mutant human oncogene differs only slightly in structure from the native protein that initiates normal cell division, a finding that may complicate efforts to develop inhibitors of the mutant protein. Previously, the x-ray structure of the protein encoded by the normal c-Ha-ras gene, a protein believed to signal cells to start or stop dividing through its interaction with guanosine triphosphate (GTP), was reported. The structure of the protein encoded by a transforming c-Ha-ras oncogene, in which a valine codon replaces the normal glycine codon at position 12 in the gene, has now been determined. The differences in the structures of the mutant and normal proteins are located primarily in a loop that interacts with the /beta/-phosphate of a bound guanosine diphosphate (GDP) molecule.
Structure determination of molecules of biochemical interest
NASA Astrophysics Data System (ADS)
Honzatko, R. B.
1985-10-01
In the past year we have established a new laboratory for the determination of macromolecular structure. Currently, facilities are in place for data collection, data processing, molecular modeling and X-ray refinement of structures of up to 100,000 molecular weight in their crystallographic asymmetric unit. In parallel with establishing a new laboratory, we have pursued structure investigations of hemoglobin from the sea lamprey, aspartate carbamoyltransferase from Escherichia coli and p-nitrobenzylidine aminoguanidine, a small molecule which is an acceptor of the adenosine diphosphate ribosyl group in an enzyme mediated reaction. In addition to the structural studies above we have made a theoretical study by techniques of energy minimization of possible modes of aggregation of lamprey hemoglobin and the relationship between aggregate formation and cooperativity expressed in solutions by lamprey hemoglobin.
NASA Astrophysics Data System (ADS)
Zhou, Bing; Sun, Zhaohua; Yao, Yefeng; Pan, Yuanming
2012-05-01
Borates consisting of diverse fundamental building blocks (FBB) formed from complex polymerization of planar triangular [Bϕ3] groups and tetrahedral [Bϕ4] groups, where ϕ = O and OH, provide an excellent opportunity for investigation of correlations between the NMR parameters and local structures. However, previous studies suggested that the 11B NMR parameters in borates are insensitive to local structural environments other than the B coordination number, in contrast to those documented for 29Si, 23Na and 27Al in silicates, and no correlation between 11B chemical shifts and the sum of bond valences has been established for borate minerals with hydroxyl groups or molecular water in the structures. In this study, high-resolution NMR spectra have been acquired at the ultra high field of 21 T as well as at 14 T for selected borate and borosilicate minerals, and have been used to extract high-precision NMR parameters by using combined ab initio theoretical calculations and spectral simulations. These new NMR parameters reveal subtle correlations with various structural characters, especially the effects of the 11B chemical shifts from the bridging oxygen atom(s), site symmetry, symmetry of FBB, the sum of bond valences, as well as the next-nearest-neighbor cations and hydrogen bonding. Also, these results provide new insights into the shielding mechanism for 11B in borate and borosilicate minerals. In particular, this study demonstrates that the small variation in 11B chemical shifts can still be used to probe the local structural environments and that the established correlations can be used to investigate the structural details in borates and amorphous materials.
Amberger, Brent K.; Esselman, Brian J.; Woods, R. Claude; McMahon, Robert J.; Stanton, John F.
2015-09-14
The millimeter-wave spectrum of hydrazoic acid (HN{sub 3}) was analyzed in the frequency region of 235-450 GHz. Transitions from a total of 14 isotopologues were observed and fit using the A-reduced or S-reduced Hamiltonian. Coupled-cluster calculations were performed to obtain a theoretical geometry, as well as rotation-vibration interaction corrections. These calculated vibration-rotation correction terms were applied to the experimental rotational constants to obtain mixed theoretical/experimental equilibrium rotational constants (A{sub e}, B{sub e}, and C{sub e}). These equilibrium rotational constants were then used to obtain an equilibrium (R{sub e}) structure using a least-squares fitting routine. The R{sub e} structural parameters are consistent with a previously published R{sub s} structure, largely falling within the uncertainty limits of that R{sub s} structure. The present R{sub e} geometric parameters of HN{sub 3} are determined with exceptionally high accuracy, as a consequence of the large number of isotopologues measured experimentally and the sophisticated (coupled-cluster theoretical treatment (CCSD(T))/ANO2) of the vibration-rotation interactions. The R{sub e} structure exhibits remarkable agreement with the CCSD(T)/cc-pCV5Z predicted structure, validating both the accuracy of the ab initio method and the claimed uncertainties of the theoretical/experimental structure determination.
Crystal structure of methane oxidation enzyme determined
Baum, R.
1994-01-10
A team of chemists has determined to 2.2-[angstrom] resolution the crystal structure of the hydroxylase protein of methane monooxygenase, the enzyme system responsible for the biological oxidation of methane. The hydroxylase, at a molecular weight of 251,000 daltons, if by far the largest component of methane monooxygenase. Although the crystal structure of the hydroxylase did not reveal any startling surprises about the enzyme-many features of the hydroxylase had been inferred previously from modeling and spectroscopic studies -- obtaining it is a significant achievement. For one thing, the crystal structure unambiguously confirms aspects of the enzyme structure that been at least somewhat speculative. The three-dimensional structure of the enzyme, the chemist say, also provides important insight into biological methane oxidation, including how methane, a relatively inert gas, might diffuse to and bind near the active site of the enzyme. The structure points to particular amino acid residues that are likely to participate in catalysis, and clarifies the structure of the dinuclear iron core of the enzyme.
NASA Astrophysics Data System (ADS)
Pamuk, Betül; Allen, Philip B.; Soler, Jose M.; Fernández-Serra, Marivi
2014-03-01
The contributions of nuclear zero point vibrations to the structures of liquid water and ice are not negligible. Recently, we have explained the source of an anomalous isotope shift in hexagonal ice, representing itself as an increase in the lattice volume when H is replaced by D, by calculating free energy within the quasiharmonic approximation, with ab initio density functional theory. In this work, we extend our studies to analyze the zero point effect in other ice-like structures under different densities: clathrate hydrates, LDL and HDL-like amorphous ices with different densities, and a highly dense ice phase, ice VIII. We show that there is a transition from anomalous isotope effect to normal isotope effect as the density increases. We also analyze nuclear zero point effects in liquid water using different vdW-DFs and make connections to this anomalous-normal isotope effect transition in ice. This work is supported by DOE Early Career Award No. DE-SC0003871.
NASA Astrophysics Data System (ADS)
Fathi, M. B.; Kanjouri, F.; Farhadi, G.
2015-07-01
Nitinol as a superelastic shape memory alloy (SMA) has been the focus of physical-chemical studies in recent decades in respect to functionality of biocompatibility in the body. Superelastic properties of nitinol are the direct results of the electronic structure of this material while dealing with the ab initio behavior of microstructure. In the present work, the elastic properties and electronic structure of B2-phase binary TiNi(1-x)Cux (x = 0, 0.25 and 0.75) shape memory alloys are discussed aiming at understanding of the physical properties underlying superelastic behavior. The calculations have been performed with the program package WIEN2K, in the framework of first-principle, all-electron density functional theory (DFT) within the scheme of the generalized gradient approximation (GGA). The optimized lattice parameters and independent elastic constants are obtained for use in the calculation of the bulk and shear moduli, Young modulus, Poisson ratio and Zener anisotropy parameter. For different alloying fractions x, the tetragonal (C‧) and trigonal (C44) shear constants are calculated and brittle/ductile behavior of these compounds is discussed. Finally, a qualitative discussion of dependence of elastic behavior of these compounds upon the electronic density of states (DOS) is presented.
Wang, Xue B.; Fu, Qiang; Yang, Jinlong
2010-09-02
Hydroxyl substituted phenoxide, o-, m-, p- HO(C6H4)O– and the corresponding neutral radicals are important species, in particularly, the p- isomer pair is directly involved in the proton-coupled electron transfer in biological photosynthetic centers. Here we report the first spectroscopic study of these species in the gas phase by means of low-temperature photoelectron spectroscopy (PES) and ab initio calculations. Vibrationally resolved PES spectra were obtained at 70 K and several photon energies for each anion, directly yielding electron affinity (EA) and electronic structure information of the corresponding hydroxyphenoxyl radical. The EAs are found to vary with OH positions, from 1.990 ± 0.010 eV (p-) to 2.315 ± 0.010 (o-) and 2.330 ± 0.010 (m-). Theoretical calculations were carried out to identify the optimized molecular structures for both anions and neutral radicals. The electron binding energies and excited state energies were also calculated to compare with experimental data. Excellent agreement is found between calculations and experiments. Molecular orbital analyses indicate strong OH anti-bonding interaction with the phenoxide moiety for o- as well as p- isomers, whereas such interaction is largely missing for the m- anion. The variance of EAs among three isomers is interpreted primarily due to the interplay between two competing factors: the OH anti-bonding interaction and H-bonding stabilization (existed only in the o- anion).
NASA Astrophysics Data System (ADS)
Hamioud, Farida; Alghamdi, Ghadah S.; Al-Omari, Saleh; Mubarak, A. A.
2016-03-01
We have performed ab initio investigation of some physical properties of the perovskite TlMnX3 (X = F, Cl) compounds using the full-potential linearized augmented plane wave (FP-LAPW) method. The generalized gradient approximation (GGA) is employed as exchange-correlation potential. The calculated lattice constant and bulk modulus agree with previous studies. Both compounds are found to be elastically stable. TlMnF3 and TlMnCl3 are classified as anisotropic and ductile compounds. The calculations of the band structure of the studied compounds showed the semiconductor behavior with the indirect (M-X) energy gap. Both compounds are classified as a ferromagnetic due to the integer value of the total magnetic moment of the compounds. The different optical spectra are calculated from the real and the imaginary parts of the dielectric function and connected to the electronic structure of the compounds. The static refractive index n(0) is inversely proportional to the energy bandgap of the two compounds. Beneficial optics technology applications are predicted based on the optical spectra.
Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S. E-mail: hochlaf@univ-mlv.fr; Linguerri, Roberto; Hochlaf, Majdi E-mail: hochlaf@univ-mlv.fr
2013-11-07
Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.
Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; Martínez, Todd J.; Gordon, Mark S.
2014-10-20
This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitation on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.
NASA Astrophysics Data System (ADS)
Tu, Qing; Lange, Björn; Lopes, J. Marcelo J.; Zauscher, Stefan; Blum, Volker
Contact resonance AFM is demonstrated as a powerful tool for mapping differences in the mechanical properties of 2D materials and heterostructures, permitting to resolve surface and subsurface structural differences of different domains. Measured contact resonance frequencies are related to the contact stiffness of the combined tip-sample system. Based on first principles predicted elastic properties and a continuum approach to model the mechanical impedance, we find contact stiffness ratios between different domains of few-layer graphene on 3C-SiC(111) in excellent agreement with experiment. We next demonstrate that the approach is able to quantitatively resolve differences between other 2D materials domains, e.g., for h-BN, MoS2 and MoO3 on graphene on SiC. We show that the combined effect of several materials parameters, especially the in-plane elastic properties and the layer thickness, determines the contact stiffness, therefore boosting the sensitivity even if the out-of-plane elastic properties are similar.
Membrane protein structure determination by electron crystallography
Ubarretxena-Belandia, Iban; Stokes, David L.
2012-01-01
During the past year, electron crystallography of membrane proteins has provided structural insights into the mechanism of several different transporters and into their interactions with lipid molecules within the bilayer. From a technical perspective there have been important advances in high-throughput screening of crystallization trials and in automated imaging of membrane crystals with the electron microscope. There have also been key developments in software, and in molecular replacement and phase extension methods designed to facilitate the process of structure determination. PMID:22572457
Choudhary, Ashu; Chandra, Amalendu
2016-02-17
The anisotropic structure and dynamics of the hydration shell of a benzene solute in liquid water have been investigated by means of ab initio molecular dynamics simulations using the BLYP (Becke-Lee-Yang-Parr) and dispersion corrected BLYP-D functionals. The main focus has been to look at the influence of π-hydrogen-bonding and hydrophobic interactions on the distance and angle resolved various structural and dynamic properties of solvation shell. The structure of hydration shell water molecules around benzene is found to be highly anisotropic as revealed by the radial distribution functions of different conical regions and joint radial/angular distribution functions. The benzene-water dimer potential energy curves are calculated for a variety of orientations of water along the axial and equatorial directions for both BLYP and BLYP-D functionals. The simulation results of the hydration shell structure of benzene, particularly the axial and equatorial benzene-water RDFs are discussed based on the differences in the benzene-water potential energies for different orientations and functionals. The inter-particle distance/angle correlations show an enhanced water structure in the solvation shell of benzene compared to that between the solvation shell and bulk and also between the bulk molecules. On average, a single πH-bond is found to be formed between water and benzene in the 45° axial conical region of the solvation shell. The πH-bonded water molecules are found to have faster translational dynamics and also found to follow a fast jump mechanism of reorientation to change their hydrogen bonded partners. The presence of π-hydrogen-bonded water makes the overall dynamics of the axial region faster than that of the equatorial region where the water molecules are hydrophobically solvated and hydrogen bonded to other water molecules. PMID:26847163
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.
Structural determinants of sigma receptor affinity
Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.
1987-12-01
The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.
Hura, Greg; Russo, Daniela; Glaeser, Robert M.; Head-Gordon,Teresa; Krack, Matthias; Parrinello, Michele
2003-03-01
We present high-quality X-ray scattering experiments on pure water taken over a temperature range of 2 to 77 C using a synchrotron beam line at the advanced light source (ALS) at Lawrence Berkeley National Laboratory. The ALS X-ray scattering intensities are qualitatively different in trend of maximum intensity over this temperature range compared to older X-ray experiments. While the common procedure is to report both the intensity curve and radial distribution function(s), the proper extraction of the real-space pair correlation functions from the experimental scattering is very difficult due to uncertainty introduced in the experimental corrections, the proper weighting of OO, OH, and HH contributions, and numerical problems of Fourier transforming truncated data in Q-space. Instead, we consider the direct calculation of X-ray scattering spectra using electron densities derived from density functional theory based on real-space configurations generated with classical water models. The simulation of the experimental intensity is therefore definitive for determining radial distribution functions over a smaller Q-range. We find that the TIP4P, TIP5P and polarizable TIP4P-Pol2 water models, with DFT-LDA densities, show very good agreement with the experimental intensities, and TIP4P-Pol2 in particular shows quantitative agreement over the full temperature range. The resulting radial distribution functions from TIP4P-Pol2 provide the current best benchmarks for real-space water structure over the biologically relevant temperature range studied here.
NASA Astrophysics Data System (ADS)
Pan, Yong; Guan, Weiming
2016-09-01
MoS3 has attracted considerable attention as potential hydrogen storage material due to the interaction between the hydrogen and unsaturated sulfur atoms. However, its structure and physical properties are unknown. By means of first-principles approach and Inorganic crystal structure Database (ISCD), we systematically investigated the structure, relevant physical and thermodynamic properties of MoS3. Phonon dispersion, electronic structure, band structure and heat capacity are calculated in detail. We predicted the orthorhombic B2ab (SrS3-type) and tetragonal P-421m (BaS3-type) structures of MoS3, which prefers to form the SrS3-type (Space group: B2ab, No.41) structure at the ground state. High pressure results in structural transition from SrS3-type structure to BaS3-type structure. This sulfide exhibits a degree of metallic behavior. The calculated heat capacity of MoS3 with SrS3-type structure is about of 39 J/(mol·K).
NASA Astrophysics Data System (ADS)
Demkov, Alexander A.; Navrotsky, Alexandra
2001-03-01
The International Technology Roadmap for Semiconductors (ITRS) predicts that the strategy of scaling complementary metal-oxide-semiconductor (CMOS) devices will come to an abrupt end around the year 2012. The main reason for this will be the unacceptably high leakage current through the silicon dioxide gate with a thickness below 20 ÅFinding a gate insulator alternative to SiO2 has proven to be far from trivial. Hafnium and zirconium dioxides and silicates have been recently considered as gate dielectrics with intermediate dielectric constants. Hafnia and ziconia are important ceramic materials as well, and their phase relations are rather well studied. There is also interest in hafnia as a constituent of ceramic waste forms for plutonium, based on its refractory nature and high neutron absorption cross section. We use a combination of the ab-initio calculations and calorimetry to investigate thermodynamic and electronic properties of hafnia and zirconia. We describe the cubic to tetragonal phase transition in the fluorite structure by computing the total energy surface for zone-edge distortions correct to fourth order in the soft-mode displacement with the strain coupling renormalization included. We compare the two materials using some simple chemical concepts.
NASA Astrophysics Data System (ADS)
Tian, T.; Wang, X. F.; Li, W.
2013-03-01
As high-temperature structural materials, L12 intermetallic compounds have attracted the strong interest from both fundamental and industrial aspects. Understanding of elastic property is a basis for the complete investigations of mechanical behavior of L12 alloys. In an effort to explore the electronic origin of elastic properties of L12 intermetallics, we have performed a systematic study on elastic constants for single crystals, and Young's modulus, shear modulus, bulk modulus and Poisson's ratio for poly-crystals of 22 known Al3X and X3Al-type (X=transition or main group metal) intermetallics using the ab initio calculations. Based on the calculations of elastic constants and extreme (both positive and negative) Poisson's ratios, we found a pronounced correlation between the extreme Poisson's ratio and the elastic anisotropy, i.e., approximate 40% of the investigated L12 intermetallics exhibit intrinsic auxetic behavior. Furthermore, based on the distribution of bonding charge densities, we revealed that the ductility and extreme Poisson's ratios were attributable to the directionality of bonds of these alloys. Our findings provide a new method to predict mechanical behavior of intermetallics.
NASA Astrophysics Data System (ADS)
Vincent, Mark A.; Hillier, Ian H.; Morgado, Claudio A.; Burton, Neil A.; Shan, Xiao
2008-01-01
We have investigated, using both ab initio and density functional theory methods, the minimum energy structures and corresponding binding energies of the van der Waals complexes between phenol and argon or the nitrogen molecule, and the corresponding complexes involving the phenol cation. Structures were obtained at the MP2 level using a large basis, and the corresponding energies were corrected for basis set superposition error (BSSE), higher order electron correlation effects, and for basis set size. The structures of the global minima were further refined for the effects of BSSE and the corresponding binding energies were evaluated. For each neutral species, we find only a single true minimum, π bonded for argon and OH bonded for nitrogen. For both cationic species, we find that the OH-bonded complex is preferred over other minima which we have identified as having Ar or N2 between exogeneous atoms. The ab initio calculations are generally in excellent agreement with experimental binding energies and rotational constants. We find that the B3LYP functional is particularly poor at describing these complexes, while a density functional theory (DFT) method with an empirical correction for dispersive interactions (DFT-D) is very successful, as are some of the new functionals proposed by Zhao and Truhlar [J. Phys. Chem. A 109, 5656 (2005); J. Chem. Theory Comput. 2, 1009 (2006); Phys. Chem. Chem. Phys. 7, 2701 (2005); J. Phys. Chem. A 108, 6908 (2004)]. Both the ab initio and DFT-D methods accurately predict the intermolecular vibrational modes.
Computational tools for experimental determination and theoretical prediction of protein structure
O`Donoghue, S.; Rost, B.
1995-12-31
This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. The authors intend to review the state of the art in the experimental determination of protein 3D structure (focus on nuclear magnetic resonance), and in the theoretical prediction of protein function and of protein structure in 1D, 2D and 3D from sequence. All the atomic resolution structures determined so far have been derived from either X-ray crystallography (the majority so far) or Nuclear Magnetic Resonance (NMR) Spectroscopy (becoming increasingly more important). The authors briefly describe the physical methods behind both of these techniques; the major computational methods involved will be covered in some detail. They highlight parallels and differences between the methods, and also the current limitations. Special emphasis will be given to techniques which have application to ab initio structure prediction. Large scale sequencing techniques increase the gap between the number of known proteins sequences and that of known protein structures. They describe the scope and principles of methods that contribute successfully to closing that gap. Emphasis will be given on the specification of adequate testing procedures to validate such methods.
Biomolecular Structure Determination with Divide and Concur
NASA Astrophysics Data System (ADS)
Kallus, Yoav; Elser, Veit
2009-03-01
Divide and concur (D-C) is a general computational approach, designed for the solution of highly frustrated problems. Recently applied to the problems of disk packing, the kissing number problem, and 3-SAT, it was competitive or outperformed special-purpose methods.ootnotetextS. Gravel and V. Elser, Phys. Rev. E 78, 036706 (2008) We present a method for applying the D-C framework to the problem of biomolecular structure determination. From a list of geometric constraints on groups of atoms in the molecule, we construct a deterministic iterative map that efficiently searches for structures simultaneously satisfying all constraints. As our method eschews an energy function and its minimization to focus on geometric constraints, it can very naturally integrate with the geometric constraints due to chemistry and physics, experimental constraints due to NMR data or many other experimental or biological hints. We present some results of our method.
Structural phase transition and 5f-electrons localization of PuSe explored by ab initio calculations
Cui Shouxin; Feng Wenxia; Hu Haiquan; Gong Zizheng; Liu Hong
2010-04-15
An investigation into the structural phase transformation, electronic and optical properties of PuSe under high pressure was conducted by using the full potential linearized augmented plane wave plus local orbitals (FP-LAPW+lo) method, in the presence and in the absence of spin-orbit coupling (SOC). Our results demonstrate that there exists a structural phase transition from rocksalt (B 1) structure to CsCl-type (B 2) structure at the transition pressure of 36.3 GPa (without SOC) and 51.3 GPa (with SOC). The electronic density of states (DOS) for PuSe show that the f-electrons of Pu are more localized and concentrated in a narrow peak near the Fermi level, which is consistent with the experimental studies. The band structure shows that B 1-PuSe is metallic. A pseudogap appears around the Fermi level of the total density of states of B 1 phase PuSe, which may contribute to its stability. The calculated reflectivity R(omega) shows agreement with the available experimental results. Furthermore, the absorption spectrum, refractive index, extinction coefficient, energy-loss spectrum and dielectric function were calculated. The origin of the spectral peaks was interpreted based on the electronic structures. - Abstract: Graphical Abstract Legend (TOC Figure): 5f-electrons are more localized by the analysis of the density of states (SOC). The origin spectra peaks was interpreted based on electronic structures.
Ab initio vibrational and dielectric properties of Y V O
NASA Astrophysics Data System (ADS)
Vali, R.
2009-10-01
For the yttrium orthovanadate Y V O with a tetragonal zircon-type structure, the first complete set of Raman-active and IR-active phonon modes has been calculated using ab initio density functional perturbation theory. The calculated IR reflectivity spectra are in good agreement with available experimental data. We report the calculated frequencies of three Raman-active modes that could not be detected experimentally and a new assignment of the experimental Raman data. The contributions of each IR-active phonon modes to static dielectric tensor have been determined.
NASA Astrophysics Data System (ADS)
Tsumuraya, Takao; Shishidou, Tatsuya; Oguchi, Tamio
2009-05-01
We study the electronic structure and vibrational modes of several amides M(NH2)n and alanates M(AlH4)n (M = K, Na, Li, Ca and Mg), focusing on the role of cation states. Calculated breathing stretching vibration modes for these compounds are compared with measured infrared and Raman spectra. In the amides, we find a significant tendency such that the breathing mode frequencies and the structural parameters of NH2 vary in accordance with the ionization energy of cation. The tendency may be explained by the strength in hybridization between cation orbitals and molecular orbitals of (NH2)-. The microscopic mechanism of correlations between the vibration frequencies and structural parameters is elucidated in relation to the electronic structure. A possible similar tendency in the alanates is also discussed.
Ab initio investigation of competing antiferromagnetic structures in low Si-content FeMn(PSi) alloy
NASA Astrophysics Data System (ADS)
Li, Guijiang; Eriksson, Olle; Johansson, Börje; Vitos, Levente
2016-06-01
The antiferromagnetic structures of a low Si-content FeMn(PSi) alloy were investigated by first principles calculations. One possible antiferromagnetic structure in supercell along the c-axis was revealed in FeMnP0.75Si0.25 alloy. It was found that atomic disorder occupation between Fe atom on 3f and Mn atoms on 3g sites is responsible for the formation of antiferromagnetic structures. Furthermore the magnetic competition and the coupling between possible AFM supercells along the c and a-axis can promote a non-collinear antiferromagnetic structure. These theoretical investigations help to deeply understand the magnetic order in FeMn(PSi) alloys and benefit to explore the potential magnetocaloric materials in Fe2P-type alloys.
Ab initio investigation of competing antiferromagnetic structures in low Si-content FeMn(PSi) alloy.
Li, Guijiang; Eriksson, Olle; Johansson, Börje; Vitos, Levente
2016-06-01
The antiferromagnetic structures of a low Si-content FeMn(PSi) alloy were investigated by first principles calculations. One possible antiferromagnetic structure in supercell along the c-axis was revealed in FeMnP0.75Si0.25 alloy. It was found that atomic disorder occupation between Fe atom on 3f and Mn atoms on 3g sites is responsible for the formation of antiferromagnetic structures. Furthermore the magnetic competition and the coupling between possible AFM supercells along the c and a-axis can promote a non-collinear antiferromagnetic structure. These theoretical investigations help to deeply understand the magnetic order in FeMn(PSi) alloys and benefit to explore the potential magnetocaloric materials in Fe2P-type alloys. PMID:27143642
Electronic structure, magnetism and stability of Co2CrX (X =Al, Ga, In) ab initio study
NASA Astrophysics Data System (ADS)
Dahmane, F.; Mesri, D.; Tadjer, A.; Khenata, R.; Benalia, S.; Djoudi, L.; Doumi, B.; Boumia, L.; Aourag, H.
2016-01-01
The structural, electronic as well as the magnetic properties of the Co2CrX (X =Al, Ga and In) full-Heusler alloy have been studied using first-principles calculations performed in the framework of density functional theory (DFT) within the generalized gradient approximation (GGA). It was taken into account both possible L21 structures (i.e. Hg2CuTi- and Cu2MnAl-type). Basically, for all compounds, the Cu2MnAl-type structure is energetically more stable than Hg2CuTi-type structure at the equilibrium volume. The electronic structure calculations for Co2CrAl reveal that half-metallic (HM) character in Cu2MnAl-type structure, Co2CrGa show nearly HM behavior and Co2CrIn has a metallic character. The predicted total magnetic moment is 3μB for Co2CrX (X =Al, Ga) which is in good convergence with the Slater-Pauling (SP) rule.
Sharma, Sheetal; Verma, A.S.; Jindal, V.K.
2014-05-01
Graphical abstract: - Highlights: • FP-LAPW method has been used to compute the solid state properties of AgGaX{sub 2} (X = S, Se, Te). • Electronic and optical properties reported with recently developed mBJ potential. • Thermal expansion, heat capacity, Debye temperature, entropy and Grüneisen parameter were evaluated. • Hardness was calculated for the first time at different temperature and pressure. - Abstract: We have performed ab initio calculations for the structural, electronic, optical, elastic and thermal properties of the silver gallium dichalcogenides (AgGaX{sub 2}: X = S, Se, Te). In this study, we have used the accurate full potential linearized augmented plane wave (FP-LAPW) method to find the equilibrium structural parameters and to compute the six elastic constants (C{sub 11}, C{sub 12}, C{sub 13}, C{sub 33}, C{sub 44} and C{sub 66}). We have reported electronic and optical properties with the recently developed density functional theory of Tran and Blaha, and this theory is used along with the Wu-Cohen generalized gradient approximation (WC-GGA) for the exchange-correlation potential. Furthermore, optical features such as dielectric functions, refractive indices, extinction coefficient, optical reflectivity, absorption coefficients and optical conductivities were calculated for photon energies up to 40 eV. The thermodynamical properties such as thermal expansion, heat capacity, debye temperature, entropy, Grüneisen parameter and bulk modulus were calculated employing the quasi-harmonic Debye model at different temperatures (0–900 K) and pressures (0–8 GPa) and the silent results were interpreted. Hardness of the materials was calculated for the first time at different temperatures and pressures.
Marquez, A.; Sanz, J.F. )
1992-12-02
Experimental and theoretical research on the electronic and geometric structure of transition-metal-carbenes and -alkylidenes is an active area in chemistry nowadays due to their potential activity in catalysis and in organic and organometallic synthesis. A theoretical investigation of the electronic structure of the high-valent, transition-metal, alkylidene-like complexes MoM[prime]H[sub 2] (M[prime] = C, Si, Ge, and Sn) is reported. Based on ab initio calculations carried out at the complete active space multiconfiguration self-consistent field (CASSCF) level, the molecular structure of the ground state and some low-lying excited states have been determined. For M[prime] = C, Si, and Ge, the ground state has C[sub 2v] symmetry (state [sup 5]B[sub 1]) and corresponds to pairing each electron of the M[prime]H[sub 2] triplet [sup 3]B[sub 1] with an electron of Mo ([sup 7]S). In the case of MoSnH[sub 2], the lowest state is bent (C[sub s] symmetry, state [sup 7]A[prime]), the out-of-plane angle being 68[degrees], and dissociates into SnH[sub 2] ([sup 1]A[sub 1]) + Mo ([sup 7]S). Dissociation energies, potential energy profiles for the dissociation, harmonic force constants in terms of internal symmetry coordinates, and vibrational frequencies are reported. The comparison of these properties with those of their pentacarbonylated homologous (CO)[sub 5]M[double bond]M[prime]H[sub 2] shows that the carbene-like (Fischer) type of complexation is stronger than the alkylidene-like one (Schrock). 28 refs., 4 figs., 6 tabs.
Liebschner, Dorothee; Brzezinski, Krzysztof; Dauter, Miroslawa; Dauter, Zbigniew; Nowak, Marta; Kur, Józef; Olszewski, Marcin
2012-12-01
The N-terminal domain of the PriB protein from the thermophilic bacterium T. tengcongensis (TtePriB) was expressed and its crystal structure has been solved at the atomic resolution of 1.09 Å by direct methods. PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded β-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel β-sheet. The structure of the N-terminal OB domain of T. tengcongensis shows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains, TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains of TtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains.
NASA Astrophysics Data System (ADS)
Ramanna, J.; Yedukondalu, N.; Ramesh Babu, K.; Vaitheeswaran, G.
2013-06-01
We report the structural, elastic, electronic, and optical properties of antiperovskite alkali metal oxyhalides Na3OCl, Na3OBr, and K3OBr using two different density functional methods within generalized gradient approximation (GGA). Plane wave pseudo potential (PW-PP) method has been used to calculate the ground state structural and elastic properties while the electronic structure and optical properties are calculated explicitly using full potential-linearized augmented plane wave (FP-LAPW) method. The calculated ground state properties of the investigated compounds agree quite well with the available experimental data. The predicted elastic constants using both PW-PP and FP-LAPW methods are in good accord with each other and show that the materials are mechanically stable. The low values of the elastic moduli indicate that these materials are soft in nature. The bulk properties such as shear moduli, Young's moduli, and Poisson's ratio are derived from the calculated elastic constants. Tran-Blaha modified Becke-Johnson (TB-mBJ) potential improves the band gaps over GGA and Engel-Vosko GGA. The computed TB-mBJ electronic band structure reveals that these materials are direct band gap insulators. The complex dielectric function of the metal oxyhalide compounds have been calculated and the observed prominent peaks are analyzed through the TB-mBJ electronic structures. By using the knowledge of complex dielectric function other important optical properties including absorption, reflectivity, refractive index and loss function have been obtained as a function of energy.
NASA Astrophysics Data System (ADS)
Benassi, R.; Bertarini, C.; Hilfert, L.; Kempter, G.; Kleinpeter, E.; Spindler, J.; Taddei, F.; Thomas, S.
2000-03-01
The structure of a number of 2- exo-methylene substituted quinazolines and benzodiazepines, respectively, 1, 3a, b, 4( X=-CN, -COOEt ) and their 2-cyanoimino substituted analogues 2, 3c, d( X=-CN, -SO 2C 6H 4-Me (p) was completely assigned by the whole arsenal of 1D and 2D NMR spectroscopic methods. The E/ Z isomerism at the exo-cyclic double bond was determined by both NMR spectroscopy and confirmed by ab initio quantum chemical calculations; the Z isomer is the preferred one, its amount proved dependent on steric hindrance. Due to the push-pull effect in this part of the molecules the restricted rotation about the partial C 2,C 11 and C 2,N 11 double bonds, could also be studied and the barrier to rotation measured by dynamic NMR spectroscopy. The free energies of activation of this dynamic process proved very similar along the compounds studied but being dependent on the polarity of the solvent. Quantum chemical calculations at the ab initio level were employed to prove the stereochemistry at the exo-cyclic partial double bonds of 1- 4, to calculate the barriers to rotation but also to discuss in detail both the ground and the transition state of the latter dynamic process in order to better understand electronic, inter- and intramolecular effects on the barrier to rotation which could be determined experimentally. In the cyanoimino substituted compounds 2, 3c, d, the MO ab initio calculations evidence the isomer interconversion to be better described by the internal rotation process than by the lateral shift mechanism.
Oscillation Laue Analysis (OLA) - A new crystal structure determination method for mineral physics
NASA Astrophysics Data System (ADS)
Dera, P.; Downs, R. T.; Liermann, H.; Yang, W.
2006-12-01
We present a new approach for collection and interpretation of polychromatic radiation diffraction images, called Oscillation Laue Analysis, which combines capabilities of single crystal X-ray diffraction and X-ray absorption spectroscopy. The method is based on smearing Laue reflections into variable-energy curves by slight oscillation of the crystal during the exposure. The OLA method allows for simple and precise peak energy determination and harmonic overlap deconvolution through measurement of X-ray attenuation coefficient of metal foils inserted into incident beam. The method provides an easy reliable way of determining unit cells of unknown single-crystal phases, yields multiple monochromatic structure factor sets covering wide range of energies, which can be used for Multiple Anomalous Dispersion (MAD) based structure solution or enhancement of contrast between neighboring elements in the periodic table, and allows the routine ab initio solution of unknown structures. The results of our first experiments, performed at sector 16 of the Advanced Photon Source Laboratory, and aimed at determination of the compression mechanism of escolite (Cr2O3) will be presented and discussed in the context of application of the new approach in micromineralogy, characterization of meteoritic samples, and high-pressure mineral physics.
Shi, Jingming; Cui, Wenwen; Flores-Livas, José A; San-Miguel, Alfonso; Botti, Silvana; Marques, Miguel A L
2016-03-01
Barium silicides are versatile materials that have attracted attention for a variety of applications in electronics and optoelectronics. Using an unbiased structural search based on a particle-swarm optimization algorithm combined with density functional theory calculations, we investigate systematically the ground-state phase stability and the structural diversity of Ba-Si binaries under high pressure. The phase diagram turns out to be quite intricate, with several compositions stabilizing/destabilizing as a function of pressure. In particular, we identify novel phases of BaSi, BaSi2, BaSi3, and BaSi5 that might be synthesizable experimentally over a wide range of pressures. Our results not only clarify and complete the previously known structural phase diagram, but also provide new insights for understanding the Ba-Si binary system. PMID:26923068
NASA Astrophysics Data System (ADS)
Kürkçü, Cihan; Merdan, Ziya; Öztürk, Hülya
2016-04-01
The crystal structure of CoF2 was studied theoretically using first-principles density functional theory (DFT) methods within the generalized gradient approximation (GGA) and local density approximation (LDA) under rapid hydrostatic pressure up to 144 GPa. CoF2 undergoes a structural phase transformation from the rutile-type tetragonal parent phase with space group P42/mnm to the CaCl2-type orthorhombic parent phase with space group Pnnm at 64 GPa with GGA and at 96 GPa with LDA methods. Another phase transformation occurs from the CaCl2-type structure to monoclinic parent phase with space group P21/c at 96 GPa with a GGA method. These phase transitions are also studied by enthalpy and total energy calculations. According to these calculations, we obtained the first phase transformation at about 6.5 GPa both GGA and LDA methods and the later phase transformation at about 45 GPa with the GGA method.
Exploiting Microbeams for Membrane Protein Structure Determination.
Warren, Anna J; Axford, Danny; Paterson, Neil G; Owen, Robin L
2016-01-01
A reproducible, and sample independent means of predictably obtaining large, well-ordered crystals has proven elusive in macromolecular crystallography. In the structure determination pipeline, crystallisation often proves to be a rate-limiting step, and the process of obtaining even small or badly ordered crystals can prove time-consuming and laborious. This is particularly true in the field of membrane protein crystallography and this is reflected in the limited number of unique membrane protein structures deposited in the protein data bank (less than 650 by June 2016 - http://blanco.biomol.uci.edu/mpstruc ). Over recent years the requirement for, and time and cost associated with obtaining, large crystals has been partially alleviated through the development of beamline instrumentation allowing data collection, and structure solution, from ever-smaller crystals. Advances in several areas have led to a step change in what might be considered achievable during a synchrotron trip over the last decade. This chapter will briefly review the current status of the field, the tools available to ease data collection and processing, and give some examples of exploitation of these for membrane protein microfocus macromolecular crystallography. PMID:27553238
NASA Astrophysics Data System (ADS)
Caetano, C.; Pela, R. R.; Martini, S.; Marques, M.; Teles, L. K.
2016-05-01
First-principles calculations and statistical methods were combined to study electronic, magnetic, thermodynamic and structural properties of zincblende (III,Mn)V and (III,Cr)V magnetic semiconductor alloys, including both nitride and arsenide alloys. From phase diagrams it was observed that nitride alloys are much less stable than arsenide ones, although the former ones have more localized d-states at the Fermi level. It was observed that all alloys present an anisotropic behavior, with the strongest magnetic interaction in the < 110 > direction. The relationship between the structural properties of these alloys and their electronic and magnetic characteristics (i.e., their half-metallicity) was investigated.
Structural and magnetic properties of MnPd/Fe grown on MgO(100) substrate: Ab initio studies
NASA Astrophysics Data System (ADS)
Malonda-Boungou, B. R.; Magnoungou, J. H. J.; M'Passi-Mabiala, B.; Demangeat, C.
2016-07-01
Structural and magnetic properties of ultrathin films MnPd/Fe grown on MgO(001) are investigated using a self-consistent pseudopotential plane waves method based on density functional theory in the Perdew-Burke-Ernzerhof generalized gradient approximation. The results obtained reveal the presence of an antiferromagnetic coupling between successive Mn [100] rows, combined with a ripple where Mn outward atoms exhibit a positive magnetic moment, in the case of Mn overlayer on Fe/MgO(001). In the case of MnPd monolayer ordered alloy, the c(2 × 2) structure formation is more favorable than the p(1 × 2) one, exhibiting a ferromagnetic coupling between Mn neighbor atoms with a positive induced ferromagnetic moment on Pd atoms. Pd atoms are pushed outward. For 1-ML MnxPd1 - x on Fe/MgO, the Mn absolute mean magnetization per atom increases as x coverage increases, whereas the Pd mean induced magnetic moment decreases. For systems alternating Mn and Pd monolayers on Fe/MgO(001), a complex magnetic structure is shown on Mn monolayers: changing from Mn neighboring antiferromagnetic coupling to Mn [010] rows antiferromagnetic behavior. The correlation is made between the electronic structure and the magnetic properties, by comparing filled with partially filled components (Pd, Mn and Fe) d-bands. The magnetization easy-axis changes between the in-plane and the out-of-plane orientations from Fe/MgO to MnPd/Fe/MgO systems.
Structural Determinants of Misfolding in Multidomain Proteins
Tian, Pengfei; Best, Robert B.
2016-01-01
Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669
Proton assisted recoupling and protein structure determination
De Paëpe, Gaël; Lewandowski, Józef R.; Loquet, Antoine; Böckmann, Anja; Griffin, Robert G.
2008-01-01
We introduce a homonuclear version of third spin assisted recoupling, a second-order mechanism that can be used for polarization transfer between 13C or 15N spins in magic angle spinning (MAS) NMR experiments, particularly at high spinning frequencies employed in contemporary high field MAS experiments. The resulting sequence, which we refer to as proton assisted recoupling (PAR), relies on a cross-term between 1H–13C (or 1H–15N) couplings to mediate zero quantum 13C–13C (or 15N–15N recoupling). In particular, using average Hamiltonian theory we derive an effective Hamiltonian for PAR and show that the transfer is mediated by trilinear terms of the form C1±C2∓HZ for 13C–13C recoupling experiments (or N1±N2∓HZ for 15N–15N). We use analytical and numerical simulations to explain the structure of the PAR optimization maps and to delineate the PAR matching conditions. We also detail the PAR polarization transfer dependence with respect to the local molecular geometry and explain the observed reduction in dipolar truncation. Finally, we demonstrate the utility of PAR in structural studies of proteins with 13C–13C spectra of uniformly 13C, 15N labeled microcrystalline Crh, a 85 amino acid model protein that forms a domain swapped dimer (MW=2×10.4 kDa). The spectra, which were acquired at high MAS frequencies (ωr2π>20 kHz) and magnetic fields (750–900 MHz 1H frequencies) using moderate rf fields, exhibit numerous cross peaks corresponding to long (up to 6–7 Å) 13C–13C distances which are particularly useful in protein structure determination. Using results from PAR spectra we calculate the structure of the Crh protein. PMID:19123534
Proton assisted recoupling and protein structure determination
NASA Astrophysics Data System (ADS)
de Paëpe, Gaël; Lewandowski, Józef R.; Loquet, Antoine; Böckmann, Anja; Griffin, Robert G.
2008-12-01
We introduce a homonuclear version of third spin assisted recoupling, a second-order mechanism that can be used for polarization transfer between 13C or 15N spins in magic angle spinning (MAS) NMR experiments, particularly at high spinning frequencies employed in contemporary high field MAS experiments. The resulting sequence, which we refer to as proton assisted recoupling (PAR), relies on a cross-term between 1H-13C (or 1H-15N) couplings to mediate zero quantum 13C-13C (or 15N-15N recoupling). In particular, using average Hamiltonian theory we derive an effective Hamiltonian for PAR and show that the transfer is mediated by trilinear terms of the form C1+/-C2-/+HZ for 13C-13C recoupling experiments (or N1+/-N2-/+HZ for 15N-15N). We use analytical and numerical simulations to explain the structure of the PAR optimization maps and to delineate the PAR matching conditions. We also detail the PAR polarization transfer dependence with respect to the local molecular geometry and explain the observed reduction in dipolar truncation. Finally, we demonstrate the utility of PAR in structural studies of proteins with 13C-13C spectra of uniformly 13C, 15N labeled microcrystalline Crh, a 85 amino acid model protein that forms a domain swapped dimer (MW=2×10.4 kDa). The spectra, which were acquired at high MAS frequencies (ωr2π>20 kHz) and magnetic fields (750-900 MHz 1H frequencies) using moderate rf fields, exhibit numerous cross peaks corresponding to long (up to 6-7 A˚) 13C-13C distances which are particularly useful in protein structure determination. Using results from PAR spectra we calculate the structure of the Crh protein.
Structural Determinants of Misfolding in Multidomain Proteins.
Tian, Pengfei; Best, Robert B
2016-05-01
Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins. PMID:27163669
Ab Initio Studies of Calcium Carbonate Hydration.
Lopez-Berganza, Josue A; Diao, Yijue; Pamidighantam, Sudhakar; Espinosa-Marzal, Rosa M
2015-11-25
Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance. PMID:26505205
NASA Astrophysics Data System (ADS)
Craco, L.; Laad, M. S.; Müller-Hartmann, E.
2003-12-01
Motivated by a study of various experiments describing the electronic and magnetic properties of the diluted magnetic semiconductor Ga1-xMnxAs, we investigate its physical response in detail using a combination of first-principles band structure with methods based on dynamical mean field theory to incorporate strong, dynamical correlations, and intrinsic as well as extrinsic disorder in one single theoretical picture. We show how ferromagnetism is driven by double exchange (DE), in agreement with very recent observations, along with a good quantitative description of the details of the electronic structure, as probed by scanning tunneling microscopy and optical conductivity. Our results show how ferromagnetism can be driven by DE even in diluted magnetic semiconductors with small carrier concentration.
NASA Astrophysics Data System (ADS)
Prasetyo, Niko; Armunanto, Ria
2016-05-01
Structures and dynamics of Ag+ in 18.6% aqueous ammonia have been studied using Quantum Mechanical Charge Field Molecular Dynamics (QMCF-MD) simulation at the Hartree-Fock (HF) level theory employing LANL2DZ ECP basis set for Ag+ and Dunning DZP for solvent molecules. Structural properties are in excellent agreement with previous QM/MM and experiments studies. [Ag(NH3)2(H2O)3]+ was found as dominant species during simulation time. For 20 ps of simulation time, a labile first solvation shell was observed with both fast ammonia and water ligands exchanges. QMCF-MD framework describes first solvation shell more labile than conventional QM/MM MD simulation.
NASA Astrophysics Data System (ADS)
Jadidi, Khosrow; Khaligh, Nader Ghaffari; Islami, Parisa; Aryan, Reza; Arvin-Nezhad, Hamid
2009-02-01
A detailed study of structural parameters and internal rotational barriers in α-stannyl, germanium and silicon carbamates 1 [H 3 CX-CH 2-N(Me)CO 2Me X dbnd C, Si, Ge, Sn] were calculated at HF/6-311G, HF/3-21G and B3LYP/3-21G//HF/3-21G levels and compared with DNMR data of synthesized molecules and a literature X-ray data. Two minimum-energy conformers, namely A and B, with almost similar energies were found for these molecules. Effect of heteroatom on structure and relative energies ( Erel) between the participants in the conformational equilibrium (A ↔ B) of these carbamates has been investigated.
McClendon, Christopher L.; Huang, Lily Jun-shen; Huang, Niu
2013-01-01
The Janus Kinase 2 (JAK2) plays essential roles in transmitting signals from multiple cytokine receptors, and constitutive activation of JAK2 results in hematopoietic disorders and oncogenesis. JAK2 kinase activity is negatively regulated by its pseudokinase domain (JH2), where the gain-of-function mutation V617F that causes myeloproliferative neoplasms resides. In the absence of a crystal structure of full-length JAK2, how JH2 inhibits the kinase domain (JH1), and how V617F hyperactivates JAK2 remain elusive. We modeled the JAK2 JH1–JH2 complex structure using a novel informatics-guided protein-protein docking strategy. A detailed JAK2 JH2-mediated auto-inhibition mechanism is proposed, where JH2 traps the activation loop of JH1 in an inactive conformation and blocks the movement of kinase αC helix through critical hydrophobic contacts and extensive electrostatic interactions. These stabilizing interactions are less favorable in JAK2-V617F. Notably, several predicted binding interfacial residues in JH2 were confirmed to hyperactivate JAK2 kinase activity in site-directed mutagenesis and BaF3/EpoR cell transformation studies. Although there may exist other JH2-mediated mechanisms to control JH1, our JH1–JH2 structural model represents a verifiable working hypothesis for further experimental studies to elucidate the role of JH2 in regulating JAK2 in both normal and pathological settings. PMID:23592968
NASA Astrophysics Data System (ADS)
Lantsuzskaya (Krisilova), E. V.; Krisilov, A. V.; Levina, A. M.
2015-09-01
Ion-mobility spectra of a set of aliphatic linear aldehydes with the number of carbon atoms from 3 to 7 are obtained. Values of the mobility corresponding to two most intense peaks, considered to be those of a monomer and dimer, are determined according the spectra. Based on mobility, collision cross sections are calculated using the Mason-Schamp equation. The linear increase in the collision cross sections upon an increase in molecular weight is determined. According to the experimental results, the contribution to the cross section that has no dependence on molecular weight diminishes with the formation of dimers. It is established using quantum chemical calculations that this is associated with a reduction in the dipole moment upon the formation of dimers.
Granular structure determined by terahertz scattering
NASA Astrophysics Data System (ADS)
Born, Philip; Rothbart, Nick; Sperl, Matthias; Hübers, Heinz-Wilhelm
2014-05-01
Light scattering from particles reveals static and dynamical information about the particles and their correlations. Such methods are particularly powerful when the wavelength of the light is chosen similar to the sizes and distances of the particles. To apply scattering to investigate granular matter in particular —or other objects of similar submillimeter size— light of suitable wavelength in the terahertz regime needs to be chosen. By using a quantum cascade laser in a benchtop setup we determine the angle-dependent scattering of spherical particles as well as coffee powder and sugar grains. The scattering from single particles can be interpreted by form factors derived within the Mie theory. In addition, collective correlations can be extracted as static structure factors and compared to recent computer simulations.
CVRQD ab initio ground-state adiabatic potential energy surfaces for the water molecule.
Barletta, Paolo; Shirin, Sergei V; Zobov, Nikolai F; Polyansky, Oleg L; Tennyson, Jonathan; Valeev, Edward F; Császár, Attila G
2006-11-28
The high accuracy ab initio adiabatic potential energy surfaces (PESs) of the ground electronic state of the water molecule, determined originally by Polyansky et al. [Science 299, 539 (2003)] and called CVRQD, are extended and carefully characterized and analyzed. The CVRQD potential energy surfaces are obtained from extrapolation to the complete basis set of nearly full configuration interaction valence-only electronic structure computations, augmented by core, relativistic, quantum electrodynamics, and diagonal Born-Oppenheimer corrections. We also report ab initio calculations of several quantities characterizing the CVRQD PESs, including equilibrium and vibrationally averaged (0 K) structures, harmonic and anharmonic force fields, harmonic vibrational frequencies, vibrational fundamentals, and zero-point energies. They can be considered as the best ab initio estimates of these quantities available today. Results of first-principles computations on the rovibrational energy levels of several isotopologues of the water molecule are also presented, based on the CVRQD PESs and the use of variational nuclear motion calculations employing an exact kinetic energy operator given in orthogonal internal coordinates. The variational nuclear motion calculations also include a simplified treatment of nonadiabatic effects. This sophisticated procedure to compute rovibrational energy levels reproduces all the known rovibrational levels of the water isotopologues considered, H(2) (16)O, H(2) (17)O, H(2) (18)O, and D(2) (16)O, to better than 1 cm(-1) on average. Finally, prospects for further improvement of the ground-state adiabatic ab initio PESs of water are discussed. PMID:17144700
Atta-Fynn, Raymond; Johnson, Donald F.; Bylaska, Eric J.; Ilton, Eugene S.; Schenter, Gregory K.; De Jong, Wibe A.
2012-03-05
Ab initio molecular dynamics simulations at 300 K based on density functional theory have been used to study the hydration shell geometries, solvent dipole, and first hydrolysis of the Uranium(IV) (U{sup 4+}) and Uranyl(V) (UO{sub 2}{sup +}) ions in aqueous solution. The solvent dipole and first of hydrolysis of aqueous Uranium(VI) (UO{sub 2}{sup 2+}) has also been probed. The first shell of U{sup 4+} is coordinated by 8-9 water ligands with an average U-O distance of 2.42 {angstrom}. The average first shell coordination number and distance are in agreement with experimental estimates of 8-11 and 2.40-2.44 {angstrom} respectively. The simulated EXAFS spectra of U{sup 4+} matched well with recent experimental data. The first shell of UO{sub 2}{sup +} is coordinated by 5 water ligands in the equatorial plane, with the average U=O{sub ax} and U-O distances being 1.85 {angstrom} and 2.54 {angstrom} respectively. Overall, the hydration shell structure of UO{sub 2}{sup +} matches closely with that of UO{sub 2}{sup 2+} except for small expansions in the average U=O{sub ax} and U-O distances. Each ion strongly polarizes their respective first shell water ligands. The computed acidity constant (pK{sub a}) of U{sup 4+} and UO{sub 2}{sup 2+} are 0.93 and 4.95, in good agreement with the experimental values of 0.54 and 5.24 respectively. The predicted pK{sub a} of UO{sub 2}{sup +} is 8.5.
NASA Astrophysics Data System (ADS)
Boilleau, Corentin; Suaud, Nicolas; Guihéry, Nathalie
2012-12-01
In spin-crossover (SCO) compounds exhibiting a light induced excited spin state trapping (LIESST) effect, the thermodynamic T1/2 and kinetic T(LIESST) temperature values depend on the features of the potential energy surfaces (PES) of the two lowest singlet and quintet states but also on vibrational contributions, collective effects, such as electrostatics, for instance, spin-orbit couplings to a lesser extent, etc. In this work, the question of the link between the shape of the PES of SCO compounds exhibiting a LIESST effect and their first coordination sphere structure is addressed from wave function theory based ab initio calculations. Fe(II) complexes based on model ligands suited to reproduce the main characteristics of the PES of such compounds are distorted to emphasize selectively the role played by the metal-ligand distances and the ligand-metal-ligand angles. The studied angular deformations are those usually observed in many Fe(L)2(NCS)2 complexes. It is shown that the larger the deformation between the low spin and high spin equilibrium geometries, the higher the energy barrier from the high spin state and the weaker the energy difference between the bottom of the wells. These results corroborate observations made by experimentalists on a large number of complexes. While the PES features only constitutes one of the contributions to these temperatures, it is worth noticing that, relating T1/2 to the energy difference between the bottoms of the singlet and quintet wells and the T(LIESST) to the energy barrier from the quintet bottom well, the same slope of the empirical law T(LIESST) = -0.3T1/2+T0 is observed.
An ab initio investigation into the elastic, structural and electronic properties of MoS2 nanotubes
NASA Astrophysics Data System (ADS)
Ansari, R.; Malakpour, S.; Faghihnasiri, M.; Sahmani, S.
2015-06-01
Molybdenum disulfide (MoS2) is a unique semiconductor with a honeycomb structure like graphite, which has the ability to form various nanostructures with distinct characteristics. In the present study, the elastic, structural and electronic properties of armchair and zigzag MoS2 nanotubes with different diameters are investigated using the density functional theory (DFT). The DFT calculations are performed within the framework of generalized gradient approximation and using the Perdew-Burke-Ernzerhof (PBE) exchange model. It is demonstrated that for all of the considered MoS2 nanotubes anharmonicity exists, except for (6,6) MoS2 nanotube. Moreover, it is found that by increasing the tube diameter, Young's modulus of both armchair and zigzag MoS2 nanotubes increases. Also, it is observed that all of armchair MoS2 nanotubes are indirect band gap-type. On the other hand, all of zigzag MoS2 nanotubes have band gaps with the type of direct in Γ point.
NASA Astrophysics Data System (ADS)
Mallia, Giuseppe; Dovesi, Roberto; Corà, Furio
2006-10-01
The effects of an electric field on the electronic properties of a typical ionic-covalent compound, Anhydrite (CaSO4), are investigated within the HF level of theory and two different formulations of hybrid DFT functionals (B3LYP [A. Becke, J. Chem. Phys. 98, 5648 (1993)] and F 0.6-BLYP [F. Corà et al., Structure and Bonding 113, 171-232 (2004)]). An external electric field is applied along each of the three periodic lattice vectors of the orthorhombic and hexagonal structures in order to detect the anisotropy of the response. The perturbation introduced by the field is analysed in terms of Mulliken charges and electron density maps. The largest response is due to a polarisation of the covalent SO bonds of the sulfate ions. The high frequency dielectric tensor, , is computed and compared with the experimental value; its anisotropy can be rationalised by the orientation of the sulfate ions relative to the three crystallographic directions. We find that the calculated value of decreases on increasing the percentage of HF exchange in the Hamiltonian; the best match with experiment is given by B3LYP, but a higher percentage of HF exchange is required to reproduce the anisotropy in , a feature that we attribute to the better representation of the equilibrium geometry and bond distances in the latter case.
NASA Astrophysics Data System (ADS)
Benlamari, S.; Amara Korba, S.; Lakel, S.; Meradji, H.; Ghemid, S.; El Haj Hassan, F.
2016-01-01
The structural, elastic, thermal and electronic properties of perovskite hydrides SrLiH3 and SrPdH3 have been investigated using the all-electron full-potential linear augmented plane wave (FP-LAPW) method based on the density functional theory (DFT). For the exchange-correlation potential, local-density approximation (LDA) and generalized gradient approximation (GGA) have been used to calculate theoretical lattice parameters, bulk modulus, and its pressure derivative. The present results are in good agreement with available theoretical and experimental data. The three independent elastic constants (C11, C12 and C44) are also reported. From electronic band structure and density of states (DOSs), it is found that SrLiH3 is an insulator characterized by an indirect gap of 3.48 eV, while SrPdH3 is metallic with a calculated DOSs at Fermi energy of 0.745 states/eV-unit cell. Poisson’s ratio (σ), Young’s modulus (E), shear modulus (G), anisotropy factor (A), average sound velocities (vm) and density (ρ) of these compounds are also estimated for the first time. The Debye temperature is deduced from the average sound velocity. Variation of elastic constants and bulk modulus of these compounds as a function of pressure is also reported. Pressure and thermal effects on some macroscopic properties are predicted using the quasi-harmonic Debye model.
Implications of a New Ab-Initio H-He Equation of State for Giant Planet Structure (Invited)
NASA Astrophysics Data System (ADS)
Hubbard, W. B.
2013-12-01
I report results from a continuing study of the structure and evolution of hydrogen-dominated giant planets with masses of ~ 100 to 600 Earth masses (collaboration with B. Militzer and J. Fortney). Our initial study is of the radii and cooling history of giant planets in this mass range, assuming simplified isentropic structures and constant hydrogen-helium mixing ratio; no heavier elements are included. Unlike in previous studies, our equation of state is thermodynamically consistent, tied to an absolute entropy scale, and based on a full density-functional molecular-dynamics simulation of a strongly interacting hydrogen-helium fluid. We reference our suite of models to an equivalent suite calculated using the widely-used equation of state of Saumon, Chabrier, and Van Horn (1995, ApJ. Suppl. 99:713; SCVH). Our models cover an entropy range from 7 Boltzmann constants per electron (similar to the entropy in the atmospheres of Jupiter and Saturn) up to about 12 Boltzmann constants per electron (comparable to the entropy in the atmospheres of the hottest giant exoplanets), thus permitting a general treatment of cooling models for giant planets. To infer giant-planet "metallicity" (astrophysical term for the object's fractional content of elements heavier than H-He), particularly for exoplanets, one relies on measurement of the giant planet's mean radius, which decreases as the metallicity rises. However the mean radius depends not only on metallicity, but also on the object's mean entropy, its rotation, and on uncertainties in the equation of state. For H-He objects in the mass range we have studied, all of these effects can increase or decrease the mean radius by up to a few tenths of a Jupiter radius (R_J). Importantly, the new equation of state causes low-entropy giant-planets such as Jupiter and Saturn to shrink in comparison to SCVH models by up to 0.08 R_J. Thus one might infer that Jupiter and Saturn are of lower metallicity than SCVH models would imply, unless
NASA Astrophysics Data System (ADS)
Behzad, Somayeh
2016-09-01
Monolayer α-graphyne is a new two-dimensional carbon allotrope with many special features. In this work the electronic properties of AA- and AB-stacked bilayers of this material and then the optical properties are studied, using first principle plane wave method. The electronic spectrum has two Dirac cones for AA stacked bilayer α-graphyne. For AB-stacked bilayer, the interlayer interaction changes the linear bands into parabolic bands. The optical spectra of the most stable AB-stacked bilayer closely resemble to that of the monolayer, except for small shifts of peak positions and increasing of their intensity. For AB-stacked bilayer, a pronounced peak has been found at low energies under the perpendicular polarization. This peak can be clearly ascribed to the transitions at the Dirac point as a result of the small degeneracy lift in the band structure.
DFT and ab initio study of structure of dyes derived from 2-hydroxy and 2,4-dihydroxy benzoic acids
NASA Astrophysics Data System (ADS)
Dabbagh, Hossein A.; Teimouri, Abbas; Najafi Chermahini, Alireza; Shahraki, Maryam
2008-02-01
We present a detailed analysis of the structural, infrared spectra and visible spectra of a series of azo dyes preparation of salicylic acid and 2,4-dihydroxy benzoic acid derivatives as the coupling component. The preparation of these azo dyes with salicylic acid and 2,4-dihydroxy benzoic acid derivatives (salicylic acid, methyl salicylate, ethyl salicylate, butyl salicylate, methyl 2,4-dihydroxy benzoate, ethyl 2,4-dihydroxy benzoate, salicylaldehyde, salicylamide, 2,4-dihydroxy benzamide, salicylaldoxime) have been investigated theoretically by performing HF and DFT levels of theory using the standard 6-31G* basis set. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from solid phase FT-IR spectra are assigned modes based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with the calculations.
Atomic and electronic structure of hydrogen on ZnO (1bar 100) surface: ab initio hybrid calculations
NASA Astrophysics Data System (ADS)
Usseinov, A. B.; Kotomin, E. A.; Zhukovskii, Yu F.; Purans, J.; Sorokin, A. V.; Akilbekov, A. T.
2013-12-01
Hydrogen atoms unavoidably incorporated into ZnO during growth of bulk samples and thin films considerably affect their electrical conductivity. The results of first principles hybrid LCAO calculations are discussed for hydrogen atoms in the bulk and on the non-polar ZnO (1bar 100) surface. The incorporation energy, the atomic relaxation, the electronic density redistribution and the electronic structure modifications are compared for the surface adsorption and bulk interstitial H positions. It is shown that hydrogen has a strong binding with the surface O ions (2.7 eV) whereas its incorporation into bulk is energetically unfavorable. Surface hydrogen atoms are very shallow donors, thus, contributing to the electronic conductivity.
NASA Astrophysics Data System (ADS)
Bureau, Christophe; Deniau, Guy; Valin, Françoise; Guittet, Marie-Joseph; Lécayon, Gérard; Delhalle, Joseph
1996-06-01
The aim of the present paper is to contribute to the elucidation of the molecular structures obtained on a platinum surface as this surface is submitted to an anodic potential (with respect to a silver reference electrode) when dipped into pure 2-methyl 2-propenenitrile (methacrylonitrile). Modified surfaces are examined using X- and UV-photoelectron spectroscopies (UPS and XPS). The results evidence the formation of an ultra-thin (20-40 Å) grafted oligomer film, which is not classical polymethacrylonitrile (PMAN), as obtained through a radical or anionic mechanism: spectral characteristics argue in the sense of a cationic polymerization of methacrylonitrile through its nitrile groups, as evidenced by a lowering of the gap as well as by the UPS and XPS (N 1s region) spectra. Molecular models of the reactants and reaction intermediates are proposed for the cationic polymerization of methacrylonitrile, and show that this polymerization is about as feasible as that of acetonitrile, at least on kinetic control grounds. Two different mechanisms are nonetheless possible, leading either to a quasi conjugated poly-imine type -(N C) n-, or to a poly-cumulene type -(N C C) n- network. Theoretical consierations on reactants properties lead us to select the poly-imine way as the most plausible. Along with literature data concerning chemisorbed nitriles on platinum surfaces, a molecular model of the final state of the poly-imine reaction is then designed, comprising a three atom cluster to render the grafting site, and a dimer to render the grafted structure. A full geometry optimization is performed on the organic moiety at the Hartree-Fock (ab initio) level of theory, and a rough evaluation of the spectral footprint of the interface bond in the N 1s region is performed on the basis of Koopmans theorem with calibration on the bulk polymer peak. A preliminary 2.7 eV downward shift is predicted for N 1s interface nitrogens with respect to the polymer peak, which can
Structural Determinants of Individual Behavior in Organizations
ERIC Educational Resources Information Center
Rice, Linda E.; Mitchell, Terence R.
1973-01-01
A new conceptual view of organizational structure is presented, which integrates the two implicit views of structure found in the literature. In addition, some unique measures of a person's position in the organizational structure are shown. (Author)
Ab initio molecular-orbital study of structures and energetics of Si3H3 neutral and anion
NASA Astrophysics Data System (ADS)
Saitoh, Toshiaki; Naoe, Toshimasa; Ikuta, Shigeru
2005-05-01
The geometric structures and isomeric stabilities of various stationary points in Si3H3 neutral and its anion are investigated at the coupled-cluster singles, doubles (triples) [CCSD(T)] level of theory. For geometrical surveys, the basis sets used are of the Dunning's correlation consistent basis sets of triple-zeta quality for the neutral. To the anions, the Dunning's correlation consistent basis sets of double-zeta quality with diffuse functions are applied. For the three lower-lying anion isomers, the Dunning's correlation consistent basis sets of triple-zeta quality with diffuse functions (aug-cc-pVTZ) are also used. The final energies for the optimized stationary points are calculated at the CCSD(T) level of theory with the aug-cc-pVTZ basis sets. The basis sets of 6-311++G(3df,2pd) were also used for the lower-lying anion isomers. The Gaussian-2 method was performed only for the lower-lying anion isomers to clarify the relative stabilities. The global minimum neutral 1 (C1:A2) has an unsymmetrical hydrogen-bridged bond; the conformer 2 in Cs symmetry is a saddle point connecting the two equivalent isomers 1. Two lower-lying isomers (3 and 4) are also predicted within the energy range of 20kJ/mol. In the anion, however, the conformer 4 (Cs:A'1) with five formal valence electrons is a global minimum. Two more isomers (2 and 3) lie within 20kJ/mol as in the neutral; the conformer 1 converts to the isomer 2. The quartets for the neutrals and diradical triplets for the anions were further studied; lower-lying quartets and triplets, competing with the corresponding doublet and singlet, respectively, were not found in the present systems. The vertical and adiabatic electron affinities of the global minimum neutral 1, producing the second lowest-lying anion isomer 2, amount to 2.18 and 2.35 eV, respectively, at the CCSD(T)/aug-cc-pVTZ level of theory. The electron addition to the third lowest-lying neutral isomer 4 produces the largest vertical electron affinities
NASA Astrophysics Data System (ADS)
Nayak, Vikas; Verma, Udai Pratap
2016-06-01
The structural stability, electronic and optical properties of BeH2 under high pressure have been studied using the density functional theory (DFT) employing full potential-linearized augmented plane wave (FP-LAPW) method. The exchange correlation functional has been solved using the generalized gradient approximation. The calculations show that BeH2 becomes unstable upon application of pressure. At a pressure of 29.40 GPa the ground state α-BeH2 transforms to hypothetical phase β-BeH2 and further at a pressure of 53.77 GPa (with respect to the ground state α-BeH2) β-BeH2 transforms to γ-BeH2. In α-BeH2 phase it remains as an insulator while in β-BeH2 phase its behavior becomes metallic. But upon further increase in pressure it becomes a semiconductor in γ-BeH2 phase. Hence the possibility of obtaining high-pressure phases with superconducting properties cannot be ruled out. There occurs a huge equilibrium volume collapse at α- to β-phase transition and relatively smaller volume changes at β- to γ-phase transition. Our obtained value of dielectric constant (3.0) for α-BeH2 is in excellent agreement with earlier reported value (3.1). Also BeH2 shows anisotropic behavior in all three studied phases.
NASA Astrophysics Data System (ADS)
Toprek, Dragan; Belosevic-Cavor, Jelena; Koteski, Vasil
2015-10-01
First principles calculations were performed in the framework of the density functional theory (DFT) using the Full Potential-Linear Augment Plane Wave method (FP-LAPW) within the generalized gradient approximation (GGA) to predict the structural, electronic, elastic and thermal properties of NiTi2 intermetallic compound. By using the Wien2k all-electron code, calculations of the ground state and electronic properties such as lattice constants, bulk modulus, presure derivative of bulk modulus, total energies and density of states were also included. The elastic constants and mechanical properties such as Poisson's ratio, Young's modulus and shear modulus are estimated from the calculated elastic constants of the single crystal. Through the quasi-harmonic Debye model, the preasure and temperature dependences of the linear expansion coefficient, bulk modulus and heat capacity have been investigated. Finally, the Debye temperature has been estimated from the average sound velocity according to the predicted polycrystal bulk properties and from the single crystal elastic constants.
Lau, E Y; Lightstone, F C; Colvin, M E
2006-02-10
Quantum mechanical calculations were performed to study the differences between the important radiopharmaceutical metals yttrium (Y) and indium (In) bound by DOTA and modified DOTA molecules. Energies were calculated at the MP2/6-31+G(d)//HF/6-31G(d) levels, using effective core potentials on the Y and In ions. Although the minimum energy structures obtained are similar for both metal ion-DOTA complexes, changes in coordination and local environment significantly affect the geometries and energies of these complexes. Coordination by a single water molecule causes a change in the coordination number and a change in the position of the metal ion in In-DOTA; but, Y-DOTA is hardly affected by water coordination. When one of the DOTA carboxylates is replaced by an amide, the coordination energy for the amide arm shows a large variation between the Y and In ions. Optimizations including water and guandinium moieties to approximate the effects of antibody binding indicate a large energy cost for the DOTA-chelated In to adopt the ideal conformation for antibody binding.
Ab initio study of the structural, vibrational and thermal properties of Ge2Sb2Te5
NASA Astrophysics Data System (ADS)
Odhiambo, Henry; Othieno, Herick
2015-05-01
The structural, vibrational and thermal properties of hexagonal as well as cubic Ge2Sb2Te5 (GST) have been calculated from first principles. The relative stability of the possible stacking sequences of hexagonal GST has been confirmed to depend on the choice for the exchange-correlation (XC) energy functional. It is apparent that without the inclusion of the Te 4d orbitals in the valence states, the lattice parameters can be underestimated by as much as 3.9% compared to experiment and all-electron calculations. From phonon dispersion curves, it has been confirmed that the hexagonal phase is, indeed, stable whereas the cubic phase is metastable. In particular, calculations based on the quasi-harmonic approximation (QHA) reveal an extra heat capacity beyond the Dulong-Petit limit at high temperatures for both hexagonal and cubic GST. Moreover, cubic GST exhibits a residual entropy at 0 K, in agreement with experimental studies which attribute this phenomenon to substitutional disorder on the Sb/Ge/v sublattice.
NASA Astrophysics Data System (ADS)
Bock, Charles W.; Trachtman, Mendel; George, Philip
1981-09-01
The structures, dipole moments, force fields, and anharmonic frequencies for the planar conformation of formamide and thioformamide were calculated using the unscaled 4-31G basis set, augmented with a full set of d functions on the sulfur, and full geometry optimization. Extensive comparison of the geometries are made, especially the CO and CS bond lengths, with both the experimental values for the amides and values calculated in previous studies on the acids and other carbonyl compounds. Comparison of the dipole moments calculated using the optimized and experimental geometries with the experimental values suggest there is some inconsistancy in the experimental geometry for thioformamide. Quadratic, cubic, and quartic force constants are calculated for both amides, and hence the fundamental vibration frequencies. Critical comparisons are made with the assignments based on experimental observations. Differences in the bond lengths and stretching force constants for the two NH bonds are shown to be consistent with a hydrogen-bonding type of interaction between the proximal NH and CO and CS groups, like that in the acids.
NASA Astrophysics Data System (ADS)
Bock, Charles W.; George, Philip; Trachtman, Mendel
1981-02-01
Calculations on performic acid at the 4-31G level, with and without bond functions with complete geometry optimization, and at the (9, 5) level, with and without polarization functions and rigid rotation, all give no sign of a well in the potential energy curve for rotation about the O/O bond axis in the region of 50° - 90° ; and all but the unaugmented 4-31G basis set find the cis- cis planar conformer to be the most stable form. Calculations at the (9,5) level with rigid rotation find the energies of the other planar conformers, relative to the cis- cis conformer, to be 0.94, 1.50 and 14.80 kcal mol -1 for the trans- trans, cis- trans and trans- cis structures respectively. These energies and also that for the barrier separating the cis- cis and cis- trans conformers, 1-2 kcal mol -1, are discussed in relation to corresponding data for formic acid, hydrogen peroxide and several planar four heavy-atom molecules. Dipole moment calculations using the same basis sets would seem to favor a skew conformation as the most stable for performic acid, but comparisons between calculated and experimental values for formic acid and for hydrogen peroxide cast doubt on the validity of such results.
NASA Astrophysics Data System (ADS)
Rustad, James R.; Dixon, David A.; Felmy, Andrew R.
2000-05-01
Density functional calculations are performed on M 3(OH) 7(H 2O) 62+ and M 3O(OH) 6(H 2O) 6+ clusters for MAl, Cr(III), and Fe(III), allowing determination of the relative acidities of the μ 3-hydroxo and aquo functional groups. Contrary to previous predictions and rationalizations, Fe 3OH and Al 3OH groups have nearly the same intrinsic acidity, while Cr 3OH groups are significantly more acidic. The gas-phase acidity of the Fe 3OH site is in good agreement with the value predicted by the molecular mechanics model previously used to estimate the relative acidities of surface sites on iron oxides. [ J. R. Rustad et al. (1996)Geochim. Cosmochim. Acta 60, 1563]. Acidities of aquo functional groups were also computed for Al and Cr. The AlOH 2 site is more acidic than the Al 3OH site, whereas the Cr 3OH site is more acidic than the CrOH 2 site. These findings predict that the surface charging behavior of chromium oxides/oxyhydroxides should be distinguishable from their Fe, Al counterparts. The calculations also provide insight into why the lepidocrocite/boehmite polymorph is not observed for CrOOH.
Woon, D.E.; Dunning, T.H. Jr.; Peterson, K.A.
1996-04-01
Augmented correlation consistent basis sets of double (aug-cc-pVDZ), triple (aug-cc-pVTZ), and modified quadruple zeta (aug-cc-pVQZ{prime}) quality have been employed to describe the N{sub 2}{endash}HF potential energy surface at the Hartree{endash}Fock level and with single reference correlated wave functions including Mo/ller{endash}Plesset perturbation theory (MP2, MP3, MP4) and coupled cluster methods [CCSD, CCSD(T)]. The most accurate computed equilibrium binding energies {ital D}{sub {ital e}} are (with counterpoise correction) 810 cm{sup {minus}1} (MP4/aug-cc-pVQZ{prime}) and 788 cm{sup {minus}1} [CCSD(T)/aug-cc-pVQZ{prime}]. Estimated complete basis set limits of 814 cm{sup {minus}1} (MP4) and 793 cm{sup {minus}1} [CCSD(T)] indicate that the large basis set results are essentially converged. Harmonic frequencies and zero-point energies were determined through the aug-cc-pVTZ level. Combining the zero point energies computed at the aug-cc-pVTZ level with the equilibrium binding energies computed at the aug-cc-pVQZ{prime} level, we predict {ital D}{sub 0} values of 322 and 296 cm{sup {minus}1}, respectively, at the MP4 and CCSD(T) levels of theory. Using experimental anharmonic frequencies, on the other hand, the CCSD(T) value of {ital D}{sub 0} is increased to 415 cm{sup {minus}1}, in good agreement with the experimental value recently reported by Miller and co-workers, 398{plus_minus}2 cm{sup {minus}1}. {copyright} {ital 1996 American Institute of Physics.}
Determining structure and function in nanomaterial biocomposites
NASA Astrophysics Data System (ADS)
Griffin, David M.
Polymeric biomaterials represent the leading technologies available today for the repair of tissue damage and for targeted drug delivery. Perhaps the most valuable aspect of polymer-based systems is the extent to which their physical properties (e.g. elasticity, porosity, etc.) can be controlled and tuned by regulating experimental parameters during their synthesis. Biomaterial performance can be improved further still by including supplementary components resulting in a composite material. Synergetic interactions between the constituents of composite materials often results in bulk physical properties that are substantially more than the sum of individual parts. Through understanding and exploiting these sympathetic relationships, novel biocomposites can be developed which exhibit improved efficacy and biocompatibility. Here we report on the synthesis strategies and characterization of novel biocomposites from our laboratory. We look specifically at hydrogel composites containing a physically-associated network of PluronicRTM block copolymer along with a calcium-phosphate mineral component. Rheological results show that composites containing an in situ deposited mineral exhibit a significantly higher elastic modulus than composites of similar composition formed by conventional means. Moreover, analysis of the calcium-phosphate phase of in situ composites revealed that system parameters such as acidity play an integral role in determining the size and stability of the resultant mineral and subsequently the materials' expected in vivo performance. Changes to the structure in PluronicRTM/calcium-phosphate composite hydrogels during dehydration was investigated to provide a look into the mechanisms involved in composite formation. Small angle X-ray scattering analysis of these systems shows that hydrogen bonding interactions between phosphate ions and the polyethylene oxide (PEO) polymer block significantly impact the nanoscale structure and long-range order contained
Cargnoni, Fausto; Nishibori, Eiji; Rabiller, Philippe; Bertini, Luca; Snyder, G Jeffrey; Christensen, Mogens; Gatti, Carlo; Iversen, Bo Brummerstadt
2004-08-20
The experimental electron density of the high-performance thermoelectric material Zn4Sb3 has been determined by maximum entropy (MEM) analysis of short-wavelength synchrotron powder diffraction data. These data are found to be more accurate than conventional single-crystal data due to the reduction of common systematic errors, such as absorption, extinction and anomalous scattering. Analysis of the MEM electron density directly reveals interstitial Zn atoms and a partially occupied main Zn site. Two types of Sb atoms are observed: a free spherical ion (Sb3-) and Sb2(4-) dimers. Analysis of the MEM electron density also reveals possible Sb disorder along the c axis. The disorder, defects and vacancies are all features that contribute to the drastic reduction of the thermal conductivity of the material. Topological analysis of the thermally smeared MEM density has been carried out. Starting with the X-ray structure ab initio computational methods have been used to deconvolute structural information from the space-time data averaging inherent to the XRD experiment. The analysis reveals how interstitial Zn atoms and vacancies affect the electronic structure and transport properties of beta-Zn4Sb3. The structure consists of an ideal A12Sb10 framework in which point defects are distributed. We propose that the material is a 0.184:0.420:0.396 mixture of A12Sb10, A11BCSb10 and A10BCDSb10 cells, in which A, B, C and D are the four Zn sites in the X-ray structure. Given the similar density of states (DOS) of the A12Sb10, A11BCSb10 and A10BCDSb10 cells, one may electronically model the defective stoichiometry of the real system either by n-doping the 12-Zn atom cell or by p-doping the two 13-Zn atom cells. This leads to similar calculated Seebeck coefficients for the A12Sb10, A11BCSb10 and A10BCDSb10 cells (115.0, 123.0 and 110.3 microV K(-1) at T=670 K). The model system is therefore a p-doped semiconductor as found experimentally. The effect is dramatic if these cells are
Ab initio thermodynamic model for magnesium carbonates and hydrates.
Chaka, Anne M; Felmy, Andrew R
2014-09-01
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation. PMID:24679248
Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates
Chaka, Anne M.; Felmy, Andrew R.
2014-03-28
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.
Ab initio derivation of model energy density functionals
NASA Astrophysics Data System (ADS)
Dobaczewski, Jacek
2016-08-01
I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.
Ab initio study of II-(VI)2 dichalcogenides.
Olsson, P; Vidal, J; Lincot, D
2011-10-12
The structural stabilities of the (Zn,Cd)(S,Se,Te)(2) dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe(2) pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications. PMID:21937783
Recarte, V; Zbiri, M; Jiménez-Ruiz, M; Sánchez-Alarcos, V; Pérez-Landazábal, J I
2016-05-25
The different contributions to the entropy change linked to the austenite-martensitic transition in a Ni-Mn-Sn metamagnetic shape memory alloy have been determined by combining different experimental techniques. The vibrational contribution has been inferred from the vibrational density of states of both the martensitic and austenite phases. This has been accomplished by combining time-of-flight neutron scattering measurements and ab initio calculations. Further, the electronic part of the entropy change has also been calculated. Since the martensitic transformation takes place between two paramagnetic phases, the magnetic contribution can be neglected and the entropy change can be reduced to the sum of two terms: vibrational and electronic. The obtained value of the vibrational contribution ([Formula: see text]) nearly provides the total entropy change measured by calorimetry ([Formula: see text]), the difference being the electronic contribution within the experimental error. PMID:27120315
Le, Hung M; Dinh, Thach S; Le, Hieu V
2011-10-13
The singlet-triplet transformation and molecular dissociation of ozone (O(3)) gas is investigated by performing quasi-classical molecular dynamics (MD) simulations on an ab initio potential energy surface (PES) with visible and near-infrared excitations. MP4(SDQ) level of theory with the 6-311g(2d,2p) basis set is executed for three different electronic spin states (singlet, triplet, and quintet). In order to simplify the potential energy function, an approximation is adopted by ignoring the spin-orbit coupling and allowing the molecule to switch favorably and instantaneously to the spin state that is more energetically stable (lowest in energy among the three spin states). This assumption has previously been utilized to study the SiO(2) system as reported by Agrawal et al. (J. Chem. Phys. 2006, 124 (13), 134306). The use of such assumption in this study probably makes the upper limits of computed rate coefficients the true rate coefficients. The global PES for ozone is constructed by fitting 5906 ab initio data points using a 60-neuron two-layer feed-forward neural network. The mean-absolute error and root-mean-squared error of this fit are 0.0446 eV (1.03 kcal/mol) and 0.0756 eV (1.74 kcal/mol), respectively, which reveal very good fitting accuracy. The parameter coefficients of the global PES are reported in this paper. In order to identify the spin state with high confidence, we propose the use of a pattern-recognition neural network, which is trained to predict the spin state of a given configuration (with a prediction accuracy being 95.6% on a set of testing data points). To enhance the prediction effectiveness, a buffer series of five points are validated to confirm the spin state during the MD process to gain better confidence. Quasi-classical MD simulations from 1.2 to 2.4 eV of total internal energy (including zero-point energy) result in rate coefficients of singlet-triplet transformation in the range of 0.027 ps(-1) to 1.21 ps(-1). Also, we find very
Large-scale ab initio configuration interaction calculations for light nuclei
NASA Astrophysics Data System (ADS)
Maris, Pieter; Metin Aktulga, H.; Caprio, Mark A.; Çatalyürek, Ümit V.; Ng, Esmond G.; Oryspayev, Dossay; Potter, Hugh; Saule, Erik; Sosonkina, Masha; Vary, James P.; Yang, Chao; Zhou, Zheng
2012-12-01
In ab-initio Configuration Interaction calculations, the nuclear wavefunction is expanded in Slater determinants of single-nucleon wavefunctions and the many-body Schrodinger equation becomes a large sparse matrix problem. The challenge is to reach numerical convergence to within quantified numerical uncertainties for physical observables using finite truncations of the infinite-dimensional basis space. We discuss strategies for constructing and solving the resulting large sparse matrix eigenvalue problems on current multicore computer architectures. Several of these strategies have been implemented in the code MFDn, a hybrid MPI/OpenMP Fortran code for ab-initio nuclear structure calculations that can scale to 100,000 cores and more. Finally, we will conclude with some recent results for 12C including emerging collective phenomena such as rotational band structures using SRG evolved chiral N3LO interactions.
NASA Astrophysics Data System (ADS)
Neeman, Elias M.; Dréan, Pascal; Huet, Thérèse R.
2016-04-01
Camphene (C10H16) is a bicyclic monoterpene of atmospheric interest. The structure of the unique stable conformer was optimized using density functional theory and ab initio calculations. The rotational spectrum of camphene was recorded in a supersonic jet expansion with a Fourier transform microwave spectrometer over the range 2-20 GHz. Signals from the parent species and from the ten 13C isotopomers were observed in natural abundance. The rotational and centrifugal distortion parameters were fitted to a Watson's Hamiltonian in the A-reduction. Complex line-shapes resulting from a magnetic interaction associated with the pairs of hydrogen nuclei in the methylene groups was observed and modeled. The rotational constants were used together with equilibrium structure to determine the r0 and the rm(1) gas-phase geometries of the carbon skeleton. The present work provides the first spectroscopic characterization of camphene in the gas phase.
Structural Determinants of Juvenile Offenses in School.
ERIC Educational Resources Information Center
Kowalski, Gregory S.; And Others
1983-01-01
Using multiple regression techniques, evaluates the relative contributions of community structure, school structure, and crime prevention efforts to delinquency in public schools. Finds that distance from central business district, school size, and region are of predictive value, when crimes against persons, property, and perceived crime are…
NASA Astrophysics Data System (ADS)
Menezla, S.; Kadri, A.; Zitouni, K.; Djelal, A.; Djermouni, M.; Hallouche, A.; Zaoui, A.
2015-12-01
We present an ab-initio theoretical study of structural and elastic properties of GaAs1-xBix alloys in the Zinc-Blende (ZB) phase. We use a recent version of Wien2k package code based on Density Functional Theory (DFT) Full Potential and Linearized Augmented Plane Waves (FP-LAPW) method including recent Tran-Blaha modified Becke-Johnson correction of the exchange potential (TB-mBJ) and the spin-orbit interaction (SO). The calculations are performed within the Local Density Approximation (LDA) as well as the Generalized Gradient Approximation (GGA). We study first the structural properties of GaAs1-xBix alloys by solving Murnaghan equation of state. Our results show that the ZB phase is the lowest equilibrium crystal structure of GaAs1-xBix in the whole alloy composition range, in agreement with previous theoretical predictions. The variations versus Bi contents of the ZB GaAs1-xBix lattice constant a0, bulk modulus B0 and its pressure derivative B0‧ are also found very close to other theoretical and experimental data, but with much smaller bowing effects indicating a better resolution thanks to TB-mBJ correction. The variations of B0 versus the reverse equilibrium volume of the unit cell (1/V0) are found to be described by the simple linear empirical expression B0 = -0.21068 + 0.16695/V0 which is close to the theoretical prediction for III-V semiconductors with, however, somewhat lower linear coefficients values, suggesting a more metallic behavior. In a second part of this work, we use Birch-Murnaghan approach to study the elastic properties of GaAs1-xBix alloys. The elastic stiffness coefficients, C11, C12 and C44, and their variations versus alloy composition were determined for ZB GaAs1-xBix alloy. Their values in GaAs and GaBi binary compounds are found in very good agreement with available experimental and/or theoretical data. Their variations in GaAs1-xBix alloy show a monotonic decrease with increasing Bi contents, indicating a softening behavior as is
Takeuchi, Hiroshi; Enmi, Jun-ichiro; Onozaki, Manabu; Egawa, Toru; Konaka, Shigehiro
1994-09-01
Gas electron diffusion and HF/4-21 G calculations on geometric parameters and harmonic force constants are used to study the molecular structure of tert-butyl acetate. This determined that C{sub 1} = O{sub 2} is (cis) to O{sub 4}-C{sub 5} and the tert-butyl group is staggered to the C{sub 1}-O{sub 4} bond. The structural parameters are also determined. C{sub 1}-O{sub 4} bond length shortening is rationalized in terms of the resonance effect and the electron-releasing inductive effect of substituents. 29 refs., 4 figs., 4 tabs.
Shape Determination for Large Static Structures
NASA Technical Reports Server (NTRS)
Rodriguez, G.; Scheid, Robert E., Jr.
1986-01-01
Parameter and shape estimates updated from new measurements. Involves statistical structural analysis, statistical electromagneticfield analysis, filtering, measurement modeling, and iterative prediction/correction procedures. Estimating algorithms result from generalizations of Kalman statistical-filter theory.
Determining Probabilities by Examining Underlying Structure.
ERIC Educational Resources Information Center
Norton, Robert M.
2001-01-01
Discusses how dice games pose fairness issues that appeal to students and examines a structure for three games involving two dice in a way that leads directly to the theoretical probabilities for all possible outcomes. (YDS)
NASA Astrophysics Data System (ADS)
Pliego, Josefredo R.; Riveros, José M.
2000-03-01
Clusters of hydroxide ion, HO-(H2O)n=1-4, have been studied by high level ab initio calculations in order to better understand the first coordination shell of OH- ions. Geometry optimizations were performed at Hartree-Fock, density functional theory and second order Møller-Plesset perturbation theory levels using the 6-31+G(d,p) basis set. Single point energy calculations were carried out on the optimized geometries using the more extended 6-311+G(2df,2p) basis set and a higher level of electron correlation, namely fourth-order Møller-Plesset perturbation theory. For the n=1-3 clusters, only structures with the hydroxide ion hydrogen bonded to all waters molecules were considered. For the n=4 cluster, three minima were found; the most stable species has all four waters directly bound to the hydroxide ion, while the other two clusters have only three waters in the first coordination shell. In addition, the transition state connecting the cluster containing four waters in the first coordination shell to the species having three waters in the coordination shell was characterized. The barrier for this rearrangement is very low (1.82 kcal/mol), and we predict this process to occur on the picosecond time scale. The thermodynamic properties (enthalpy, entropy and Gibbs free energy) for the formation of the clusters have been calculated for all the species (including the fully deuterated clusters). Comparison of our calculations with experimental data reveals good agreement in the free energy. Nevertheless, our ab initio results suggest that for the n>1 clusters, both -ΔH0 and -ΔS0 are larger than those reported from experiment and new experiments may be necessary to obtain accurate experimental values.
NASA Astrophysics Data System (ADS)
Resat, Marianne Sowa; Smolanoff, Jason N.; Goldman, Ilyse B.; Anderson, Scott L.
1994-06-01
We report a combined experimental and theoretical study of the reaction of small carbon cluster cations with N2O aimed at understanding the reaction mechanism and how it is affected by the electronic and geometric structure of the C+n reactants. Cross sections for reaction of C+n (n=3-12) with N2O were measured over a collision energy range from 0.1-10 eV, using a guided ion beam tandem mass spectrometer. Ab initio calculations were used to examine the structure and energetics of reactant and product species. Small clusters, which are linear, react with no activation barrier, resulting in either oxide or nitride formation. The branching between oxide and nitride channels shows a strong even-odd alternation, with even clusters preferentially forming nitrides. This appears to be correlated with an even/odd alternation in the ionization potential of the CnN. The larger, monocyclic C+n have activation barriers for reaction, and a completely different product distribution. Secondary reactions of the primary oxide and nitride products were studied at high N2O pressures. Products containing two O or two N atoms are not observed, but it is possible to add one of each. Possible reaction mechanisms are discussed and supported by thermochemistry derived from spin restricted ab initio calculations.
NASA Astrophysics Data System (ADS)
Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela
2015-06-01
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.
Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela
2015-06-17
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding. PMID:25993396
NASA Astrophysics Data System (ADS)
Bannikov, V. V.; Beketov, A. R.; Baranov, M. V.; Elagin, A. A.; Kudyakova, V. S.; Shishkin, R. A.
2016-05-01
The phase stability, electronic structure, and magnetic properties of Al1- x Ti x N compositions based on the metastable aluminum nitride modification with the rock-salt structure at low ( x = 0.03) and high ( x = 0.25) concentrations of titanium in the system have been investigated using the results of ab initio band calculations. It has been shown that, at low values of x, the partial substitution is characterized by a positive enthalpy, which, however, changes sign with an increase in the titanium concentration. According to the results of the band structure calculations, the doped compositions have electronic conductivity. For x = 0.03, titanium impurity atoms have local magnetic moments (˜0.6 μB), and the electronic spectrum is characterized by a 100% spin polarization of near-Fermi states. Some of the specific features of the chemical bonding in Al1- x Ti x N cubic phases have been considered.
The ab initio potential energy surface and spectroscopic constants of HOCl
NASA Astrophysics Data System (ADS)
Koput, Jacek; Peterson, Kirk A.
1998-02-01
The potential energy surface of hypochlorous acid, HOCl, has been determined from large-scale ab initio calculations using the coupled-cluster method CCSD(T), with basis sets of quadruple- and quintuple-zeta quality. The effect of core-electron correlation on the calculated structural parameters has been investigated. The vibrational-rotational energy levels of the three isotopic species of HOCl have then been calculated using the variational method and have been further characterized by the spectroscopic constants determined using the perturbational approach. The spectroscopic constants determined, are found to be in excellent agreement with experimental data.
Electron Diffraction Determination of Nanoscale Structures
Parks, Joel H
2013-03-01
Dominant research results on adsorption on gold clusters are reviewed, including adsorption of H{sub 2}O and O{sub 2} on gold cluster cations and anions, kinetics of CO adsorption to middle sized gold cluster cations, adsorption of CO on Au{sub n}{sup +} with induced changes in structure, and H{sub 2}O enhancement of CO adsorption.
Contemporary Methodology for Protein Structure Determination.
ERIC Educational Resources Information Center
Hunkapiller, Michael W.; And Others
1984-01-01
Describes the nature and capabilities of methods used to characterize protein and peptide structure, indicating that they have undergone changes which have improved the speed, reliability, and applicability of the process. Also indicates that high-performance liquid chromatography and gel electrophoresis have made purifying proteins and peptides a…
Structural Determinants of Publicly Subsidized Adult Education.
ERIC Educational Resources Information Center
Nordhaug, Odd
1990-01-01
Data on the amount of adult education activity were collected from 454 Norwegian municipalities. Variables were geographic centrality, population density, commuting status, educational resources, municipal finances, and municipal subsidies for adult education. Material and population structures had more effect on activity level than did economic…
Vascular structure determines pulmonary blood flow distribution
NASA Technical Reports Server (NTRS)
Hlastala, M. P.; Glenny, R. W.
1999-01-01
Scientific knowledge develops through the evolution of new concepts. This process is usually driven by new methodologies that provide observations not previously available. Understanding of pulmonary blood flow determinants advanced significantly in the 1960s and is now changing rapidly again, because of increased spatial resolution of regional pulmonary blood flow measurements.
Determining Factor Structure in a Multidimensional Inventory.
ERIC Educational Resources Information Center
Deeter, Thomas E.; Gill, Diane L.
A two-step procedure is described and used to revise a multidimensional inventory in its developmental stages. First, the latent factors influencing the observed variables on the inventory are determined and justified using the following five methods: Kaiser's criterion, root staring, examination of difference values, examination of root mean…
Campetella, Marco; Bodo, Enrico; Montagna, Maria; De Santis, Serena; Gontrani, Lorenzo
2016-03-14
We have explored by means of ab initio molecular dynamics the homologue series of 11 different ionic liquids based on the combination of the cholinium cation with deprotonated amino acid anions. We present a structural analysis of the liquid states of these compounds as revealed by accurate ab initio computations of the forces. We highlight the persistent structural motifs that see the ionic couple as the basic building block of the liquid whereby a strong hydrogen bonding network substantially determines the short range structural behavior of the bulk state. Other minor docking features of the interaction network are also discovered and described. Special cases along the series such as Cysteine and Phenylalanine are discussed in the view of their peculiar properties due to zwitterion formation and additional long-range structural organization. PMID:26979694
NASA Astrophysics Data System (ADS)
Campetella, Marco; Bodo, Enrico; Montagna, Maria; De Santis, Serena; Gontrani, Lorenzo
2016-03-01
We have explored by means of ab initio molecular dynamics the homologue series of 11 different ionic liquids based on the combination of the cholinium cation with deprotonated amino acid anions. We present a structural analysis of the liquid states of these compounds as revealed by accurate ab initio computations of the forces. We highlight the persistent structural motifs that see the ionic couple as the basic building block of the liquid whereby a strong hydrogen bonding network substantially determines the short range structural behavior of the bulk state. Other minor docking features of the interaction network are also discovered and described. Special cases along the series such as Cysteine and Phenylalanine are discussed in the view of their peculiar properties due to zwitterion formation and additional long-range structural organization.
Some structural determinants of melody recall.
Boltz, M
1991-05-01
Sophisticated musicians were asked to recall, using musical notation, a set of unfamiliar folk tunes that varied in rhythmic structure and referents of tonality. The results showed that memory was facilitated by tonic triad members marking phrase endings, but only when their presence was highlighted by a corresponding pattern of temporal accents. Conversely, recall significantly declined when tonal information was either absent or obscured by rhythmic structure. Error analyses further revealed that the retention of overall pitch contour and information at phrase ending points varied as a function of these manipulations. The results are discussed in terms of a framework that links the acts of perceiving and remembering to a common attentional scheme. PMID:1861610
Structural features determining thermal adaptation of esterases.
Kovacic, Filip; Mandrysch, Agathe; Poojari, Chetan; Strodel, Birgit; Jaeger, Karl-Erich
2016-02-01
The adaptation of microorganisms to extreme living temperatures requires the evolution of enzymes with a high catalytic efficiency under these conditions. Such extremophilic enzymes represent valuable tools to study the relationship between protein stability, dynamics and function. Nevertheless, the multiple effects of temperature on the structure and function of enzymes are still poorly understood at the molecular level. Our analysis of four homologous esterases isolated from bacteria living at temperatures ranging from 10°C to 70°C suggested an adaptation route for the modulation of protein thermal properties through the optimization of local flexibility at the protein surface. While the biochemical properties of the recombinant esterases are conserved, their thermal properties have evolved to resemble those of the respective bacterial habitats. Molecular dynamics simulations at temperatures around the optimal temperatures for enzyme catalysis revealed temperature-dependent flexibility of four surface-exposed loops. While the flexibility of some loops increased with raising the temperature and decreased with lowering the temperature, as expected for those loops contributing to the protein stability, other loops showed an increment of flexibility upon lowering and raising the temperature. Preserved flexibility in these regions seems to be important for proper enzyme function. The structural differences of these four loops, distant from the active site, are substantially larger than for the overall protein structure, indicating that amino acid exchanges within these loops occurred more frequently thereby allowing the bacteria to tune atomic interactions for different temperature requirements without interfering with the overall enzyme function. PMID:26647400
AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT
French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes
2012-09-15
We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.
Structural determinants of proton blockage in aquaporins.
Chakrabarti, Nilmadhab; Roux, Benoît; Pomès, Régis
2004-10-15
Aquaporins are an important class of membrane channels selective for water and linear polyols but impermeable to ions, including protons. Recent computational studies have revealed that the relay of protons through the water-conduction pathway of aquaporin channels is opposed by a substantial free energy barrier peaking at the signature NPA motifs. Here, free-energy simulations and continuum electrostatic calculations are combined to examine the nature and the magnitude of the contribution of specific structural elements to proton blockage in the bacterial glycerol uptake facilitator, GlpF. Potential of mean-force profiles for both hop and turn steps of structural diffusion in the narrow pore are obtained for artificial variants of the GlpF channel in which coulombic interactions between the pore contents and conserved residues Asn68 and Asn203 at the NPA signature motifs, Arg206 at the selectivity filter, and the peptidic backbone of the two half-helices M3 and M7, which are arranged in head-to-head fashion around the NPA motifs, are turned off selectively. A comparison of these results with electrostatic energy profiles for the translocation of a probe cation throughout the water permeation pathway indicates that the free-energy profile for proton movement inside the narrow pore is dominated by static effects arising from the distribution of charged and polar groups of the channel, whereas dielectric effects contribute primarily to opposing the access of H+ to the pore mouths (desolvation penalty). The single most effective way to abolish the free-energy gradients opposing the movement of H+ around the NPA motif is to turn off the dipole moments of helices M3 and M7. Mutation of either of the two NPA Asn residues to Asp compensates for charge-dipole and dipole-dipole effects opposing the hop and turn steps of structural diffusion, respectively, and dramatically reduces the free energy barrier of proton translocation, suggesting that these single mutants could
Structure of the Sevoflurane-Benzene Complex as Determined by Chirped-Pulse Ftmw Spectroscopy
NASA Astrophysics Data System (ADS)
Seifert, Nathan A.; Zaleski, Daniel P.; Neill, Justin L.; Pate, Brooks H.; Lesarri, Alberto; Vallejo, Montserrat; Cocinero, Emilio J.; Castano, Fernando
2012-06-01
Following previous microwave studies on sevoflurane monomer by Suenram {et al.} and Vega-Toribio et al. we report the broadband rotational spectrum of sevoflurane clustered with benzene. The structure assigned is consistent with a C-H...π interaction between the benzene ring and the (CF_3)_2C-H hydrogen on sevoflurane. The spectrum of this species is complicated by the six-fold internal rotation of the benzene ring over the C_1 framework of sevoflurane. The six-fold tunneling falls into a high effective barrier case where there are several bound torsional levels. The tunneling spectrum has been successfully analyzed using the BELGI internal rotation program and a barrier to internal rotation of the benzene against sevoflurane of 32.5 cm-1 has been determined. Structural information about the complex has been obtained by studying the complex of sevoflurane with benzene-{d_1}. For this complex, six unique isomers are observed making it possible to determine the positions of the benzene H-atoms in the complex. Combination of these hydrogen r_s positions with the sevoflurane monomer r_s coordinates reported by Lesarri {et al.} results in a substitution structure in excellent agreement with the ab initio results. Finally, initial microwave results on two sevoflurane dimer species will also be presented. R. D. Suenram, D. J. Brugh, F. J. Lovas and C. Chu, 51st OSU Int. Symp. On Mol. Spectrosc., Columbus, OH, 1999, RB07. A. Vega-Toribio, A. Lesarri, R.D. Suenram, J. Grabow, 64th OSU Int. Symp. On Mol. Spectrosc., Columbus, OH, 2009, MH07. A. Lesarri, A. Vega-Toribio, R. D. Suenram, D. J. Brugh, J.-U. Grabow, Phys. Chem. Chem. Phys., 12, 9624-9631 (2010).
Collective rotation from ab initio theory
NASA Astrophysics Data System (ADS)
Caprio, Mark A.; Maris, Pieter; Vary, James P.
2015-10-01
The challenge of ab initio nuclear theory is to quantitatively predict the complex and highly-correlated behavior of the nuclear many-body system, starting from the underlying internucleon interactions. We may now seek to understand the wealth of nuclear collective phenomena through ab initio approaches. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. In this talk, the intrinsic structure of these bands is discussed, and the predicted rotational bands are compared to experiment. Supported by the US DOE under Award Nos. DE-FG02-95ER-40934, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371 and the US NSF under Award No. 0904782. Computational resources provided by NERSC (US DOE Contract No. DE-AC02-05CH11231).
NASA Astrophysics Data System (ADS)
Brause, Robert; Krügler, Daniel; Schmitt, Michael; Kleinermanns, Karl; Nakajima, Atsushi; Miller, Terry A.
2005-12-01
The change of the 7-azaindole-water cluster structure upon electronic excitation was determined by a Franck-Condon analysis of the intensities in the fluorescence emission spectra obtained via excitation of five different vibronic bands. A total of 105 emission band intensities were fitted, together with the changes of rotational constants of one isotopomer. These rotational constants have been obtained from a fit to the rovibronic contour of the cluster. The geometry change upon electronic excitation to the ππ* state can be described by a strong and asymmetric shortening of the hydrogen bonds and a deformation of both the pyridine and the pyrrole rings of 7-azaindole. The resulting geometry changes are interpreted on the basis of ab initio calculations.
Magnetic Structure Determinations at NBS/NIST
Lynn, J. W.; Borchers, J. A.; Huang, Q.; Santoro, A.; Erwin, R. W.
2001-01-01
Magnetic neutron scattering plays a central role in determining and understanding the microscopic properties of a vast variety of magnetic systems, from the fundamental nature, symmetry, and dynamics of magnetically ordered materials to elucidating the magnetic characteristics essential in technological applications. From the early days of neutron scattering measurements at NBS/NIST, magnetic diffraction studies have been a central theme involving many universities, industrial and government labs from around the United States and worldwide. Such measurements have been used to determine the spatial arrangement and directions of the atomic magnetic moments, the atomic magnetization density of the individual atoms in the material, and the value of the ordered moments as a function of thermodynamic parameters such as temperature, pressure, and applied magnetic field. These types of measurements have been carried out on single crystals, powders, thin films, and artificially grown multilayers, and often the information collected can be obtained by no other experimental technique. This article presents, in an historical perspective, a few examples of work carried out at the NIST Center for Neutron Research (NCNR), and discusses the key role that the Center can expect to play in future magnetism research.
Photoelectron holography applied to surface structural determination
Petersen, B.L.
1995-05-01
Photoemitted electron waves are used as coherent source waves for angstrom-scale holographic imaging of local atomic geometry at surfaces. Electron angular distribution patterns are collected above a sample surface and serve as a record of the interference between source wave and waves scattered from surrounding ion cores. Using a mathematical imaging integral transformation, the three-dimensional structural information is obtained directly from these collected patterns. Patterns measured with different electron kinetic energies are phase-summed for image improvement. Pt (111) surface is used as a model system. A pattern 9.6{angstrom}{sup {minus}1} (351 eV) is used to generate a full 3-D image of atom locations around an emitter with nearest neighbors within 0.l{angstrom} of the expected bulk positions. Atoms several layers beyond the nearest neighbors are also apparent. Twin-image reduction and artifact suppression is obtained by phase-summing eight patterns measured from 8.8 to 10.2{angstrom}{sup {minus}1} (295 to 396 eV). 32 were measured in 0.2{angstrom}{sup {minus}1} steps from 6.0 to 12.2{angstrom}{sup {minus}1} (137 to 567 eV) are presented here. Simple models of two-slit interference are compared with electron scattering to illuminate understanding of holographic recording of the structural information. This also shows why it sometimes fails due to destructive interferences. Simple theoretical models of electron scattering are compared to experiment to show the origin of the structural information and the differences that result from atomic scattering and from the source wave. Experimental parameters and their relation to imaging is discussed. Comparison is made to the Pt pattern measured at 351 eV using the simple theoretical model. The remaining data set is also modeled, and the eight appropriate theoretical patterns are used to regenerate the multiple-wavenumber experimental result. A clean Cu (001) surface is also measured and imaged.
NASA Astrophysics Data System (ADS)
Tarighi Ahmadpour, Mahdi; Hashemifar, S. Javad; Rostamnejadi, Ali
2016-07-01
We use density functional computations to study the zero temperature structural, electronic, magnetic, and optical properties of (5,0) finite carbon nanotubes (FCNT), with length in the range of 4-44 Å. It is found that the structural and electronic properties of (5,0) FCNTs, in the ground state, converge at a length of about 30 Å, while the excited state properties exhibit long-range edge effects. We discuss that curvature effects enhance energy gap of FCNTs, in contrast to the known trend in the periodic limit. It is seen that compensation of curvature effects in two special small sizes may give rise to spontaneous magnetization. The obtained cohesive energies provide some insights into the effects of environment on the growth of FCNTs. The second-order difference of the total energies reveals an important magic size of about 15 Å. The optical and dynamical magnetic responses of the FCNTs to polarized electromagnetic pulses are studied by time dependent density functional theory. The results show that the static and dynamic magnetic properties mainly come from the edge carbon atoms. The optical absorption properties are described in terms of local field effects and characterized by Casida linear response method.
Oka, Hideyuki; Ohki, Hiroshi
2010-01-01
The host-guest interaction in high-silica ferrierite (FER) with different structure-directing agents (SDA), pyridine and piperidine, was analyzed by solid-state (29)Si NMR relaxation experiments and molecular-orbital calculations. Qualitative and quantitative knowledge of the SDA structure obtained by these methods provides significant insight for understanding the functions in a template, and the stabilizing role of the SDA. Relaxation experiments show a larger magnetic dipolar interaction between the silicon and hydrogen atoms in piperidine as compared to that in pyridine, and the results correlate with the bonding property in terms of the distance between the zeolite framework and the SDA. The (1)H MAS NMR spectrum shows that the pyridine molecules mainly act as pore fillers in the pyridine-FER. In contrast, it was presumed that piperidine, adjacent to the aluminosilicate framework and framework defects, acted as a counter cation to balance the charge in the piperidine-FER. H(+)-FER synthesized with piperidine shows a lower hydrothermal stability as compared to that synthesized with pyridine. The hydrothermal stability of H(+)-FER is discussed by considering the contributions of framework defects and the different properties pertaining to the bonding between the zeolite framework and the SDA. PMID:20410561
Ab initio infrared and Raman spectra
NASA Astrophysics Data System (ADS)
Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.
1983-06-01
mechanically, using gradient techniques step by step along a classical trajectory whose path is determined by these quantum forces. We believe the QFCT method to be a more practical ab initio route to spectral band contours for large molecules, clusters, and solutions, and it can be equally applied to equilibrium and nonequilibrium systems. It is pointed out that a similar ab initio QFCT molecular dynamic approach could be used to compute other types of spectra, e.g., electronic absorption, as well as other parameters such as transport properties and thermodynamic functions and their quantum corrections. For parameters not depending on momenta, a parallel ab initio Monte Carlo approach would use electronic energies and other parameters of interest generated quantum mechanically, and ``classical'' trial moves of the nuclei.
Determining 3-D motion and structure from image sequences
NASA Technical Reports Server (NTRS)
Huang, T. S.
1982-01-01
A method of determining three-dimensional motion and structure from two image frames is presented. The method requires eight point correspondences between the two frames, from which motion and structure parameters are determined by solving a set of eight linear equations and a singular value decomposition of a 3x3 matrix. It is shown that the solution thus obtained is unique.
Structural determinants of criticality in biological networks
Valverde, Sergi; Ohse, Sebastian; Turalska, Malgorzata; West, Bruce J.; Garcia-Ojalvo, Jordi
2015-01-01
Many adaptive evolutionary systems display spatial and temporal features, such as long-range correlations, typically associated with the critical point of a phase transition in statistical physics. Empirical and theoretical studies suggest that operating near criticality enhances the functionality of biological networks, such as brain and gene networks, in terms for instance of information processing, robustness, and evolvability. While previous studies have explained criticality with specific system features, we still lack a general theory of critical behavior in biological systems. Here we look at this problem from the complex systems perspective, since in principle all critical biological circuits have in common the fact that their internal organization can be described as a complex network. An important question is how self-similar structure influences self-similar dynamics. Modularity and heterogeneity, for instance, affect the location of critical points and can be used to tune the system toward criticality. We review and discuss recent studies on the criticality of neuronal and genetic networks, and discuss the implications of network theory when assessing the evolutionary features of criticality. PMID:26005422
Atmospheric structure determined from satellite data
NASA Technical Reports Server (NTRS)
Knight, K. S.; Scoggins, J. R.
1981-01-01
The capabilities of the Nimbus 6 satellite sounding data for use in synoptic analysis were considered and interpreted. An evaluation of the ability of the satellite sounding data to detect and depict structural features of the atmosphere was made on the basis of vertical profiles of average difference and standard deviation of differences between satellite and rawinsonde data at nine pressure levels from 850 to 100 mb; and constant pressure charts and cross sections of satellite, rawinsonde and difference values. Results indicate that satellite measurements of temperature as well as the vertical lapse rate and horizontal gradient of temperature are accurate enough to show large scale patterns but not to precisely define fronts or tropopauses; satellite measurements of dew point temperature are smoothed enough to severely reduce contrasts between air masses across fronts; the magnitude of the standard deviation of differences between rawinsonde and satellite data for most variables increases with the synoptic activity in the region; and the most reliable variables to examine from satellite data for depiction of synoptic features are the temperature equivalent potential temperature and mixing ratio.
Structural Determinants of Sleeping Beauty Transposase Activity.
Abrusán, György; Yant, Stephen R; Szilágyi, András; Marsh, Joseph A; Mátés, Lajos; Izsvák, Zsuzsanna; Barabás, Orsolya; Ivics, Zoltán
2016-08-01
Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold. PMID:27401040
Structure of catalase determined by MicroED.
Nannenga, Brent L; Shi, Dan; Hattne, Johan; Reyes, Francis E; Gonen, Tamir
2014-01-01
MicroED is a recently developed method that uses electron diffraction for structure determination from very small three-dimensional crystals of biological material. Previously we used a series of still diffraction patterns to determine the structure of lysozyme at 2.9 Å resolution with MicroED (Shi et al., 2013). Here we present the structure of bovine liver catalase determined from a single crystal at 3.2 Å resolution by MicroED. The data were collected by continuous rotation of the sample under constant exposure and were processed and refined using standard programs for X-ray crystallography. The ability of MicroED to determine the structure of bovine liver catalase, a protein that has long resisted atomic analysis by traditional electron crystallography, demonstrates the potential of this method for structure determination. PMID:25303172
Rajeswaran, Manju; Blanton, Thomas N; Zumbulyadis, Nicholas; Giesen, David J; Conesa-Moratilla, Carlota; Misture, Scott T; Stephens, Peter W; Huq, Ashfia
2002-12-01
The three-dimensional structure, conformation, and packing of molecules in the solid state are crucial components used in the optimization of many technologically useful materials properties. Single-crystal X-ray diffraction is the traditional and most effective method of determining 3-D structures in the solid state. Obtaining single crystals that are sufficiently large and free of imperfections is often laborious, time-consuming, and, occasionally, impossible. The feasibility of an integrated approach to the determination and verification of a complete three-dimensional structure for a medium-sized organic molecule without using single crystals is demonstrated for the case of an organic stabilizer compound N-(p-tolyl)-dodecylsulfonamide. The approach uses a combination of powder XRD data, several computational packages involving Monte Carlo simulations and ab initio quantum mechanical calculations, and experimental solid-state NMR chemical shifts. Structure elucidation of N-(p-tolyl)-dodecylsulfonamide revealed that the Bravais lattice is monoclinic, with cell dimensions of a = 38.773 A, b = 5.507 A, c = 9.509 A, and beta = 86.35 degrees, and a space group of P21/c. PMID:12452721
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Rohlfing, Celeste MCM.; Rice, Julia E.
1992-01-01
Quantum mechanical computational methods are employed for an ab initio investigation of: (1) the molecular properties of the lowest isomers of the ClO dimer; and (2) predicted molecular and thermochemical properties. Techniques employed include electron correlation and particularly singles and doubles coupled-cluster (CCSD) theory with or without perturbational estimates of the effects of connected triple excitations. The isomers ClOClO and ClClO2 are found to have higher energies than the ClOOCl isomer, and the theoretical vibrational frequencies of the isomers are well correlated with experimental data. Experimental values of the heat of formation for the isomers are also compared with calculations based on an isodesmic reaction with Cl2O, H2O, and HOOH.
Ab initio Bogoliubov coupled cluster theory
NASA Astrophysics Data System (ADS)
Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas
2014-09-01
Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.
Automating the determination of 3D protein structure
Rayl, K.D.
1993-12-31
The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.