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
2015-08-24
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.
Ab initio structure determination of new compound Ba 3(BO 3)(PO 4)
NASA Astrophysics Data System (ADS)
Ma, H. W.; Liang, J. K.; Wu, L.; Liu, G. Y.; Rao, G. H.; Chen, X. L.
2004-10-01
The crystal structure of new compound Ba3BPO7 was determined by ab initio method from high-resolution conventional X-ray powder diffraction data. The Rietveld refinement converged to Rp=5.92%, Rwp=8.87%, Rexp=5.00% with the following details: Hexagonal, space group P63mc, a=5.4898 (1) Å, c=14.7551(1) Å, Z=2. The basic unit of the structure is the [BaO10]-[BO3]-[PO4] polar polyhedra-chain composed of Ba1-B-P-O cluster. These chains, running along c-axis, stack in a HCP mode to build the whole structure with triangular prism channels. The channels are parallel to c-axis too, in which Ba2 and Ba3 are located.
Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED
Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; Collazo, Michael J.; Shi, Dan; Reyes, Francis E.; Gonen, Tamir; Eisenberg, David S.
2016-01-01
Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods. PMID:27647903
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.
Fang, Wei-Hai
2008-03-01
photoexcitation of aromatic carbonyl compounds. The importance of ab initio determination of transient structures in the photodissociation dynamics has been demonstrated for the case of the aromatic carbonyl compounds. In addition, the detailed knowledge of mechanistic photochemistry for aromatic carbonyl compounds forms the basis for further investigating photodissociation dynamics of a polyatomic molecule.
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.
Ab initio structure determination and refinement of a scorpion protein toxin.
Smith, G D; Blessing, R H; Ealick, S E; Fontecilla-Camps, J C; Hauptman, H A; Housset, D; Langs, D A; Miller, R
1997-09-01
The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 A resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F >or= 2sigma(F) in the resolution range 8.0-0.964 A. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date.
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
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
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 β-La 2WO 6
NASA Astrophysics Data System (ADS)
Chambrier, M.-H.; Kodjikian, S.; Ibberson, R. M.; Goutenoire, F.
2009-02-01
The structure of the low-temperature form of β-La 2WO 6 has been determined from laboratory X-ray, neutron time-of-flight and electron diffraction data. This tungstate crystallizes in the non-centrosymmetric orthorhombic space group (no. 19) P2 12 12 1, with Z=8, a=7.5196(1) Å, b=10.3476(1) Å, c=12.7944(2) Å, and a measured density 7.37(1) g cm -3. The structure consists of tungsten [WO 6] octahedra and tetrahedral [OLa 4]. Tungsten polyhedra are connected such that [W 2O 11] 10- units are formed.
Ab-initio structure determination of {beta}-La{sub 2}WO{sub 6}
Chambrier, M-H.; Kodjikian, S.; Ibberson, R.M.; Goutenoire, F.
2009-02-15
The structure of the low-temperature form of {beta}-La{sub 2}WO{sub 6} has been determined from laboratory X-ray, neutron time-of-flight and electron diffraction data. This tungstate crystallizes in the non-centrosymmetric orthorhombic space group (no. 19) P2{sub 1}2{sub 1}2{sub 1}, with Z=8, a=7.5196(1) A, b=10.3476(1) A, c=12.7944(2) A, and a measured density 7.37(1) g cm{sup -3}. The structure consists of tungsten [WO{sub 6}] octahedra and tetrahedral [OLa{sub 4}]. Tungsten polyhedra are connected such that [W{sub 2}O{sub 11}]{sup 10-} units are formed. - Graphical abstract: Projection of La{sub 2}WO{sub 6} structure along [100]. The structure could be described by [W{sub 2}O{sub 11}]{sup -10} structural unit formed by two corner-sharing octahedra.
Ab-Initio Determination of Novel Crystal Structures of the Thermoelectric Material MgAgSb
Kirkham, Melanie J; Moreira Dos Santos, Antonio F; Rawn, Claudia J; Lara-Curzio, Edgar; Sharp, Jeff W.; Thompson, Alan
2012-01-01
Materials with the half-Heusler structure possess interesting electrical and magnetic properties, including potential for thermoelectric applications. MgAgSb is compositionally and structurally related to many half-Heusler materials, but has not been extensively studied. This work presents the high-temperature X-ray diffraction analysis of MgAgSb between 27 and 420 C, complemented with thermoelectric property measurements. MgAgSb is found to exist in three different structures in this temperature region, taking the half-Heusler structure at high temperatures, a Cu2Sb-related structure at intermediate temperatures, and a previously unreported tetragonal structure at room temperature. All three structures are related by a distorted Mg-Sb rocksalt-type sublattice, differing primarily in the Ag location among the available tetrahedral sites. Transition temperatures between the three phases correlate well with discontinuities in the Seebeck coefficient and electrical conductivity; the best performance occurs with the novel room temperature phase. For application of MgAgSb as a thermoelectric material, it may be desirable to develop methods to stabilize the room temperature phase at higher temperatures.
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.
Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar
2015-12-01
A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data.
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
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
2016-03-01
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
NASA Astrophysics Data System (ADS)
Dakkouri, Marwan; Grosser, Martin
2002-06-01
As a continuation of our systematic investigation of the effect of substituents on the ring geometry and dynamics in silacyclobutanes and in order to explore the role of the silicon atom as a mediator for electronic interactions between the attached fragments, we studied the molecular structure of 1,1-diethynylsilacyclobutane (DESCB) by means of gas-phase electron diffraction and ab initio calculations. The structural refinement of the electron diffraction data yielded the following bond lengths ( ra) and bond angles (uncertainties are 3σ): r( Si- C)=1.874(2) Å, r( Si- C)=1.817(1) Å, r(- C C-)=1.209(1) Å, r( C- C)=1.563(2) Å, ∠(C-Si-C)=79.2(6)°, ∠(C-Si-C)=106.5(6)°. The geminal Si-CC moieties were found to be bent outwards by 3.1(15)° and the puckering angle was determined to be 30.0(15)°. The evidently short Si-C bond length, which was also reproduced by the ab initio calculations, could be rationalized as being the consequence of the electronic interaction between the outer π charges of the triple bond and the 3pπ orbitals at the silicon atom. It is also likely that the conjugation of the geminal ethynyl groups leads to an enhancement of this bond contraction. Electrostatic interactions and the subsequent reduction of the covalent radius of the silicon atom may also contribute to this bond shortening. It has been found that the endocyclic Si-C bond length fits nicely within a scheme describing a monotonous decrease of the Si-C bond length with the increase of the electronegativity of the substituent in various geminally substituted silacyclobutanes. A series of related silacyclobutanes and acyclic diethynylsilanes have been studied by applying various ab initio methods and their optimized structures were compared to the structure of DESCB. Among these compounds are 1,1-dicyanosilacyclobutane (DCYSCB), which is isoelectronic to DESCB, 1,1-diethynylcyclobutane (DECB) which is isovalent to DESCB, monoethynylsilacyclobutane (MESCB
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.
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
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.
Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung
2014-01-01
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 (ϕ1 and ϕ2) 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 θDS list as a criterion to select optimized phases ϕam from ϕ1 or ϕ2 of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕSAD has been developed. Based on this work, reflections with an angle θDS in the range 35–145° are selected for an optimized improvement, where θDS is the angle between the initial phase ϕSAD and a preliminary density-modification (DM) phase ϕDM 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. PMID:25195747
Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung
2014-09-01
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 (φ1 and φ2) 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(DS) list as a criterion to select optimized phases φ(am) from φ1 or φ2 of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases φ(SAD) has been developed. Based on this work, reflections with an angle θ(DS) in the range 35-145° are selected for an optimized improvement, where θ(DS) is the angle between the initial phase φ(SAD) and a preliminary density-modification (DM) phase φ(DM)(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 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).
NASA Astrophysics Data System (ADS)
Bénard-Rocherullé, P.; Louër, D.
2000-01-01
Two new mixed zirconium hydroxide nitrates ZrM(OH)2(NO3)3 (M=K, Rb) have been synthesized through a wet chemical process. The two crystal structures have been solved ab initio from powder diffraction data collected with conventional monochromatic X-rays. ZrK(OH)2(NO3)3 crystallizes with a monoclinic symmetry [a=16.569(3) Å, b=5.791(1) Å, c=9.813(2) Å, β=90.17(2)°, P21/n, Z=4) and ZrRb(OH)2(NO3)3 with an orthorhombic symmetry [a=10.126(3) Å, b=16.492(3) Å, c=5.855(2) Å, Pbcn, Z=4]. The heavy atoms have been located from an interpretation of Patterson functions. The coordinates of the remaining light atoms have been determined from successive three-dimensional Fourier maps. The final Rietveld refinement indicators were RF=0.042, Rp=0.077 (M=K) and RF=0.064, Rp=0.115 (M=Rb). Like the structures of α-Zr(OH)2(NO3)2·1.65H2O and β-Zr(OH)2(NO3)2·H2O, the structures of the mixed basic zirconium nitrates are built from edge-sharing ZrO8 polyhedra to form infinite neutral zigzag chains of chemical composition [Zr(OH)4/2(NO3)2]n. The main difference with respect to the hydrated phases is the nature of the cohesion in the structures based on ionic contacts involving intercalated K+ or Rb+ and NO-3 species in the mixed compounds and on a complex hydrogen-bonding network in the hydrated phases. The crystal chemistry of the zirconium hydroxide nitrates is discussed and three structure types are identified.
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
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.
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.
Finite Elements in Ab Initio Electronic-Structure Calulations
NASA Astrophysics Data System (ADS)
Pask, J. E.; Sterne, P. A.
Over the course of the past two decades, the density functional theory (DFT) (see e.g., [1]) of Hohenberg, Kohn, and Sham has proven to be an accurate and reliable basis for the understanding and prediction of a wide range of materials properties from first principles (ab initio), with no experimental input or empirical parameters. However, the solution of the Kohn-Sham equations of DFT is a formidable task and this has limited the range of physical systems which can be investigated by such rigorous, quantum mechanical means. In order to extend the interpretive and predictive power of such quantum mechanical theories further into the domain of "real materials", involving nonstoichiometric deviations, defects, grain boundaries, surfaces, interfaces, and the like; robust and efficient methods for the solution of the associated quantum mechanical equations are critical. The finite-element (FE) method (see e.g., [2]) is a general method for the solution of partial differential and integral equations which has found wide application in diverse fields ranging from particle physics to civil engineering. Here, we discuss its application to large-scale ab initio electronic-structure calculations.
Ab initio X-Ray Absorption Fine Structure Cumulants
NASA Astrophysics Data System (ADS)
Vila, F.; Rehr, J. J.; Rossner, H. H.; Krappe, H. J.
2006-03-01
Theoretical calculations of vibrational effects in x-ray absorption spectra typically employ semi-phenomenological models, e.g. empirical force constants or correlated Debye or Einstein models. Instead we introduce an efficient and generally applicable ab initio approach based on electronic structure calculations of the dynamical matrix together with the Lanczos recursion algorithm [1] and relations between the cumulants. The approach yields 1) the thermal expansion coefficients (first cumulant of the vibrational distribution function); 2) correlated Debye-Waller factors (second cumulants) and 3) anharmonic contributions (third cumulants). Results are presented for crystalline (Cu, Au, Ge, GaAs) and molecular (GeCl4, C6H6) systems. Our results for the Debye-Waller factors agree well with experiment. [1]H.J. Krappe and H.H. Rossner, Phys. Rev. B70, 104102 (2004).
NASA Astrophysics Data System (ADS)
Xu, Li-Hong; Liu, Qiang; Suenram, R. D.; Lovas, F. J.; Hight Walker, A. R.; Jensen, J. O.; Samuels, A. C.
2004-12-01
The rotational spectra of three low-energy conformers of thiodiglycol (TDG) (HOCH 2CH 2SCH 2CH 2OH) have been measured in a molecular beam using a pulsed-nozzle Fourier-transform microwave spectrometer. To determine the likely conformational structures with ab initio approach, conformational structures of 2-(ethylthio)ethanol (HOEES) (CH 3CH 2SCH 2CH 2OH) were used as starting points together with the consideration of possible intramolecular hydrogen bonding in TDG. Three lower-energy conformers have been found for TDG at the MP2=Full/6311G** level and ab initio results agree nicely with experimentally determined rotational constants. In addition, Stark measurements were performed for two of the three conformers for dipole moment determinations, adding to our confidence of the conformational structure matches between experimental observations and ab initio calculations. Of the three lower-energy conformers, one displays a compact folded-like structure with strong hydrogen bonding between the two hydroxyl groups and the central sulfide atom. Two other conformers have relatively open chain-like structures with hydrogen bonding between each of the hydroxyl groups to the central sulfur atom, of which one has pure b-type dipole moment according to the ab initio results.
Summation of Parquet diagrams as an ab initio method in nuclear structure calculations
Bergli, Elise; Hjorth-Jensen, Morten
2011-05-15
Research Highlights: > We present a Green's function based approach for doing ab initio nuclear structure calculations. > In particular the sum the subset of so-called Parquet diagrams. > Applying the theory to a simple but realistic model, results in good agreement with other ab initio methods. > This opens up for ab initio calculations for medium-heavy nuclei. - Abstract: In this work we discuss the summation of the Parquet class of diagrams within Green's function theory as a possible framework for ab initio nuclear structure calculations. The theory is presented and some numerical details are discussed, in particular the approximations employed. We apply the Parquet method to a simple model, and compare our results with those from an exact solution. The main conclusion is that even at the level of approximation presented here, the results shows good agreement with other comparable ab initio approaches.
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.
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.
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 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.
Szostak, Roman; Aubé, Jeffrey; Szostak, Michal
2015-08-21
Twisted amides containing nitrogen at the bridgehead position are attractive practical prototypes for the investigation of the electronic and structural properties of nonplanar amide linkages. Changes that occur during rotation around the N-C(O) axis in one-carbon-bridged twisted amides have been studied using ab initio molecular orbital methods. Calculations at the MP2/6-311++G(d,p) level performed on a set of one-carbon-bridged lactams, including 20 distinct scaffolds ranging from [2.2.1] to [6.3.1] ring systems, with the C═O bond on the shortest bridge indicate significant variations in structures, resonance energies, proton affinities, core ionization energies, frontier molecular orbitals, atomic charges, and infrared frequencies that reflect structural changes corresponding to the extent of resonance stabilization during rotation along the N-C(O) axis. The results are discussed in the context of resonance theory and activation of amides toward N-protonation (N-activation) by distortion. This study demonstrates that one-carbon-bridged lactams-a class of readily available, hydrolytically robust twisted amides-are ideally suited to span the whole spectrum of the amide bond distortion energy surface. Notably, this study provides a blueprint for the rational design and application of nonplanar amides in organic synthesis. The presented findings strongly support the classical amide bond resonance model in predicting the properties of nonplanar amides.
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.
NASA Astrophysics Data System (ADS)
Van Nuffel, P.; Van Den Enden, L.; Van Alsenoy, C.; Geise, H. J.
1984-04-01
The structure and conformational equilibrium of CH 3-SYN and CH 3-SKEW conformers of propanal were studied by joint analysis of gas electron diffraction, microwave and infrared data, including constraints obtained after ab-initio relaxations (4-21G basis set) of the molecule. A valence force field was calculated for both conformers and scaled upon experimental IR frequencies; theoretical frequencies and band intensities are compared to experimental ones. Rotamer populations of CH 3-SYN and CH 3-SKEW were found to be 81 and 19%, respectively, at 300 K. The following best-fitting rg/ rα parameters were obtained as: r(OC) = 1.209(4) Å, r(C2C3) = 1.515(9) Å, r(C3C4) = 1.521(9) Å for CH 3-SYN and (with lower reliability) 1.569(45) Å for CH 3-SKEW,
van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira
2014-07-01
The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.
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.
NASA Astrophysics Data System (ADS)
Chudoba, C.; Kummrow, A.; Dreyer, J.; Stenger, J.; Nibbering, E. T. J.; Elsaesser, T.; Zachariasse, K. A.
1999-08-01
Combining femtosecond transient vibrational spectroscopy and high-level calculations is a powerful tool in the determination of excited-state structures. Striking differences in the experimental vibrational pattern of the locally excited states of 4-(dimethylamino)benzonitrile (DMABN) and 4-aminobenzonitrile (ABN) are explained on the basis of molecular structures obtained from ab initio complete-active-space self-consistent-field (CASSCF) calculations, giving evidence for a strong sensitivity of the molecular structure on modest changes in the substituents. The 4.0 ps charge-transfer time for DMABN in acetonitrile is resolved for the first time by tracking the downshifted CN stretching mode.
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
Kafka, Graeme R; Masters, Sarah L; Rankin, David W H
2007-07-01
A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).
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.
Structures of 13-atom clusters of fcc transition metals by ab initio and semiempirical calculations
NASA Astrophysics Data System (ADS)
Longo, R. C.; Gallego, L. J.
2006-11-01
We report the results of ab initio calculations of the structures and magnetic moments of Ni13 , Pd13 , Pt13 , Cu13 , Ag13 , and Au13 that were performed using a density-functional method that employs linear combinations of pseudoatomic orbitals as basis sets (SIESTA). Our structural results for Pt13 , Cu13 , Ag13 , and Au13 show that a buckled biplanar structure (BBP) is more stable than the icosahedral configuration, in keeping with results obtained recently by Chang and Chou [Phys. Rev. Lett. 93, 133401 (2004)] using the Vienna ab initio simulation package with a plane-wave basis. However, for Ni13 and Pd13 we found that the icosahedral structure is more stable than BBP. For all these clusters, two semiempirical methods based on spherically symmetric potentials both found the icosahedral structure to be the more stable, while the modified embedded atom model method, which uses a direction-dependent potential, found BBP to be the more stable structure. When low-energy structures found in recent ab initio studies of Pt13 , Cu13 , and Au13 other than Chang and Chou were optimized with SIESTA, those reported for Pt13 and Cu13 were found to be less stable than BBP, but the two-dimensional planar configuration reported for Au13 proved to be more stable than BBP.
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
New developments in the ``ab initio`` determination of transition metal alloy phase diagrams
Wolverton, C.; Asta, M.; Quannasser, S.; Dreysse, H.; de Fontaine, D.
1992-04-01
Certain classes of temperature-composition binary alloy phase diagrams can now be computed in an ``ab-initio`` approach. No adjustable or experimentally fitted parameter is used. The expectation value of the energy is expressed in terms of an expansion of cluster probabilities, where the prefactors, the Effective Cluster Interaction, are related to the alloy electronic structure. This framework is used to study the MoRe alloy for two situations: bulk and semi-infinite crystal bounded by a (001) surface. In both cases, good agreement with experimental data is found.
New developments in the ab initio'' determination of transition metal alloy phase diagrams
Wolverton, C.; Asta, M. . Dept. of Physics); Quannasser, S.; Dreysse, H. . Lab. de Physique des Solides); de Fontaine, D. . Dept. of Materials Science and Mineral Engineering)
1992-04-01
Certain classes of temperature-composition binary alloy phase diagrams can now be computed in an ab-initio'' approach. No adjustable or experimentally fitted parameter is used. The expectation value of the energy is expressed in terms of an expansion of cluster probabilities, where the prefactors, the Effective Cluster Interaction, are related to the alloy electronic structure. This framework is used to study the MoRe alloy for two situations: bulk and semi-infinite crystal bounded by a (001) surface. In both cases, good agreement with experimental data is found.
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.
Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Yasuoka, Kenji
2012-10-14
Vibrational spectra of guest molecules in clathrate hydrates are frequently measured to determine the characteristic signatures of the molecular environment and dynamical properties of guest-host interactions. Here, we present results of our study on the vibrational frequencies of methane molecules in structure H clathrate hydrates, namely, in the 5(12) and 4(3)5(6)6(3) cages, as the frequencies of stretching vibrational modes in these environments are still unclear. The vibrational spectra of methane molecules in structure H clathrate hydrate were obtained from ab initio molecular dynamics simulation and computed from Fourier transform of autocorrelation functions for each distinct vibrational mode. The calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules were found to be lower in the 4(3)5(6)6(3) cages than in the 5(12) cages (3.8 cm(-1) for symmetric stretching and 6.0 cm(-1) for asymmetric stretching). The C-H bond length and average distance between methane molecules and host-water molecules in 4(3)5(6)6(3) cages were slightly longer than those in the 5(12) cages.
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.
Incorporating Ab Initio energy into threading approaches for protein structure prediction
2011-01-01
Background Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the Ab Initio energy function can be used to improve threading, especially for the weakly/distant homologous templates. Results In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an Ab Initio energy function to evaluate the “partial” decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function. Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison. Conclusions Incorporating Ab Initio energy functions into threading can greatly improve alignment accuracy. PMID:21342587
NASA Astrophysics Data System (ADS)
Kiyono, Hajime; Kuze, Nobuhiko; Fujiwara, Hideo; Takeuchi, Hiroshi; Egawa, Toru; Konaka, Shigehiro
1996-02-01
The molecular structure of methyl isonicotinate was studied by gas phase electron diffraction combined with ab initio calculations. The molecular skeleton was assumed to be planar. The determined values of principal structure parameters ( rg and ∠ α) are as follows: r( NC) = 1.343(5) Å, r( C…C) ring = 1.401(3) Å, r( Cγ C) = 1.499(9) Å, r( C O) = 1.205(5) Å, r( C( O) O) = 1.331(8) Å, r( OC Me) = 1.430(8) Å,
NASA Astrophysics Data System (ADS)
Kirchhoff, F.; Holender, J. M.; Gillan, M. J.
1996-07-01
Ab initio molecular-dynamics simulations have been used to investigate the structure, dynamics, and electronic properties of the liquid alloy Ag1-xSex at 1350 K and at the three compositions x=0.33, 0.42, and 0.65. To provide a point of reference, calculations are also presented for the equilibrium structure and the electronic structure of the α-Ag2Se crystal. The calculations are based on density-functional theory in the local-density approximation and on the pseudopotential plane-wave method. For the solid, we find excellent agreement with experiment for the equilibrium lattice parameters and the atomic coordinates of the 12-atom orthorhombic unit cell, and we present an analysis of the electronic density of states and density distribution. The reliability of the liquid simulations is confirmed by detailed comparisons with very recent neutron-diffraction results for the partial structure factors and radial distribution functions (RDF) of the stoichiometric liquid Ag2Se. Comparison with the predictions of an empirical interaction model due to Rino et al. is also given for l-Ag2Se. The ab initio simulations show a dramatic change of the Se-Se RDF with increasing Se content. This change is due to the formation of Se clusters bound by covalent bonds, the Se-Se bond length being almost the same as in pure c-Se and l-Se. The clusters are predominantly chainlike, but for higher x there is a significant fraction of threefold coordinated Se atoms. It is shown that the equilibrium fractions of Se present as isolated atoms and in clusters can be understood on a simple charge-balance model based on an ionic interpretation. The Ag diffusion coefficient in the simulated stoichiometric liquid is consistent with experimental values measured in the high-temperature superionic solid. The Ag and Se diffusion coefficients both increase with Se content, in spite of the Se clustering. An analysis of the Se-Se bond dynamics reveals surprisingly short bond lifetimes of less than 1 ps
NASA Astrophysics Data System (ADS)
Łodyga, Wiesław; Makarewicz, Jan
2012-05-01
Geometries, anharmonic vibrations, and torsion-wagging (TW) multiplets of hydrazine and its deuterated species are studied using high-level ab initio methods employing the second-order Møller-Plesset perturbation theory (MP2) as well as the coupled cluster singles and doubles model including connected triple corrections, CCSD(T), in conjunction with extended basis sets containing diffuse and core functions. To describe the splitting patterns caused by tunneling in TW states, the 3D potential energy surface (PES) for the large-amplitude TW modes is constructed. Stationary points in the 3D PES, including equivalent local minima and saddle points are characterized. Using this 3D PES, a flexible Hamiltonian is built numerically and then employed to solve the vibrational problem for TW coupled motion. The calculated ground state rav structure is expected to be more reliable than the experimental one that has been determined using a simplified structural model. The calculated fundamental frequencies allowed resolution of the assignment problems discussed earlier in the literature. The determined energy barriers, including the contributions from the small-amplitude vibrations, to the tunneling of the symmetric and antisymmetric wagging mode of 1997 cm-1 and 3454 cm-1, respectively, are in reasonable agreement with the empirical estimates of 2072 cm-1 and 3312 cm-1, respectively [W. Łodyga et al. J. Mol. Spectrosc. 183, 374 (1997), 10.1006/jmsp.1997.7271]. However, the empirical torsion barrier of 934 cm-1 appears to be overestimated. The ab initio calculations yield two torsion barriers: cis and trans of 744 cm-1 and 2706 cm-1, respectively. The multiplets of the excited torsion states are predicted from the refined 3D PES.
Structural properties of rutherfordium: An ab-initio study
NASA Astrophysics Data System (ADS)
Gyanchandani, Jyoti; Sikka, S. K.
2012-01-01
The structural and electronic properties of rutherfordium, the latest group IV B element, have been evaluated by first principles density functional theory in scalar relativistic formalism with and without spin-orbit coupling and compared with its 5d homologue Hf. It is found that Rf will crystallize in the hexagonal close packed structure as in Hf. However, under pressure, it will have different sequence of phase transitions than Hf: hcp→bcc instead of hcp→ω→bcc. An explanation is offered for this difference in terms of the competition between the band structure and the Ewald energy contributions.
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.
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.
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.
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.
2013-01-07
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.
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.
Petrenko, Y M
2015-01-01
Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.
Structural and magnetic properties of Tcn@C60 endohedral metallofullerenes: An ab initio study
NASA Astrophysics Data System (ADS)
Kim, Eunja; Weck, Philippe F.; Czerwinski, Kenneth R.; Tománek, David
2010-03-01
We use ab initio spin density functional calculations to study the equilibrium structure and magnetic properties of Tcn@C60 endohedral metallofullerenes. The radionuclide ^99mTc is well established in biomedicine as a potent in vivo diagnostic radiopharmaceutical; its encapsulation in the inert C60 shell is expected to limit possible cytotoxicity of radiometal nanoparticles catabolized by the biological host. We find that C60 can endohedrally accommodate Tcn clusters with up to n=7. The encapsulation does not change significantly the structure of the enclosed clusters, but reduces the magnetic moment due to a stronger Tc--C hybridization for the larger clusters.
NASA Astrophysics Data System (ADS)
Amokrane, S.; Ayadim, A.; Levrel, L.
2015-11-01
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.
Durig, James R; Panikar, Savitha S; Groner, Peter; Nanaie, Hossein; Bürger, Hans; Moritz, Peter
2010-04-01
The microwave spectra of seven isotopomers of fluoromethylsilane, CH(2)FSiH(3), in the ground vibrational state were measured and analyzed in the frequency range 18-40 GHz. The rotational and centrifugal distortion constants were evaluated by the least-squares treatment of the observed frequencies of a- and b-type R- and b-type Q-transitions. The values for the components of the dipole moment were obtained from the measurements of Stark effects from both a- and b-type transitions and the determined values are: |mu(a)| = 1.041(5), |mu(b)| = 1.311(6), and |mu(t)| = 1.674(4) D. Structural parameters have been determined and the heavy atom distances (r(0)) in Angstroms are: Si-C = 1.8942(57) and C-F = 1.4035(55) and the angle in degree, angleSiCF = 109.58(14). A semi-experimental r(e) structure was also determined from experimental ground state rotational constants and vibration-rotation constants derived from ab initio force fields. The internal torsional fundamental, SiH(3), was observed at 149.2 cm(-1) with two accompanying hot bands at 138.8 and 127.5 cm(-1). The barrier to internal rotation was obtained as 717.3(16) cm(-1) (2.051(46) kcal mol(-1)) by combining the analysis of the microwave A and E splittings and the torsional fundamental and hot band frequencies. Ab initio calculations have been carried out with full electron correlation by the second-order perturbation method with several different basis sets up to MP2/6-311+G(d,p) to obtain geometrical parameters, barriers to internal rotation, and centrifugal distortion constants. Adjusted r(0) structural parameters have been obtained by combining the ab initio MP2/6-311+G(d,p) predicted values with the determined rotational constants for the fluoride as well as with the previously reported microwave data for the chloro- and bromo- compounds. These experimental results are compared to the corresponding parameters for the carbon analogues.
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.
Ab Initio Electronic Structure Calculations of Cytochrome P450 -- Ligand Interactions
NASA Astrophysics Data System (ADS)
Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.
1997-03-01
The Cytochrome P450 superfamily of enzymes are of great interest in pharmacology as they participate in an enormous range of physiological processes including drug deactivation and xenobiotic detoxification. We apply ab initio electronic structure calculations to model the interactions of the haem molecule at the P450 active site with substrate and inhibitor ligands. These calculations, based on density function theory, were performed with the CETEP code which uses a plane wave basis set and pseudopotentials to perform efficient LDA, GGA and spin dependent calculations. A change in the spin state of the haem iron atom is observed on binding of a substrate molecule, consistent with the accepted reaction mechanism.
Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.
Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang
2016-09-01
We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc.
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.
NASA Astrophysics Data System (ADS)
Tilocca, Antonio
2007-12-01
Ab initio (Car-Parrinello) molecular dynamics simulations were carried out to investigate the melt precursor of a modified phosphosilicate glass with bioactive properties, and to quench the melt to the vitreous state. The properties of the 3000K liquid were extensively compared with those of the final glass structure. The melt is characterized by a significant fraction of structural defects (small rings, undercoordinated and overcoordinated ions), often combined together. The creation or removal of these coordinative defects in the liquid (through Si-O bond formation or dissociation) reflects frequent exchanges within the silicate first coordination shell, which in turn dynamically modify the intertetrahedral connectivity of silicate groups. The observed dynamical variation in both the identity and the number of silicate groups linked to a tagged Si ( Qn speciation) are considered key processes in the viscous flow of silicate melts [I. Farnan and J. F. Stebbins, Science 265, 1206 (1994)]. On the other hand, phosphate groups do not show an equally marked exchange activity in the coordination shell, but can still form links with Si. Once formed, these Si-O-P bridges are rather stable, and in fact they are retained in the glass phase obtained after cooling; their formation within the present full ab initio melt-and-quench approach strongly supports their presence in melt-derived phosphosilicate glasses with bioactive applications. On the other hand, the simulations show that the fraction of structural defects rapidly decreases during the cooling, and the glass is essentially free of miscoordinated ions and small rings.
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.
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.
Structural phase transition of CdTe: an ab initio study.
Alptekin, Sebahaddin
2013-01-01
A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in zinc-blende CdTe. We found that CdTe undergoes a structural first-order phase transition to [Formula: see text] (binary β-tin) tetragonal structure in the constant pressure molecular dynamics simulation at 20 GPa. When the pressure was increased to 50 GPa, the phase of tetragonal structure converted to a new Imm2 orthorhombic structure. These phase transformations were also calculated by using the enthalpy calculations. Transition phases, lattice parameters and bulk properties we attained are comparable with experimental and theoretical data.
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.
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 Determination of Formation Energies and Charge Transfer Levels of Charged Ions in Water
NASA Astrophysics Data System (ADS)
Vatti, Anoop Kishore; Todorova, Mira; Neugebauer, Joerg
The ability to describe the complex atomic and electronic structure of liquid water and hydrated ions on a microscopic level is a key requirement to understand and simulate electro-chemical and biological processes. Identifying theoretical concepts which enable us to achieve an accurate description in a computationally efficient way is thereby of central importance. Aiming to unravel the importance and influence of different contributions on the hydration energy of ions we perform extensive ab-initio molecular dynamics simulations for charged and neutral cations (Zn, Mg) and anions (Cl, Br, I) in water. The structural correlations and electronic properties of the studied ions are analysed and compared to experimental observations. Following an approach inspired by the defect chemistry in semiconductors and aligning the water band edges on an absolute scale allows us to benchmark the calculated formation energies, identify transition states and compare the results to experiment. Based on these results we discuss the performance of various DFT xc-functionals to predict charge transfer levels and photo-emission experiments.
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.
Ab initio study of structural and electronic properties of Cun@C60
NASA Astrophysics Data System (ADS)
Dhiman, Shobhna; Kumar, Ranjan; Dharamvir, Keya
2013-06-01
Ab initio investigation of structural and electronic properties of copper doped endohedral fullerene has been performed using numerical atomic orbital density functional theory. We have obtained the ground state structures for Cun@C60 (n=1-10). Which shows that C60 molecule can accommodate maximum of nine copper atoms, for n > 9 the cage eventually break. Encapsulated large number of copper atoms leads to deformation of cage with diameter varies from 7.00Å to 8.38Å. Binding energy/Cu atom is found to increase till n = 4 and after that it decreases with the number of Cu atoms with a sudden increase for n=10 and electronic affinity increases till n=2 then decreases uniformly till up to n=7 with a further sharp decrease for n=10. Ionization potential and Homo-Lumo gap shows a oscillatory nature. The results obtained are consistent with available theoretical and experimental results. The ab-initio calculations were performed using SIESTA code with generalized gradient approximation (GGA).
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)
Kempisty, Paweł; Strąk, Paweł; Krukowski, Stanisław
2011-04-01
Density Functional Theory (DFT) calculations indicate that energetically stable structure of clean GaN(0001) surface posses (2 × 1) reconstruction, having every second row of Ga located near plane of N atoms, that gives rise to Ga-related dispersionless surface electronic state, already identified by angle resolved photoelectron spectroscopy (ARPES) measurements [S.S. Dhesi et al. Phys. Rev. B 56 (1997) 10271, L. Plucinski et al. Surf. Sci 507-10 (2002) 223, S. M. Widstrand et al. Surf. Sci. 584 (2005) 169]. The energy reduction in reconstruction proceeds via change of the hybridization of the occupied Ga surface states from sp 3 to sp 2, transforming the empty states to p z type. It is also shown that the electric subsurface field, modeled in new slab model which allows to simulate electric fields at the semiconductor surfaces [P. Kempisty et al., J. Appl. Phys. 106 (2009) 054901], strongly affects the energy of electronic states of GaN(0001) surfaces. The change of the field may shift the energy of surface states of bare and hydrogen covered GaN(0001) surface, by several eV with respect to the band states. The phenomenon, denoted as Surface States Stark Effect (SSSE), explains various band bending values, measured at differently doped n-type GaN(0001) surfaces. It is shown also that, for the adsorbate density up to one H atom for each Ga surface atom i.e. 1 monolayer coverage (1 ML), the hydrogen adatoms are located at the on-top positions, i.e. directly above Ga atoms. For these adsorbate densities, the H-related quantum surface state is located slightly below the valence band maximum (VBM) in the case of p-type GaN surface. For n-type GaN, the H-related surface state is located deeply in the valence band, about 2 eV below VBM. For higher, 1.25 ML hydrogen coverage, the two H adatoms create either surface attached H 2 ad-molecule (energetically stable) or triple bridge configuration is created (metastable). The H 2 ad-molecule is weekly attached to the surface
Determination of the AlN Sublimation Growth Precursors from ab initio Modeling
NASA Astrophysics Data System (ADS)
Li, Yanxin; Brenner, Donald
2003-03-01
Concentrations of gas-phase species and their supersaturation with respect to crystal growth in an AlN sublimation chamber were calculated using an ab initio model that considers 16 gas-phase species. To determine the degree of supersaturation, two calculations were carried out. In the first, concentrations were calculated subject to experimental pressure and temperature conditions with no constraints on the amount of N and Al. In the second calculation, the concentrations were constrained such that the amount of N and Al matched that at the solid source, mimicking a chamber where the inlet N2 and sublimation source are the only sources of Al and N. The calculations predict that Al is supersaturated and in high concentration, and therefore is likely a growth precursor in agreement with assumptions in prior modeling studies. In contrast, while our calculations show that N2 is present in high concentrations, it is not supersaturated and therefore is not a growth precursor, in contrast to assumptions made in prior models. Instead, our calculations show that Al3N, while in lower concentration than N2, is supersaturated and therefore is likely a sourcs for N addition to the crystal. This result resolves apparent discrepancies in the literature in which the sticking coefficient for N2, which must be assumed very small to match experimental growth rates, varies from model to model.
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
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.
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.
Evolved chiral NN +3N Hamiltonians for ab initio nuclear structure calculations
NASA Astrophysics Data System (ADS)
Roth, Robert; Calci, Angelo; Langhammer, Joachim; Binder, Sven
2014-08-01
We discuss the building blocks for a consistent inclusion of chiral three-nucleon (3N) interactions into ab initio nuclear structure calculations beyond the lower p shell. We highlight important technical developments, such as the similarity renormalization group (SRG) evolution in the 3N sector, a JT-coupled storage scheme for 3N matrix elements with efficient on-the-fly decoupling, and the importance-truncated no-core shell model with 3N interactions. Together, these developments make converged ab initio calculations with explicit 3N interactions possible also beyond the lower p shell. We analyze in detail the impact of various truncations of the SRG-evolved Hamiltonian, in particular the truncation of the harmonic-oscillator model space used for solving the SRG flow equations and the omission of the induced beyond-3N contributions of the evolved Hamiltonian. Both truncations lead to sizable effects in the upper p shell and beyond and we present options to remedy these truncation effects. The analysis of the different truncations is a first step towards a systematic uncertainty quantification of all stages of the calculation.
NASA Astrophysics Data System (ADS)
Guerrero, Carlo L.; Cuesta-Lopez, Santiago; Perlado, Jose M.
2014-10-01
The phase diagram and the possible stable structures of molecular solid hydrogen are intriguing physical phenomena that still remain to be fully unveiled. Particularly, its transition to metallic hydrogen at high pressures is currently a hot topic of discussion. This letter reports a simulation method that links the ab initio, quantum molecular dynamic and mechanical properties calculations to study the relation between the structural phase transitions and sound velocity in solid molecular hydrogen. The pressure range studied is from 0.1 GPa to 180 GPa, at 15 K temperature, thereby our aim is to simulate the conditions of manufacture, handling and early stages of compression of the target fuel used in confinement inertial fusion. Phase I degeneration below 1 GPa is discussed.
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.
Guirgis, Gamil A; Klaassen, Joshua J; Deodhar, Bhushan S; Sawant, Dattatray K; Panikar, Savitha S; Dukes, Horace W; Wyatt, Justin K; Durig, James R
2012-12-01
The infrared spectra (3500-220 cm(-1)) of cyclobutylgermane, c-C(4)H(7)GeH(3) have been recorded of the gas. Also variable temperature (-65 to -100 °C) studies of the infrared spectra (3500-400 cm(-1)) of the sample dissolved in liquid xenon were recorded and both the equatorial and axial conformers were identified. The enthalpy difference has been determined from 10 band pairs 8 temperatures to give 112 ± 11 cm(-1) (1.34 ± 0.13 kJ mol(-1)) with the equatorial conformer the more stable form. The percentage of the axial conformer present at ambient temperature is estimated to be 37 ± 1%. From ab initio calculations conformational stabilities have been predicted from both MP2(full) and density functional theory calculations from a variety of basic sets. The r(0) structure parameters have been obtained for both conformers from the previously reported rotational constants from the three isotopologues. The determined heavy atom distances for the equatorial [axial] form are (Å) Ge-C(α)=1.952(3) [1.950(3)], [Formula: see text] , [Formula: see text] [1.551(3)] and angles in degrees (°) ∠GeC(α)C(β)=118.6(5) [113.4(5)], [Formula: see text] , ∠C(α)C(β)C(γ)=87.8(5) [88.8(5)], [Formula: see text] and a puckering angle of 29.1(5) [25.1(5)]. Data from ab initio calculations were used to predict vibrational harmonic force constants, fundamental wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The results are compared to the corresponding properties of some related molecules.
Structural Determination of Circulation.
ERIC Educational Resources Information Center
Blankenburg, William B.
1981-01-01
Analyzes the effects of both structural factors (demographics, economic conditions, and competition) and discretionary factors (content, design, and marketing techniques) and concludes that it is the former that determine a newspaper's circulation. (FL)
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
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.
Ab Initio Investigation of the Structures of Fe-Doped Carbon Clusters
NASA Astrophysics Data System (ADS)
Lovato, Christella; Brownrigg, Clifton; Hira, Ajit
2012-02-01
We continue our interest in the theoretical study of carbon clusters to examine the effects of the doping of small carbon clusters (Cn, n = 2 - 15) with iron atoms. This work applies the hybrid ab initio methods of quantum chemistry to derive the different FemCn (m = 1-3) geometries. Of particular interest are linear, fan, and cyclic geometries. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Exploration of the singlet, triplet, quintet, and septet potential energy surfaces is performed. The type of bonding in terms of competition between sp^2 and sp^3 hybridization is examined, with a view to addressing the possibility of the stabilization of the doped carbon nano-particles in a diamond type structure. The potential for the existence of new pathways to the fabrication of nanotubes is explored.
Structure and lattice dynamics of rare-earth ferroborate crystals: Ab initio calculation
NASA Astrophysics Data System (ADS)
Chernyshev, V. A.; Nikiforov, A. E.; Petrov, V. P.; Serdtsev, A. V.; Kashchenko, M. A.; Klimin, S. A.
2016-08-01
The ab initio calculation of the crystal structure and the phonon spectrum of crystals RFe3(BO3)4 ( R = Pr, Nd, Sm) has been performed in the framework of the density functional theory. The ion coordinates in the unit cell, the lattice parameters, the frequencies and the types of fundamental vibrations, and also the intensities of lines in the Raman spectrum and infrared reflection spectra have been found. The elastic constants of the crystals have been calculated. For low-frequency A 2 mode in PrFe3(BO3)4, a "seed" vibration frequency that strongly interacts with the electronic excitation on a praseodymium ion was found. The calculation results satisfactory agree with the experimental data.
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
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
Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.
Ishikawa, Tetsuya; Hayakawa, Daichi; Miyamoto, Hitomi; Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi
2015-11-19
The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).
Vazquez-Mayagoitia, Alvaro; Fuentes-Cabrera, Miguel A; Sumpter, Bobby G; Luque, Javier; Huertas, Oscar; Orozco, Modesto; Felice, Rosa; Brancolini, Giorgia; Migliore, Agostino
2009-01-01
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 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 inter-plane 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.
Ab initio random structure search for 13-atom clusters of fcc elements.
Chou, J P; Hsing, C R; Wei, C M; Cheng, C; Chang, C M
2013-03-27
The 13-atom metal clusters of fcc elements (Al, Rh, Ir, Ni, Pd, Pt, Cu, Ag, Au) were studied by density functional theory calculations. The global minima were searched for by the ab initio random structure searching method. In addition to some new lowest-energy structures for Pd13 and Au13, we found that the effective coordination numbers of the lowest-energy clusters would increase with the ratio of the dimer-to-bulk bond length. This correlation, together with the electronic structures of the lowest-energy clusters, divides the 13-atom clusters of these fcc elements into two groups (except for Au13, which prefers a two-dimensional structure due to the relativistic effect). Compact-like clusters that are composed exclusively of triangular motifs are preferred for elements without d-electrons (Al) or with (nearly) filled d-band electrons (Ni, Pd, Cu, Ag). Non-compact clusters composed mainly of square motifs connected by some triangular motifs (Rh, Ir, Pt) are favored for elements with unfilled d-band electrons.
A Parallel Framework for Multipoint Spiral Search in ab Initio Protein Structure Prediction
Rashid, Mahmood A.; Newton, M. A. Hakim; Hoque, Md Tamjidul; Sattar, Abdul
2014-01-01
Protein structure prediction is computationally a very challenging problem. A large number of existing search algorithms attempt to solve the problem by exploring possible structures and finding the one with the minimum free energy. However, these algorithms perform poorly on large sized proteins due to an astronomically wide search space. In this paper, we present a multipoint spiral search framework that uses parallel processing techniques to expedite exploration by starting from different points. In our approach, a set of random initial solutions are generated and distributed to different threads. We allow each thread to run for a predefined period of time. The improved solutions are stored threadwise. When the threads finish, the solutions are merged together and the duplicates are removed. A selected distinct set of solutions are then split to different threads again. In our ab initio protein structure prediction method, we use the three-dimensional face-centred-cubic lattice for structure-backbone mapping. We use both the low resolution hydrophobic-polar energy model and the high-resolution 20 × 20 energy model for search guiding. The experimental results show that our new parallel framework significantly improves the results obtained by the state-of-the-art single-point search approaches for both energy models on three-dimensional face-centred-cubic lattice. We also experimentally show the effectiveness of mixing energy models within parallel threads. PMID:24744779
Electronic and structural properties of nitrogen adsorbed Nb(100) surfaces: An ab initio study
NASA Astrophysics Data System (ADS)
Carvalho, P. A. S.; Miwa, R. H.
2013-08-01
We have performed an ab initio total energy investigation of the electronic and structural properties of nitrogen adsorbed Nb(100) surface, N/Nb(100). We find an energetic preference for the nitrogen adsorption on the hollow sites of the Nb(100) surface. Upon the presence of N adatoms, there is a reduction of the electronic density of states near the Fermi level. However, the metallic character of the Nb(100) surface has been maintained. The (occupied) electronic states of N adatoms are resonant within the valence band of Nb(100), mostly lying at 4 eV below the Fermi level. Further investigations reveal the formation of energetically stable N/Nb(100)-(n × 1) phase, being the (2 × 1), (5 × 1), and (10 × 1) the most likely ones. Those (n × 1) structures are composed by NbN stripes separated by N vacancy lines. Our scanning tunneling microscopy simulations indicate the formation of bright lines lying on the Nb atoms neighboring the (dark) N vacancy lines, giving rise to an anisotropic electronic structure on the N/Nb(100)-(n × 1) surface. That is, the metallic character of the surface has been strengthened along the vacancy-lines.
Ab initio calculations of the electronic structure and bonding characteristics of LaB6
NASA Astrophysics Data System (ADS)
Hossain, Faruque M.; Riley, Daniel P.; Murch, Graeme E.
2005-12-01
Lanthanum hexaboride ( LaB6 , NIST SRM-660a) is widely used as a standard reference material for calibrating the line position and line shape parameters of powder diffraction instruments. The accuracy of this calibration technique is highly dependent on how completely the reference material is characterized. Critical to x-ray diffraction, this understanding must include the valence of the La atomic position, which in turn will influence the x-ray form factor (f) and hence the diffracted intensities. The electronic structure and bonding properties of LaB6 have been investigated using ab initio plane-wave pseudopotential total energy calculations. The electronic properties and atomic bonding characteristics were analyzed by estimating the energy band structure and the density of states around the Fermi energy level. The calculated energy band structure is consistent with previously reported experimental findings; de Haas-van Alphen and two-dimensional angular correlation of electron-positron annihilation radiation. In addition, the bond strengths and types of atomic bonds in the LaB6 compound were estimated by analyzing the Mulliken charge density population. The calculated result revealed the coexistence of covalent, ionic, and metallic bonding in the LaB6 system and partially explains its high efficiency as a thermionic emitter.
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.
Experimental and ab initio structural studies of liquid Zr[subscript 2]Ni
Hao, S.G.; Kramer, M.J.; Wang, C.Z.; Ho, K.M.; Nandi, S.; Kreyssig, A.; Goldman, A.I.; Wessels, V.; Sahu, K.K.; Kelton, K.F.; Hyers, R.W.; Canepari, S.M.; Rogers, J.R.
2009-05-01
High-energy x-ray diffraction and ab initio molecular-dynamics simulations demonstrate that the short-range order in the deeply undercooled Zr{sub 2}Ni liquid is quite nuanced. The second diffuse scattering peak in the total structure factory sharpens with supercooling, revealing a shoulder on the high-Q side that is often taken to be a hallmark of increasing icosahedral order. However, a Voronoi tessellation indicates that only approximately 3.5% of all the atoms are in an icosahedral or icosahedral-like environment. In contrast, a Honeycutt-Andersen analysis indicates that a much higher fraction of the atoms is in icosahedral (15%--18%) or distorted icosahedral (25%--28%) bond-pair environments. These results indicate that the liquid contains a large population of fragmented clusters with pentagonal and distorted pentagonal faces, but the fully developed icosahedral fragments are rare. Interestingly, in both cases, the ordering changes little over the 500 K of cooling. All metrics show that the nearest-neighbor atomic configurations of the most deeply supercooled simulated liquid (1173 K) differ topologically and chemically from those in the stable C16 compound, even though the partial pair distributions are similar. The most significant structural change upon decreasing the temperature from 1673 to 1173 K is an increase in the population of Zr in Ni-centered clusters. The structural differences between the liquid and the C16 increase the nucleation barrier, explaining glass formation in the rapidly quenched alloys.
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.
Klepeis, J. L.; Floudas, C. A.
2003-01-01
The field of computational biology has been revolutionized by recent advances in genomics. The completion of a number of genome projects, including that of the human genome, has paved the way toward a variety of challenges and opportunities in bioinformatics and biological systems engineering. One of the first challenges has been the determination of the structures of proteins encoded by the individual genes. This problem, which represents the progression from sequence to structure (genomics to structural genomics), has been widely known as the structure-prediction-in-protein-folding problem. We present the development and application of ASTRO-FOLD, a novel and complete approach for the ab initio prediction of protein structures given only the amino acid sequences of the proteins. The approach exhibits many novel components and the merits of its application are examined for a suite of protein systems, including a number of targets from several critical-assessment-of-structure-prediction experiments. PMID:14507680
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
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.
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(∗)/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. PMID:26374007
Zhang, Yang
2014-02-01
We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems.
Structure, dynamics, and reactivity of hydrated electrons by ab initio molecular dynamics.
Marsalek, Ondrej; Uhlig, Frank; VandeVondele, Joost; Jungwirth, Pavel
2012-01-17
Understanding the properties of hydrated electrons, which were first observed using pulse radiolysis of water in 1962, is crucial because they are key species in many radiation chemistry processes. Although time-resolved spectroscopic studies and molecular simulations have shown that an electron in water (prepared, for example, by water photoionization) relaxes quickly to a localized, cavity-like structure ∼2.5 Å in radius, this picture has recently been questioned. In another experimental approach, negatively charged water clusters of increasing size were studied with photoelectron and IR spectroscopies. Although small water clusters can bind an excess electron, their character is very different from bulk hydrated species. As data on electron binding in liquid water have become directly accessible experimentally, the cluster-to-bulk extrapolations have become a topic of lively debate. Quantum electronic structure calculations addressing experimental measurables have, until recently, been largely limited to small clusters; extended systems were approached mainly with pseudopotential calculations combining a classical description of water with a quantum mechanical treatment of the excess electron. In this Account, we discuss our investigations of electrons solvated in water by means of ab initio molecular dynamics simulations. This approach, applied to a model system of a negatively charged cluster of 32 water molecules, allows us to characterize structural, dynamical, and reactive aspects of the hydrated electron using all of the system's valence electrons. We show that under ambient conditions, the electron localizes into a cavity close to the surface of the liquid cluster. This cavity is, however, more flexible and accessible to water molecules than an analogous area around negatively charged ions. The dynamical process of electron attachment to a neutral water cluster is strongly temperature dependent. Under ambient conditions, the electron relaxes in the
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.
Gregurick, S. K.
2001-04-20
During the period from September 1, 1998 until September 1, 2000 I was awarded a Sloan/DOE postdoctoral fellowship to work in collaboration with Professor John Moult at the Center for Advanced Research in Biotechnology (CARB). Our research project, ''Ab Initio Protein Tertiary Structure Prediction and a Comparative Genetic algorithm'', yielded promising initial results. In short, the project is designed to predict the native fold, or native tertiary structure, of a given protein by inputting only the primary sequence of the protein (one or three letter code). The algorithm is based on a general learning, or evolutionary algorithm and is called Genetic Algorithm (GAS). In our particular application of GAS, we search for native folds, or lowest energy structures, using two different descriptions for the interactions of the atoms and residues in a given protein sequence. One potential energy function is based on a free energy description, while the other function is a threading potential derived by Moult and Samudrala. This modified genetic algorithm was loosely termed a Comparative Genetic Algorithm and was designed to search for native folded structures on both potential energy surfaces, simultaneously. We tested the algorithm on a series of peptides ranging from 11 to 15 residues in length, which are thought to be independent folding units and thereby will fold to native structures independent of the larger protein environment. Our initial results indicated a modest increase in accuracy, as compared to a standard Genetic Algorithm. We are now in the process of improving the algorithm to increase the sensitivity to other inputs, such as secondary structure requirements. The project did not involve additional students and as of yet, the work has not been published.
Structure-property relationship in py-hexahydrocinchonidine diastereomers: ab initio and NMR study.
Szöllösi, György; Chatterjee, Abhijit; Forgó, Péter; Bartók, Mihály; Mizukami, Fujio
2005-02-10
Two py-hexahydrocinchonidine diastereomers were selectively obtained in the heterogeneous catalytic hydrogenation of cinchonidine over supported Pt catalyst. The two isolated compounds when used as chiral base catalysts in the Michael addition of a beta-keto ester to methyl vinyl ketone gave products of opposite configuration in excess. To trace the reason of this behavior, in the present study, the structures of the two diastereomers were fully optimized by ab initio quantum chemical calculation. These results were then compared with several nuclear Overhauser enhancement spectroscopy (NOESY) signal intensities from the spectra of the two compounds. Further we performed a conformational search on all the optimized geometries independently for the two flexible torsional angles, which are linking the quinuclidine and tetrahydroquinoline moieties present in these molecules. This study allowed us to propose the configuration of the C(4)(') chiral center. Thus, the product mixture resulted in the hydrogenation of cinchonidine containing the 4'-(S)-diastereomer in excess (de = 20%). According to the computation results the 4'-(S)-diastereomer is more stable than the 4'-(R)-diastereomer. The 4'-(S)-conformer obtained by computation has lower electronic energy than the structures obtained for the 4'-(R)-diastereomer, which may explain the excess formation of the first one. The results of the Michael addition catalyzed by these diastereomers were interpreted on the basis of these conclusions.
NASA Astrophysics Data System (ADS)
Xie, Z. L.; Dy, K. S.; Wu, S. Y.
1996-03-01
An efficient ab initio scheme has been developed by using TB LMTO method to calculate the electronic structure and the full electron density of atomic clusters. In this scheme, the real-space Green's function (RSG) is used to obtain the full electronic density which includes the correction for non-spherical effects. Meanwhile, the real space Green's function can facilitate the calculation of the electronic structure for large clusters with restricted computer memory and CPU resources by using matrix reversion method developed by Wu and his co-workers. With the full electron density of atomic clusters, the total energies of clusters can be calculated. We have applied this ab initio scheme to evaluate the structural properties for Si clusters of 11-14 atoms. Diffrent geometrical arrangements have been examined as posible candidates of the most stable structure for each size cluster, and by calculating their cohesive energies, the most stable structure can be determined for a given size cluster. Our calculations have given similar results of previous investigations using the tight-binding molecular dynamics method.
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.
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.
Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott
2011-01-01
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-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) 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. PMID:21965559
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.
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.
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.
A high-precision ab initio determination of the equilibrium geometry and force field of HOC(+)
NASA Technical Reports Server (NTRS)
Defrees, D. J.; Bunker, P. R.; Binkley, J. S.; Mclean, A. D.
1987-01-01
The results of an ab initio molecular orbital investigation of the isoformyl cation, HOC(+), shape are reported. The effects of expanding the basis set to near the Hartree-Fock limit and of electron correlation were examined, and the results indicate that near the Hartree-Fock limit the HOC(+) is linear. An analytic potential function is presented, from which the calculated rotational energies are only 0.03 percent different from the experimental values. This represents a nearly two orders of magnitude reduction in error from earlier work.
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)
Durig, J. R.; Guirgis, G. A.; Eltayeb, S.
1994-07-01
The Raman (2500 to 30 cm -1) and infrared (2500 to 60 cm 1) spectra of gaseous and solid trifluoromethyl isocyanate, CF 3NCO, have been recorded. The Raman spectrum of the liquid has also been obtained and qualitative depolarization ratios have been measured. The CNC bend has been observed in the low-frequency Raman spectrum of the gas at 130 cm -1 as a relatively strong line which is split in the spectrum of the solid. However, the CF 3 torsional mode was not observed. The infrared spectrum of CF 3NCO dissolved in liquid xenon was also obtained and the observed spectrum indicates a very small barrier to internal rotation. With the exception of the torsion, a complete assignment of the vibrational fundamentals is proposed. The structural parameters, force constants, and vibrational frequencies have been determined from ab initio calculations utilizing a variety of basis sets and the theoretical results are compared to the experimental values when appropriate. These results have been compared with the corresponding quantities obtained for some similar molecules.
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
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
Malloum, Alhadji; Fifen, Jean Jules; Dhaouadi, Zoubeida; Engo, Serge Guy Nana; Jaidane, Nejm-Eddine
2015-11-21
A hydrogen bond network in ammonia clusters plays a key role in understanding the properties of species embedded in ammonia. This network is dictated by the structures of neutral ammonia clusters. In this work, structures of neutral ammonia clusters (NH3)n(=2-10) have been studied at M06-2X/6-31++G(d,p) and MP2/6-31++g(d,p) levels of theory. The analysis of the relative stabilities of various hydrogen bond types has also been studied and vibrational spectroscopy of the ammonia pentamer and decamer is investigated. We noted that M06-2X provides lower electronic energies, greater binding energies and higher structural resolution than MP2. We also noted that at the M06-2X level of theory, the binding energy converges to the experimental vaporization enthalpy faster than that at the MP2 level of theory. As a result, it is found that the M06-2X functional could be more suitable than the MP2 ab initio method in the description of structures and energies of ammonia clusters. However, we found that the electronic energy differences obtained at both levels of computation follow a linear relation with n (number of ammonia molecules in a cluster). As far as the structures of ammonia clusters are concerned, we proposed new "significant" isomers that have not been reported previously. The most remarkable is the global minimum electronic energy structure of the ammonia hexamer, which has an inversion centre and confirms experimental observation. Moreover, we reported the relative stabilities of neutral ammonia clusters for temperatures ranging from 25 to 400 K. The stability of isomers changes with the increase of the temperature. As a result, the branched and less bonded isomers are the most favored at high temperatures and disfavored at low temperatures, while compact and symmetric isomers dominate the population of clusters at low temperatures. In fine, from this work, the global minimum energy structures of ammonia clusters are known for the first time at a given temperature
Structure and dynamics of La(III) in aqueous solution An ab initio QM/MM MD approach
NASA Astrophysics Data System (ADS)
Hofer, Thomas S.; Scharnagl, Harald; Randolf, Bernhard R.; Rode, Bernd M.
2006-08-01
Ab initio QM/MM MD simulations have allowed to clarify some of the ambiguities arising from various studies on the hydrated La(III) ion. Both nine- and ten-coordinated hydrates co-exist and interchange in a dissociative process on the nano- or even subnanosecond scale, and thus much faster than any other trivalent main group or transition metal ions. The weak ion-ligand bond (53 N/m) supplies a reasonable explanation for it. The simulation results for La(III) are also compared to those for the isoelectronic ions Cs(I) and Ba(II) obtained by the same ab initio MD procedure, leading to conclusions on the influence of central ion charge on structural and dynamic properties of hydrate complexes.
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.
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.
An ab initio study of the fcc and hcp structures of helium
NASA Astrophysics Data System (ADS)
Røeggen, I.
2006-05-01
The hexagonal close packed (hcp) and face centered cubic (fcc) structures of helium are studied by using a new ab initio computational model for large complexes comprising small subsystems. The new model is formulated within the framework of the energy incremental scheme. In the calculation of intra- and intersystem energies, model systems are introduced. To each subsystem associated is a set of partner subsystems defined by a vicinity criterion. In the independent calculations of intra- and intersystem energies, the calculations are performed on model subsystems defined by the subsystems considered and their partner subsystems. A small and a large basis set are associated with each subsystem. For partner subsystems in a model system, the small basis set is adopted. By introducing a particular decomposition scheme, the intermolecular potential is written as a sum of effective one-body potentials. The binding energy per atom in an infinite crystal of atoms is the negative value of this one-body potential. The one- body potentials for hcp and fcc structures are calculated for the following nearest neighbor distances (d0): 4.6, 5.1, 5.4, 5.435, 5.5, 5.61, and 6.1a.u. The equilibrium distance is 5.44a.u. for both structures. The equilibrium dimer distance is 5.61a.u. For the larger distances, i.e., d0>5.4a.u., the difference of the effective one-body potentials for the two structures is less than 0.2μEh. However, the hcp structure has the lowest effective one-body potential for all the distances considered. For the smallest distance the difference in the effective one-body potential is 3.9μEh. Hence, for solid helium, i.e., helium under high pressure, the hcp structure is the preferred one. The error in the calculated effective one-body potential for the distance d0=5.61a.u. is of the order of 1μEh (≈0.5%).
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
Mishin, Y.; Mehl, M. J.; Papaconstantopoulos, D. A.; Voter, A. F.; Kress, J. D.
2001-06-01
We evaluate the ability of the embedded-atom method (EAM) potentials and the tight-binding (TB) method to predict reliably energies and stability of nonequilibrium structures by taking Cu as a model material. Two EAM potentials are used here. One is constructed in this work by using more fitting parameters than usual and including ab initio energies in the fitting database. The other potential was constructed previously using a traditional scheme. Excellent agreement is observed between ab initio, TB, and EAM results for the energies and stability of several nonequilibrium structures of Cu, as well as for energies along deformation paths between different structures. We conclude that not only TB calculations but also EAM potentials can be suitable for simulations in which correct energies and stability of different atomic configurations are essential, at least for Cu. The bcc, simple cubic, and diamond structures of Cu were identified as elastically unstable, while some other structures (e.g., hcp and 9R) are metastable. As an application of this analysis, nonequilibrium structures of epitaxial Cu films on (001)-oriented fcc or bcc substrates are evaluated using a simple model and atomistic simulations with an EAM potential. In agreement with experimental data, the structure of the film can be either deformed fcc or deformed hcp. The bcc structure cannot be stabilized by epitaxial constraints.
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
Observation and Structure Determination of an Oxide Quasicrystal Approximant
NASA Astrophysics Data System (ADS)
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.
2016-08-01
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 32 .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 TiO3 clusters, leading to a fundamental edge length of the tiling 6.7 Å.
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
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.
Ab initio self-consistent x-ray absorption fine structure analysis for metalloproteins.
Dimakis, Nicholas; Bunker, Grant
2006-12-01
X-ray absorption fine structure is a powerful tool for probing the structures of metals in proteins in both crystalline and noncrystalline environments. Until recently, a fundamental problem in biological XAFS has been that ad hoc assumptions must be made concerning the vibrational properties of the amino acid residues that are coordinated to the metal to fit the data. Here, an automatic procedure for accurate structural determination of active sites of metalloproteins is presented. It is based on direct multiple-scattering simulation of experimental X-ray absorption fine structure spectra combining electron multiple scattering calculations with density functional theory calculations of vibrational modes of amino acid residues and the genetic algorithm differential evolution to determine a global minimum in the space of fitting parameters. Structure determination of the metalloprotein active site is obtained through a self-consistent iterative procedure with only minimal initial information.
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)
Yue, Sheng-Ying; Zhang, Xiaoliang; Stackhouse, Stephen; Qin, Guangzhao; Di Napoli, Edoardo; Hu, Ming
2016-08-01
Many physical properties of metals can be understood in terms of the free electron model, as proven by the Wiedemann-Franz law. According to this model, electronic thermal conductivity can be inferred from the Boltzmann transport equation (BTE). However, the BTE does not perform well for some complex metals, such as Cu. Moreover, the BTE cannot clearly describe the origin of the thermal energy carried by electrons or how this energy is transported in metals. The charge distribution of conduction electrons in metals is known to reflect the electrostatic potential of the ion cores. Based on this premise, we develop a methodology for evaluating electronic thermal conductivity of metals by combining the free electron model and nonequilibrium ab initio molecular dynamics simulations. We confirm that the kinetic energy of thermally excited electrons originates from the energy of the spatial electrostatic potential oscillation, which is induced by the thermal motion of ion cores. This method directly predicts the electronic thermal conductivity of pure metals with a high degree of accuracy, without explicitly addressing any complicated scattering processes of free electrons. Our methodology offers a route to understand the physics of heat transfer by electrons at the atomistic level. The methodology can be further extended to the study of similar electron-involved problems in materials, such as electron-phonon coupling, which is underway currently.
NASA Astrophysics Data System (ADS)
Aarset, Kirsten; Hagen, Kolbjørn; Stølevik, Reidar
2001-06-01
The structure and conformational composition of 2-chlorobutane and 2-bromobutane have been studied by gas-phase electron diffraction (GED) at 25°C, together with ab initio molecular orbital calculations (HF/6-311+G(d,p)). These molecules may exist as three distinguishable conformers (G+, A, and G-). The symbols refer to anti (A) with a torsion angle Φ2(X 8-C 2-C 3-C 4) of about 180° and gauche (G+ and G-) with torsion angles Φ2(X 8-C 2-C 3-C 4) of about +60° and 300°(-60°), respectively. It was not possible; from our GED-data alone, to accurately determine the conformational composition because the distance distributions for two of the conformers (G+ and G-) are very similar. The conformational composition for 2-chlorobutane obtained from the ab initio calculations (G+ 62%, A 25% G- 13%) was found to fit the experimental data quite well. For 2-bromobutane the ab initio calculated conformational composition (G+ 58%, A 28% G- 14%) did not, however, fit the experimental data. Here a much better fit was obtained by using only 10% of the A conformer and using the relative energy for the two gauche conformers, as obtained in the ab initio molecular orbital calculations, to calculate the relative amounts of the two gauche forms (G+ 73%, A 10% G- 17%). The results for the principal distances ( rg) and angles ∠ α for the G+ conformer of 2-chlorobutane, with estimated 2 σ uncertainties, obtained from the combined GED/ab initio study are: r( C1- C2)=1.524(3) Å, r( C2- C3)=1.528(3) Å, r( C3- C4)=1.539(3) Å, r( C- Cl)=1.812(3) Å, r( C- H) ave=1.098(4) Å, ∠C 1C 2C 3=111.5(16)°, ∠C 2C 3C 4=113.3(5)°, ∠C 1C 2C1=110.4(9)°. The results for the G+ conformer of 2-bromobutane are: r( C1- C2)=1.526(4) Å, r( C2- C3)=1.530(4) Å, r( C3- C4)=1.540(4) Å, r( C- Br)=1.982(5) Å, r( C- H) ave=1.111(8) Å, ∠C 1C 2C 3=112.5(16)°, ∠C 2C 3C 4=114.6(15)°, ∠C 1C 2Br=110.1(16)°. Only average values for r(C-C), r(C-H), ∠CCC, and ∠CCH could be determined in the
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)
Letchworth-Weaver, Kendra; Umbright, Christine; Chan, Maria; Fenter, Paul; Arias, T. A.
Understanding the physics of the interface between a charged electrode surface and a fluid electrolyte would inform design of electrochemical energy storage and conversion devices. However, such studies require a simultaneously accurate yet inherently multi-scale theory. Joint density-functional theory (JDFT) bridges the relevant length-scales by joining a fully ab initio description of the electrode with a low computational cost, yet atomically detailed classical DFT description of the liquid electrolyte structure. Leveraging JDFT within our framework to treat charged systems in periodic boundary conditions, we can predict the voltage-dependent structure and energetics of solvated ions at the interface between graphitic and single-crystalline metallic electrodes and technologically relevant liquid electrolytes. First, we elucidate the physical origin of the experimentally measured voltage-dependent differential capacitance of an Ag(111) electrode in aqueous NaF electrolyte, examining the crucial role of ion de-solvation and physisorption onto the electrode surface. We go on to compare the JDFT-predicted interfacial liquid structure next to a graphitic electrode with results obtained from X-ray reflectivity measurements and ab initio molecular dynamics simulations.
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.
Raybaud, P.; Hafner, J.; Kresse, G.; Kasztelan, S.; Toulhoat, H.
2000-02-15
The determination of the local structure of cobalt- or nickel-promoted MoS{sub 2}-based hydrodesulfurization catalysts is of interest for understanding the mechanism leading to an increased activity brought by cobalt or nickel, the so-called synergetic effect. For that reason, the authors carried out ab initio calculations using density functional theory under the generalized gradient approximation for periodic systems. The edge substitution model emerges as the most stable structure and provides an excellent agreement with local structures experimentally determined on real catalysts by in situ extended X-ray absorption fine structure. The authors studied the absorption of sulfur on the active edge surface of the promoted MoS{sub 2} catalyst and determined the equilibrium coverage under sulfiding conditions. It is demonstrated that the incorporation of promoter atoms has a strong influence on the sulfur-metal bond energy at the surface and in particular leads to a reduction of the equilibrium S coverage of the active metal sites. A comparative study on the effects of Co, Ni, and Cu atoms as promoters was performed. Detailed results on the surface electronic structure of promoted MoS{sub 2} are presented.
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.
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)
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.
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.
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.
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
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.
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.
NASA Astrophysics Data System (ADS)
Andriyevsky, B.; Doll, K.; Cakmak, G.; Jansen, M.; Niemer, A.; Betzler, K.
2011-09-01
An ab initio density functional theory-based study of the electronic band structure, the elastic, electric, elastoelectric, and linear and nonlinear optical properties of the new ion conductor LiB6O9F, has been performed. The computed band structure reveals a wide direct band gap. The coefficients of the second order nonlinear susceptibility χ(2) were found to be comparable to those of KH2PO4. Corresponding experimental investigations of second harmonic generation comply with the respective ab initio calculations.
Zhu, Tong; Zhang, John Z H; He, Xiao
2014-09-14
In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.
Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D.
2013-11-21
We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform.
NASA Astrophysics Data System (ADS)
Gaiduk, Alex P.; Zhang, Cui; Gygi, François; Galli, Giulia
2014-06-01
We present a study of a dilute solution (1 M) of NaCl in water, carried out using ab initio molecular dynamics with semilocal and hybrid functionals. We showed that the structural and electronic properties of the solute and the solvent are the same as those obtained in the infinite dilution limit, i.e. for aqueous ions in the presence of a uniform compensating background. Compared to semilocal functionals, simulations with hybrid functionals yield a less structured solution with a smaller number of hydrogen bonds and a larger coordination number for the Cl- anion. In addition, hybrid functionals predict qualitatively correct positions of the energy levels of the ions with respect to the valence band of water.
NASA Astrophysics Data System (ADS)
Binev, Ivan G.; Stamboliyska, Bistra A.; Velcheva, Evelina A.
1996-08-01
The structure of o-sulfobenzimide (saccharin) and of its nitranion has been studied on the basis of both infrared spectra and ab initio force field calculations. A good agreement has been found between the theoretical and experimental spectroscopic characteristics of the particles studied. The theoretical method used gives a good description of the strong spectral changes caused by the conversion of the saccharin molecule into the corresponding nitranion. The structural changes which accompany this conversion are essential and they spread over the whole sulfocarboximide group and the adjacent bonds. The nitranionic charge is delocalized over the phenylene group (0.29 e -), sulfonyl group (0.26 e -), nitranionic center (0.25 e -), and carbonyl group (0.20 e -).
Durig, James R; Zheng, Chao
2007-11-01
Variable temperature (-105 to -150 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylisothiocyanate, CH(3)CH(2)NCS, dissolved in liquid krypton have been recorded. Additionally the infrared spectra of the gas and solid have been re-investigated. These spectroscopic data indicate a single conformer in all physical states with a large number of molecules in the gas phase at ambient temperature in excited states of the CN torsional mode which has a very low barrier to conformational interchange. To aid in the analyses of the vibrational and rotational spectra, ab initio calculations have been carried out by the perturbation method to the second order (MP2) with valence and core electron correlation using a variety of basis sets up to 6-311+G(2df,2pd). With the smaller basis sets up to 6-311+G(d,p) and cc-PVDZ, the cis conformer is indicated as a transition state with all larger basis sets the cis conformer is the only stable form. The predicted energy difference from these calculations between the cis form and the higher energy trans conformer is about 125 cm(-1) which represents essentially the barrier to internal rotation of the NCS group (rotation around NC axis). Density functional theory calculation by the B3LYP method with the same basis sets predicts this barrier to be about 25 cm(-1). By utilizing the previously reported microwave rotational constants with the structural parameters predicted by the ab initio MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the cis form. The determined heavy atom parameters are: r(NC)=1.196(5), r(CS)=1.579(5), r(CN)=1.439(5), r(CC)=1.519(5)A for the distances and angles of angleCCN=112.1(5), angleCNC=146.2(5), angleNCS=174.0(5) degrees . The centrifugal distortion constants, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and compared to experimental
Ab Initio Determined Phase Diagram of Clean and Solvated Muscovite Mica Surfaces.
Vatti, Anoop Kishore; Todorova, Mira; Neugebauer, Jörg
2016-02-01
Focusing on muscovite mica, the most significant phyllosilicate in the mica series, we determine its surface phase diagram employing density functional theory. Surfaces in vacuum and in more realistic environmental conditions, that is, the surface in contact with water or an ionic liquid, are considered. These results naturally explain experimental observations such as the swelling of mica when it comes into contact with water.
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.
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.
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.
Ab initio investigations of the electronic structure and chemical bonding of Li2ZrN2
NASA Astrophysics Data System (ADS)
Matar, S. F.; Pöttgen, R.; Al Alam, A. F.; Ouaini, N.
2012-06-01
The electronic structure of the ternary nitride Li2ZrN2 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 Li2ZrN2 and they become less intense upon removal of Li. From energy differences the partial delithiation leading to Li2-xZrN2 (x=∼1) is favored.
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
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 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.
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.
Yin, Huabing; Ma, Yuchen Mu, Jinglin; Liu, Chengbu; Hao, Xiaotao; Yi, Zhijun
2014-06-07
The excited states of small-diameter diamond nanoparticles in the gas phase are studied using the GW method and Bethe-Salpeter equation (BSE) within the ab initio many-body perturbation theory. The calculated ionization potentials and optical gaps are in agreement with experimental results, with the average error about 0.2 eV. The electron affinity is negative and the lowest unoccupied molecular orbital is rather delocalized. Precise determination of the electron affinity requires one to take the off-diagonal matrix elements of the self-energy operator into account in the GW calculation. BSE calculations predict a large exciton binding energy which is an order of magnitude larger than that in the bulk diamond.
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.
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)
Wolff, Stephen K.; Jayatilaka, Dylan; Chandler, Graham S.
1995-09-01
Spin-orbit interaction plays a significant role in determining the magnetic density in some transition metal complexes. We present a new ab initio technique, based on an extension of unrestricted Hartree-Fock theory, which includes nonperturbatively these spin-orbit effects, and simultaneously also the effects of a finite magnetic field. We also present a new and efficient method for calculating magnetic structure factors, based on the current density rather than magnetic dipole moment density, for a crystal composed of noninteracting molecular fragments. These structure factors are directly comparable to polarized neutron diffraction experiments. Results for the Cs3CoCl5 crystal are compared with experiment and previous studies. Without one-electron spin-orbit coupling terms, the magnitudes of the predicted structure factors are on average 10-15 % too low, whereas, with the spin-orbit terms, the magnitudes are 25-30% too high. Using an effective nuclear charge for Co in the spin-orbit term brings the results into much better agreement, and suggests that the two-electron spin-orbit shielding terms omitted in the present work are important. For over one quarter of the reflections studied, the magnetic contribution to the structure factors is more than 20% of the nuclear contribution.
NASA Technical Reports Server (NTRS)
Herbst, Eric; Winnewisser, G.; Yamada, K. M. T.; Defrees, D. J.; Mclean, A. D.
1989-01-01
A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.
Anisotropic elasticity of IVB transition-metal mononitrides determined by ab initio calculations
Nagao, Shijo; Nordlund, K.; Nowak, R.
2006-04-01
Elastic parameters of IVB transition-metal mononitrides, TiN, ZrN, and HfN in the cubic NaCl crystal structure have been calculated by means of density-functional theory with the generalized gradient approximation. The elastic constants c{sub 11}, c{sub 12}, and c{sub 44} were shown to be sufficiently converged with the density of the k-point mesh in the deformed Brillouin zone to discuss the elastic anisotropy of the systems. It was found that the anisotropy coefficient {kappa}{identical_to}(c{sub 11}-c{sub 12})/2c{sub 44} increases with the atomic number of the metal element, i.e., HfN exhibits as strong anisotropy as {kappa}=2.02. The Young's modulus of HfN along <100> is approximately two times higher than that along <111>. Moreover, analysis of the deformation energy by the applied strain modes shows that this elastic anisotropy originates from the strong covalent bonding between metal and nitrogen atoms along <100>.
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.
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.
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
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.
NASA Astrophysics Data System (ADS)
Rajesh, C.; Majumder, C.; Rajan, M. G. R.; Kulshreshtha, S. K.
2005-12-01
The geometric and electronic structure of the Pbn clusters (n=2-15) has been calculated to elucidate its structural evolution and compared with other group-IV elemental clusters. The search for several low-lying isomers was carried out using the ab initio molecular dynamics simulations under the framework of the density functional theory formalism. The results suggest that unlike Si, Ge, and Sn clusters, which favor less compact prolate shape in the small size range, Pb clusters favor compact spherical structures consisting of fivefold or sixfold symmetries. The difference in the growth motif can be attributed to their bulk crystal structure, which is diamond-like for Si, Ge, and Sn but fcc for Pb. The relative stability of Pbn clusters is analyzed based on the calculated binding energies and second difference in energy. The results suggest that n=4 , 7, 10, and 13 clusters are more stable than their respective neighbors, reflecting good agreement with experimental observation. Based on the fragmentation pattern it is seen that small clusters up to n=12 favor monomer evaporation, larger ones fragment into two stable daughter products. The experimental observation of large abundance for n=7 and lowest abundance of n=14 have been demonstrated from their fragmentation pattern. Finally a good agreement of our theoretical results with that of the experimental findings reported earlier implies accurate predictions of the ground state geometries of these clusters.
NASA Astrophysics Data System (ADS)
Fausto, Rui; Quinteiro, Graciete; Breda, Susana
2001-12-01
The molecular structures and vibrational spectra of the monomeric forms of α- and γ-pyrones were investigated by ab initio MO calculations, undertaken at the HF/6-31G ∗ level of theory, and vibrational spectroscopy, including matrix-isolation FTIR spectroscopy. A complete assignment of the vibrational spectra of the studied compounds isolated in an argon matrix, at 8 K, or in the condensed phases, at room temperature, is presented and the vibrational data correlated with some important structural parameters. It is shown that the intermolecular interactions in the room temperature condensed phases do not affect the structure and vibrational properties of the studied molecules strongly, though the vibrational results clearly reveal minor changes induced in the carbonyl groups that indirectly affect the electron distribution in the whole pyrone rings, leading to an increase in their π-electron delocalization. For the isolated monomers, both structural and vibrational results point to a relatively weak π-electron delocalization in both α- and γ-pyrone moieties.
Mandal, Pankaj K; Ramdass, Dharmender J; Arunan, E
2005-07-21
This paper reports the rotational spectrum and structure of the Ar2-H2S complex and its HDS and D2S isotopomers. The ground state structure has heavy-atom C2v symmetry with the two Ar atoms indistinguishable and H2S freely rotating as evinced by the fact that asymmetric top energy levels with Kp=odd levels are missing. The rotational constants for the parent isotopomer are: A=1733.115(1) MHz, B=1617.6160(5) MHz and C=830.2951(2) MHz. Unlike the Ar-H2S complex, the Ar2-H2S does not show an anomalous isotopic shift in rotational constants on deuterium substitution. However, the intermolecular potential is still quite floppy, leading to very different centrifugal distortion constants for the three isotopomers. The Ar-Ar and Ar-c.m.(H2S) distances are determined to be 3.820 A and 4.105 A, respectively. The A rotational constants for Ar2-H2S/HDS/D2S isotopomers are very close to each other and to the B constant of free Ar2, indicating that H2S does not contribute to the moment of inertia about the a-axis. Ab initio calculations at MP2 level with aug-cc-pVQZ basis set lead to an equilibrium C2v minimum structure with the Ar-Ar line perpendicular to the H-H line and the S away from Ar2. The centrifugal distortion constants, calculated using the ab initio force field, are in reasonable agreement with the experimental values. However, they do not show the variation observed for different isotopmers. The binding energy of Ar2-H2S has been determined to be 507 cm-1(6.0 kJ mol-1) by CBS extrapolation after correcting for basis set superposition error. Potential energy scans point out that the barrier for internal rotation of H2S about its b axis is only 10 cm-1 and it is below the zero point energy (13.5 cm-1) in this torsional degree of freedom. Internal rotation of H2S about its a- and c-axes also have small barriers of about 50 cm-1 only, suggesting that H2S is extremely floppy within the complex.
Ab initio powder structure analysis and theoretical study of two thiazole derivatives
NASA Astrophysics Data System (ADS)
Hazra, Dipak K.; Mukherjee, Monika; Mukherjee, Alok K.
2013-05-01
Crystal structures of 2-amino-5-methylthiazole (1) and 4-(6-methyl-2-benzothiazolyl) aniline (2) have been determined from laboratory X-ray powder diffraction data along with an analysis of the Hirshfeld surfaces and 2D-fingerprint plots, facilitating a comparison of intermolecular interactions. The DFT optimized molecular geometries in (1) and (2) agree closely with those obtained from the crystallographic studies. An interplay of Nsbnd H⋯N/S hydrogen bonds and C/Nsbnd H⋯π interactions connects the molecules of (1) and (2) into two-dimensional framework. Hirshfeld surface analysis of (1) indicates that the H⋯H and H⋯π contacts can account for 56.9% of the Hirshfeld surface area, whereas the corresponding fraction in (2) is 80.5%.
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.
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).
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.
Vchirawongkwin, Viwat; Kritayakornupong, Chinapong; Tongraar, Anan; Rode, Bernd M
2012-10-14
Hydration structure and dynamics of an aqueous Sc(III) solution were characterized by means of an extended ab initio quantum mechanical/molecular dynamical (QM/MM) molecular dynamics simulation at Hartree-Fock level. A monocapped trigonal prismatic structure composed of seven water molecules surrounding scandium(III) ion was proposed by the QM/MM simulation including the quantum mechanical effects for the first and second hydration shells. The mean Sc(III)-O bond length of 2.14 Å was identified for six prism water molecules with one capping water located at around 2.26 Å, reproducing well the X-ray diffraction data. The Sc(III)-O stretching frequency of 432 cm(-1) corresponding to a force constant of 130 N m(-1), evaluated from the enlarged QM/MM simulation, is in good agreement with the experimentally determined value of 430 cm(-1) (128 N m(-1)). Various water exchange processes in the second hydration shell of the hydrated Sc(III) ion predict a mean ligand residence time of 7.3 ps.
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).
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…
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
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.
Ab-initio phasing in protein crystallography
NASA Astrophysics Data System (ADS)
van der Plas, J. L.; Millane, Rick P.
2000-11-01
The central problem in the determination of protein structures form x-ray diffraction dada (x-ray crystallography) corresponds to a phase retrieval problem with undersampled amplitude data. Algorithms for this problem that have an increased radius of convergence have the potential for reducing the amount of experimental work, and cost, involved in determining protein structures. We describe such an algorithm. Application of the algorithm to a simulated crystallographic problem shows that it converges to the correct solution, with no initial phase information, where currently used algorithms fail. The results lend support to the possibility of ab initio phasing in protein crystallography.
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
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.
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.
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.
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
NASA Astrophysics Data System (ADS)
Anandan, K.; Kolandaivel, P.; Kumaresan, R.
We studied molecular structural conformations and hydration of internally hydrogen-bonded salicylic acid using ab initio and density functional theory methods. Molecular geometries and energetical parameters were obtained in gaseous phase using MP2 and B3LYP levels of theory, implementing the 6-311G(2d,2p) atomic basis set. Chemical hardness and chemical potential were calculated at HF/6-311G(2d,2p) level of theory for all the optimized structures, and the principle of maximum hardness was tested. The condensed Fukui functions were calculated using the atomic charges obtained through a natural population analysis scheme for all optimized structures at B3LYP/6-311G(2d,2p) level of theory, and the most reactive sites of the molecules were identified. NMR studies were carried out for all the conformers in gaseous phase on the basis of Cheeseman et al.'s method at B3LYP/6-311G(2d,2p) level of theory; the calculated chemical shift values are discussed. The self-consistent reaction field theory (SCRF) was used to optimize all the conformers in aqueous phase (ɛ = 78.39) at B3LYP/6-311G(2d,2p) level of theory and the solvent effect was studied. The geometrical and energetical parameters of all the conformers are compared and analyzed. The dimeric structure of the most stable conformer in the gaseous phase was optimized at B3LYP/6-311G(2d,2p) level of theory and the interaction energy studied. Selected conformers were allowed to interact with water molecule; optimized parameters are discussed. Vibrational frequency analyses were performed at MP2/6-311G(2d,2p) level of theory and the stationary point corresponding to local minima without imaginary frequencies are obtained for all the optimized structures.
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.
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.
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)
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.
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.
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.
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.
Novel gene complex structure determination
Gatewood, J.M.
1997-08-01
This is the final report of a one-year, Laboratory-Directed Research and Development (LORD) project at the Los Alamos National Laboratory. `Operative` chromatin containing exclusively the minor hasten variants was successfully isolated. Linker hasten H1 is quantitatively missing from operative chromatin. One of the aims of this proposal was to determine the proteins responsible for stabilizing operative chromatin. This chromatin is stabilized by microtubule proteins tar and tubulin. Another goal of this project was the structural characterization of operate chromatin nucleosomes. Using solution scattering, nucleosomes containing the minor variants were shown to be structurally distinct from major variant containing nucleosomes. The unusual structure and stabilization of operative chromatin by microtubule proteins provides a possible mechanism for direct interaction of transcription machinery with specific chromatin domains.
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.
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
NASA Astrophysics Data System (ADS)
Lemke, Kono H.; Seward, Terry M.
2008-07-01
Reports of the high ion content of steam and low-density supercritical fluids date back to the work of Carlon [Carlon H. R. (1980) Ion content of air humidified by boiling water. J. Appl.Phys.51, 171-173], who invoked ion and neutral-water clustering as mechanism to explain why ions partition into the low-density aqueous phase. Mass spectrometric, vibrational spectroscopic measurements and quantum chemical calculations have refined this concept by proposing strongly bound ion-solvent aggregates and water clusters such as Eigen- and Zundel-type proton clusters H 3O +·(H 2O) m and the more weakly bound water oligomers (H 2O) m. The extent to which these clusters affect fluid chemistry is determined by their abundance, however, little is known regarding the stability of such moieties in natural low-density high-temperature fluids. Here we report results from quantum chemical calculations using chemical-accuracy multi-level G3 (Curtiss-Pople) and CBS-Q theory (Peterson) to address this question. In particular, we have investigated the cluster structures and clustering equilibria for the ions HO·(HO)m(HS)n,NH4+·(HO)m(HS)n and H 3S +·(H 2O) m(H 2S) n, where m ⩽ 6 and n ⩽ 4, at 300-1000 K and 1 bar as well as under vapor-liquid equilibrium conditions between 300 and 646 K. We find that incremental hydration enthalpies and entropies derived from van't Hoff analyses for the attachment of H 2O and H 2S onto H 3O +, NH4+ and H 3S + are in excellent agreement with experimental values and that the addition of water to all three ions is energetically more favorable than solvation by H 2S. As clusters grow in size, the energetic trends of cluster hydration begin to reflect those for bulk H 2O liquids, i.e. calculated hydration enthalpies and entropies approach values characteristic of the condensation of bulk water (Δ Ho = -44.0 kJ mol -1, Δ So = -118.8 J K mol -1). Water and hydrogen sulfide cluster calculations at higher temperatures indicate that a significant
NASA Astrophysics Data System (ADS)
DiStasio, Robert A.; Santra, Biswajit; Li, Zhaofeng; Wu, Xifan; Car, Roberto
2014-08-01
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.
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.
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.
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
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.
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.
Rohrer, J; Ruberto, C; Hyldgaard, P
2010-01-13
We present a strategy to identify energetically favourable oxide structures in thin-film geometries. Thin-film candidate configurations are constructed from a pool of sublattices of stable and metastable oxide bulk phases. Favourable stoichiometric compositions and atomic geometries are identified by comparing total and Gibbs free energies of the relaxed configurations. This strategy is illustrated for thin-film alumina on TiC, materials which are commonly fabricated by chemical vapour deposition (CVD) and used as wear-resistant multilayer coatings. Based on the standard implementation of ab initio thermodynamics, with an assumption of equilibrium between molecular O(2) and the oxide, we predict a stability preference of TiC/alumina configurations that show no binding across the interface. This result is seemingly in conflict with the wear-resistant character of the material and points towards a need for extending standard ab initio thermodynamics to account for relevant growth environments. PMID:21386219
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
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.
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.
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.
Structural properties of iron-phosphate glasses: spectroscopic studies and ab initio simulations.
Stoch, Pawel; Szczerba, Wojciech; Bodnar, Wiktor; Ciecinska, Malgorzata; Stoch, Agata; Burkel, Eberhard
2014-10-01
Vitrification is the most effective method for the immobilization of hazardous waste by incorporating toxic elements into a glass structure. Iron phosphate glasses are presently being considered as matrices for the storage of radioactive waste, even of those which cannot be vitrified using conventional borosilicate waste glass. In this study, a structural model of 60P2O5-40Fe2O3 glass is proposed. The model is based on the crystal structure of FePO4 which is composed of [FeO4][PO4] tetrahedral rings. The rings are optimized using the DFT method and the obtained theoretical FTIR and Raman spectra are being compared with their experimental counterparts. Moreover, the proposed model is in very good agreement with X-ray absorption fine structure spectroscopy (XANES/EXAFS) and Mössbauer spectroscopy measurements. According to the calculations the Fe(3+) is in tetrahedral and five-fold coordination. The maximal predicted load of waste constituents into the glass without rebuilding of the structure is 30 mol%. Below this content, waste constituents balance the charge of [FeO4](-) tetrahedra which leads to their strong bonding to the glass resulting in an increase of the chemical durability, transformation and melting temperatures and density. PMID:25115558
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.
Structural determinants of GAD antigenicity.
Arafat, Yasir; Fenalti, Gustavo; Whisstock, James C; Mackay, Ian R; Garcia de la Banda, Maria; Rowley, Merrill J; Buckle, Ashley M
2009-12-01
Our aim was to ascertain structural determinants of autoantigenicity based on the model of the diabetes autoantigen glutamic acid decarboxylase 65 kDa isoform (GAD65) in comparison with that of the non-autoantigenic isoform GAD67. This difference exists despite the two isoforms having the same fold and high sequence identity. Autoantibodies to GAD65 precede the development of type 1 diabetes and are clinical markers of this and certain neural autoimmune diseases. To date, epitope mapping has been based on particular amino acid differences between the two isoforms, and there is no explanation as to why autoantibodies that react with GAD65 only infrequently cross-react with GAD67. To characterize each isoform of the enzyme and gain insights into their contrasting autoantigenic properties, we have used the recently determined crystal structures of GAD65 and GAD67 to compare their structure, hydrophobicity, electrostatics, flexibility and physiochemical properties. The results revealed striking differences which appear almost exclusively at the C-terminal domain of the isoforms. Whereas GAD65 displayed a highly charged and flexible C-terminal domain containing numerous patches of high electrostatic and solvation energies, these characteristics were absent in the GAD67 molecule. Additionally, analysis indicated potential N-terminal and PLP domain binding sites surrounding the C-terminal domain of GAD65, a major region of autoantigenic activity, but not of GAD67. These features agree with good accuracy with published epitope-mapping data. Our analysis suggests that the high flexibility and charge of GAD65 in the C-terminal domain is coupled with the mobility of its catalytic loop, a property that is absolutely required for its enzymatic function. Thus, the structural features that distinguish GAD65 from GAD67 as a B cell autoantigen are related to functional requirements for its enzymatic mechanism. This could well apply to the various other enzyme autoantigens and, if
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)
Sun, Hosung; Freed, Karl F.
1984-01-01
The exact ab initio effective valence shell Hamiltonian, which is mimicked by semiempirical theories of valence, is calculated for CH at 11 bond lengths using quasidegenerate many-body perturbation theory to incorporate extensive correlation contributions. Least squares fits of the bond length dependence of the calculated CH matrix elements provide simple formulas which are compared with the intuitive forms introduced into semiempirical theories. Some of the semiempirical formulas, e.g., one-center, one-electron integrals and two-center, two-electron integrals, are in good agreement with our correlated ab initio calculations, while others display substantial departures. For example, the bond length dependence of one-center, two-electron integrals, which are assumed to be independent of bond length in semiempirical theories, is substantial but physically understandable. Corrections are found to the assumed proportionality of resonance and overlap integrals. The bond length dependence of nonclassical three-electron integrals is presented along with the hybrid and exchange integrals that are ignored in zero differential overlap methods.
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 studies of electronic and structural transitions in low-Z liquids under extreme conditions
NASA Astrophysics Data System (ADS)
Bonev, Stanimir
2007-06-01
The liquids of group I elements (H, Li, Na, and K) are studied using first principles theory. It will be shown that they undergo electronic and structural transitions analogous to that observed in their solids, but commencing at much lower pressure in the presence of disorder. These changes result in exotic melting behavior and in molten phases with unusual properties. The theoretical predictions will be compared with experimental data and ways for further experimental verification of the theoretical results will be suggested.
Ab-initio structural search in solid oxygen at high pressure: from zero to finite temperature
NASA Astrophysics Data System (ADS)
Cogollo-Olivo, B. H.; Montoya, J. A.
2016-08-01
The crystal structure of solid oxygen in the terapascal (TPa) regime has been investigated with Density Functional Theory and the Random Search algorithm at zero temperature. We also considered the effect of the entropy at finite temperatures using the QuasiHarmonic Approximation, and we found that the regime of stability of solid oxygen differs strongly from the results predicted at zero temperature. Finally, we provide some insights of oxygen as a chalcogen element.
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.
Helles, Glennie
2008-04-01
Protein structure prediction is one of the major challenges in bioinformatics today. Throughout the past five decades, many different algorithmic approaches have been attempted, and although progress has been made the problem remains unsolvable even for many small proteins. While the general objective is to predict the three-dimensional structure from primary sequence, our current knowledge and computational power are simply insufficient to solve a problem of such high complexity. Some prediction algorithms do, however, appear to perform better than others, although it is not always obvious which ones they are and it is perhaps even less obvious why that is. In this review, the reported performance results from 18 different recently published prediction algorithms are compared. Furthermore, the general algorithmic settings most likely responsible for the difference in the reported performance are identified, and the specific settings of each of the 18 prediction algorithms are also compared. The average normalized r.m.s.d. scores reported range from 11.17 to 3.48. With a performance measure including both r.m.s.d. scores and CPU time, the currently best-performing prediction algorithm is identified to be the I-TASSER algorithm. Two of the algorithmic settings--protein representation and fragment assembly--were found to have definite positive influence on the running time and the predicted structures, respectively. There thus appears to be a clear benefit from incorporating this knowledge in the design of new prediction algorithms.
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
Wang, Xue B.; Woo, Hin-koon; Wang, Lai S.; Minofar, Babak; Jungwirth, Pavel
2006-04-20
The electronic structure and electron affinity of the acetyloxyl radical (CH3COO) were investigated by low-temperature anion photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of the acetate anion (CH3COO-) were obtained at two photon energies (355 and 266 nm) and under three different temperatures (300, 70, and 20 K) using a new low temperature ion-trap photoelectron spectroscopy apparatus. In contrast to a featureless spectrum at 300 K, a well-resolved vibrational progression corresponding to the OCO bending mode was observed at low temperatures in the 355 nm spectrum, yielding an accurate electron affinity for the acetyloxyl radical as 3.250 + 0.010 eV. This experimental result is supported by ab initio calculations, which also indicate three low-lying electronic states observed in the 266 nm spectrum. The calculations suggest a 19° decrease of the OCO angle upon detaching an electron from acetate, consistent with the vibrational progression observed experimentally.
Bharadwaj, Vivek S; Vyas, Shubham; Villano, Stephanie M; Maupin, C Mark; Dean, Anthony M
2015-02-14
The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter
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.
Davis, Sergio; Gutiérrez, Gonzalo
2011-12-14
First-principles molecular dynamics calculations of the structural, elastic, vibrational and electronic properties of amorphous Al(2)O(3), in a system consisting of a supercell of 80 atoms, are reported. A detailed analysis of the interatomic correlations allows us to conclude that the short-range order is mainly composed of AlO(4) tetrahedra, but, in contrast with previous results, also an important number of AlO(6) octahedra and AlO(5) units are present. The vibrational density of states presents two frequency bands, related to bond-bending and bond-stretching modes. It also shows other recognizable features present in similar amorphous oxides. We also present the calculation of elastic properties (bulk modulus and shear modulus). The calculated electronic structure of the material, including total and partial electronic density of states, charge distribution, electron localization function and the ionicity for each species, gives evidence of correlation between the ionicity and the coordination for each Al atom.
Ab initio structural and vibrational properties of GaAs diamondoids and nanocrystals
NASA Astrophysics Data System (ADS)
Abdulsattar, Mudar Ahmed; Hussein, Mohammed T.; Hameed, Hadeel Ali
2014-12-01
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-1) compared to experimental 0.035 eV (285.2 cm-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 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.
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.
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.
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.
Ab initio calculations of quasiparticle band structure in correlated systems: LDA++ approach
NASA Astrophysics Data System (ADS)
Lichtenstein, A. I.; Katsnelson, M. I.
1998-03-01
We discuss a general approach to a realistic theory of the electronic structure in materials containing correlated d or f electrons. The main feature of this approach is the taking into account of the energy dependence of the electron self-energy with the momentum dependence being neglected (local approximation). It allows us to consider such correlation effects as the non-Fermi-step form of the distribution function, the enhancement of the effective mass including Kondo resonances,'' the appearance of the satellites in the electron spectra, etc. To specify the form of the self-energy, it is useful to distinguish (according to the ratio of the on-site Coulomb energy U to the bandwidth W) three regimes-strong, moderate, and weak correlations. In the case of strong interactions (U/W>1-rare-earth system) the Hubbard-I approach is the most suitable. Starting from an exact atomic Green function with the constrained density matrix nmm' the band-structure problem is formulated as the functional problem on nmm' for f electrons and the standard local-denisty-approximation functional for delocalized electrons. In the case of moderate correlations (U/W~1-metal-insulator regime, Kondo systems) we start from the d=∞ dynamical mean-field iterative perturbation scheme of Kotliar and co-workers and also make use of our multiband atomic Green function for constrained nmm'. Finally for the weak interactions (U/W<1-transition metals) the self-consistent diagrammatic fluctuation-exchange approach of Bickers and Scalapino is generalized to the realistic multiband case. We present two-band, two-dimensional model calculations for all three regimes. A realistic calculation in the Hubbard-I scheme with the exact solution of the on-site multielectron problem for f(d) shells was performed for mixed-valence 4f compound TmSe, and for the classical Mott insulator NiO.
NASA Astrophysics Data System (ADS)
Dacal, Luis C. O.; Cantarero, A.
2014-03-01
Most III-V semiconductors, which acquire the zinc-blende phase as bulk materials, adopt the metastable wurtzite phase when grown in the form of nanowires. These are new semiconductors with new optical properties, in particular, a different electronic band gap when compared with that grown in the zinc-blende phase. The electronic gap of wurtzite InAs at the \\Gamma -point of the Brillouin zone ({{E}_{0}} gap) has been recently measured, {{E}_{0}}=0.46 eV at low temperature. The electronic gap at the A-point of the Brillouin zone (equivalent to the L-point in the zinc-blende structure, {{E}_{1}}) has also been obtained recently based on a resonant Raman scattering experiment. In this work, we calculate the band structure of InAs in the zinc-blende and wurtzite phases, using the full potential linearized augmented plane wave method, including spin-orbit interaction. The electronic band gap has been improved through the modified Becke-Johnson exchange-correlation potential. Both the {{E}_{0}} and {{E}_{1}} gaps agree very well with the experiment. From the calculations, a crystal field splitting of 0.122 eV and a spin-orbit splitting of 0.312 eV (the experimental value in zinc-blende InAs is 0.4 eV) has been obtained. Finally, we calculate the dielectric function of InAs in both the zinc-blende and wurtzite phases and a comparative discussion is given.
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
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)
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.
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.
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.
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.
NASA Astrophysics Data System (ADS)
Jalilian, Jaafar; Kanjouri, Faramarz
2016-11-01
Using spin-polarized density functional theory calculations, we demonstrated that carbon doped boron nitride nanowire (C-doped BNNW) has diverse electronic and magnetic properties depending on position of carbon atoms and their percentages. Our results show that only when one carbon atom is situated on the edge of the nanowire, C-doped BNNW is transformed into half-metal. The calculated electronic structure of the C-doped BNNW suggests that doping carbon can induce localized edge states around the Fermi level, and the interaction among localized edge states leads to semiconductor to half-metal transition. Overall, the bond reconstruction causes of appearance of different electronic behavior such as semiconducting, half-metallicity, nonmagnetic metallic, and ferromagnetic metallic characters. The formation energy of the system shows that when a C atom is doped on surface boron site, system is more stable than the other positions of carbon impurity. Our calculations show that C-doped BNNW may offer unique opportunities for developing nanoscale spintronic materials.
Ab Initio Assessment of the Structural and Optoelectronic Properties of Organic-ZnO Nanoclusters.
Kumar, Pushpendra; Pal, Suman Kalyan
2015-10-01
Structural, electronic, and optical properties of a new coumarin dye, zinc oxide (ZnO) nanoclusters of varying sizes, and their complexes have been investigated using density functional theory (DFT). The band gap of oxide nanoclusters varies with size validating quantum confinement effect in small particles. Energy level diagrams of dye, ZnO nanoclusters, and redox electrolyte are in favor of efficient electron injection from dye to nanocluster and regeneration of the ionized dye. The adsorption of the organic dye to nanocluster is tested for anchoring through three different functional groups (cyano, carbonyl, and hydroxyl) of the dye. We have compared simulated absorption spectra of the dye, nanoclusters, and dye functionalized nanoclusters and discussed the matching with the solar irradiance spectrum. A strong new band appeared in the low energy side of the absorption spectra for dye adsorbed nanoclusters. Frontier molecular orbital calculations reveal that the first absorption band of dye-ZnO complexes is charge transfer (CT) in character. Excitation of this band leads to direct electron transfer to the conduction band (CB) of the nanocluster, making dye-ZnO complexes suitable for type II DSSCs as well. PMID:26348781
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.
NASA Astrophysics Data System (ADS)
Zhu, X. L.; Zeng, X. C.; Lei, Y. A.; Pan, B.
2004-05-01
Ab initio all-electron molecular-orbital calculations are carried out to study the structures and relative stability of low-energy silicon clusters (Sin,n=12-20). Selected geometric isomers include those predicted by Ho et al. [Nature (London) 392, 582 (1998)] based on an unbiased search with tight-binding/genetic algorithm, as well as those found by Rata et al. [Phys. Rev. Lett. 85, 546 (2000)] based on density-functional tight-binding/single-parent evolution algorithm. These geometric isomers are optimized at the Møller-Plesset (MP2) MP2/6-31G(d) level. The single-point energy at the coupled-cluster single and double substitutions (including triple excitations) [CCSD(T)] CCSD(T)/6-31G(d) level for several low-lying isomers are further computed. Harmonic vibrational frequency analysis at the MP2/6-31G(d) level of theory is also undertaken to assure that the optimized geometries are stable. For Si12-Si17 and Si19 the isomer with the lowest-energy at the CCSD(T)/6-31G(d) level is the same as that predicted by Ho et al., whereas for Si18 and Si20, the same as predicted by Rata et al. However, for Si14 and Si15, the vibrational frequency analysis indicates that the isomer with the lowest CCSD(T)/6-31G(d) single-point energy gives rise to imaginary frequencies. Small structural perturbation onto the Si14 and Si15 isomers can remove the imaginary frequencies and results in new isomers with slightly lower MP2/6-31G(d) energy; however the new isomers have a higher single-point energy at the CCSD(T)/6-31G(d) level. For most Sin (n=12-18,20) the low-lying isomers are prolate in shape, whereas for Si19 a spherical-like isomer is slightly lower in energy at the CCSD(T)/6-31G(d) level than low-lying prolate isomers.
Durig, James R; Panikar, Savitha S; Obenchain, Daniel A; Bills, Brandon J; Lohan, Patrick M; Peebles, Rebecca A; Peebles, Sean A; Groner, Peter; Guirgis, Gamil A; Johnston, Michael D
2012-01-28
The microwave spectrum (6500-18 ,500 MHz) of 1-fluoro-1-silacyclopentane, c-C(4)H(8)SiHF has been recorded and 87 transitions for the (28)Si, (29)Si, (30)Si, and (13)C isotopomers have been assigned for a single conformer. Infrared spectra (3050-350 cm(-1)) of the gas and solid and Raman spectrum (3100-40 cm(-1)) of the liquid have also been recorded. The vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twist form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers to be saddle points with nearly the same energies but much lower energy than the planar conformer. By utilizing the microwave rotational constants for seven isotopomers ((28)Si, (29)Si, (30)Si, and four (13)C) combined with the structural parameters predicted from the MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the twist conformer. The heavy atom distances in Å are: r(0)(SiC(2)) = 1.875(3); r(0)(SiC(3)) = 1.872(3); r(0)(C(2)C(4)) = 1.549(3); r(0)(C(3)C(5)) = 1.547(3); r(0)(C(4)C(5)) = 1.542(3); r(0)(SiF) = 1.598(3) and the angles in degrees are: [angle]CSiC = 96.7(5); [angle]SiC(2)C(4) = 103.6(5); [angle]SiC(3)C(5) = 102.9(5); [angle]C(2)C(4)C(5) = 108.4(5); [angle]C(3)C(5)C(4) = 108.1(5); [angle]F(6)Si(1)C(2) = 110.7(5); [angle]F(6)Si(1)C(3) = 111.6(5). The heavy atom ring parameters are compared to the corresponding r(s) parameters. Normal coordinate calculations with scaled force constants from MP2(full)/6-31G(d) calculations were carried out to predict the fundamental vibrational frequencies, infrared intensities, Raman activities, depolarization values, and infrared band contours. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings.
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
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.
Sambathkumar, K; Jeyavijayan, S; Arivazhagan, M
2015-08-01
Combined experimental and theoretical studies were conducted on the molecular structure and vibrational spectra of 4-AminoPhthalhydrazide (APH). The FT-IR and FT-Raman spectra of APH were recorded in the solid phase. The molecular geometry and vibrational frequencies of APH in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking 6-311+G(d,p) basis set. The optimized geometric bond lengths and bond angles obtained by HF and B3LYP method show best agreement with the experimental values. Comparison of the observed fundamental vibrational frequencies of APH with calculated results by HF and density functional methods indicates that B3LYP is superior to the scaled Hartree-Fock approach for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the NMR spectra of APH was also reported. The theoretical spectrograms for infrared and Raman spectra of the title molecule have been constructed. UV-vis spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies, were performed by time dependent density functional theory (TD-DFT) approach. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. And the temperature dependence of the thermodynamic properties of constant pressure (Cp), entropy (S) and enthalpy change (ΔH0→T) for APH were also determined. PMID:25829160
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.
Ab initio calculations of the 2p3/2-2p1/2 fine-structure splitting in boronlike ions
NASA Astrophysics Data System (ADS)
Artemyev, A. N.; Shabaev, V. M.; Tupitsyn, I. I.; Plunien, G.; Surzhykov, A.; Fritzsche, S.
2013-09-01
We have performed ab initio QED calculations of the (1s)2(2s)22p3/2-(1s)2(2s)22p1/2 fine-structure splitting along the boron isoelectronic sequence for all ions with 17≤Z≤100. This level splitting was evaluated within the extended Furry picture and by making use of four different screening potentials in order to estimate the effects of interelectronic correlations. The accuracy of the predicted transition energies has been improved significantly when compared with previous computations.
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
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)
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)
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.
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)
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.
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
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.
NASA Astrophysics Data System (ADS)
Ali, M. A.; Roknuzzaman, M.; Nasir, M. T.; Islam, A. K. M. A.; Naqib, S. H.
2016-04-01
The elastic, electronic, and optical properties of Cu3MTe4 (M = Nb, Ta) are investigated for the first time using the density-functional formalism. The optimized crystal structure is obtained and the lattice parameters are compared with available experimental data. Different elastic moduli are calculated. The Born criteria for mechanical stability are found to be fulfilled from the estimated values of the elastic moduli, Cij. The band structure and the electronic energy density of states (EDOS) are also determined. The band structure calculations show semiconducting behavior for both the compounds. The theoretically calculated values of the band gaps are found to be strongly dependent on the nature of the functional representing the exchange correlations. Technologically significant optical parameters (e.g., dielectric function, refractive index, absorption coefficient, optical conductivity, reflectivity, and loss function) have been determined. Important conclusions are drawn based on the theoretical findings.
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.
NASA Astrophysics Data System (ADS)
Zhu, He; Jha, Kshitij C.; Bhatta, Ram S.; Tsige, Mesfin; Dhinojwala, Ali
2015-03-01
The chemical composition and molecular structure of polymeric surfaces are important in understanding wetting, adhesion, and friction. Here, we combine interface-sensitive sum frequency generation spectroscopy (SFG), all-atom molecular dynamics (MD) simulations, and ab initio calculations to understand the composition and the orientation of chemical groups on poly(methyl methacrylate) (PMMA) surface as a function of tacticity and temperature. The SFG spectral features for isotactic and syndiotactic PMMA surfaces are similar and the dominant peak in the spectra corresponds to the ester-methyl groups. The SFG spectra for solid and melt states are very similar for both syndiotactic and isotactic PMMA. In comparison, the MD simulation results show that both the ester-methyl and the α-methyl groups of syndiotactic-PMMA are ordered and tilted towards the surface normal. For the isotactic-PMMA, the α-methyl groups are less ordered compared to their ester-methyl groups. The backbone methylene groups have a broad angular distribution and on average tilt along the surface plane, independent of tacticity and temperature. We have compared the SFG results with theoretical spectra calculated using MD simulations and ab initio calculations. National Science Foundation.
NASA Astrophysics Data System (ADS)
Lemke, Kono H.; Seward, Terry M.
2008-10-01
We present results from ab initio calculations for the structures and energetic properties of neutral clusters containing water, carbon dioxide, and nitrous oxide using the complete basis set CBS-Q multilevel procedure. Gas phase hydration energies ΔG0, enthalpies ΔH0, and entropies ΔS0 for the stepwise attachment of water onto clusters according to X·(H2O)n + H2O ↔ X·(H2O)n+1 (X = CO2, N2O, and H2O) are reported for n ≤ 4. In particular, our results demonstrate that values for the incremental hydration enthalpies and entropies of all three gases CO2, N2O, and H2O asymptotically approach values characteristic of bulk water (i.e., -44.0 kJ mol-1 for the enthalpy and -118.8 J K-1 mol-1 for the entropy of condensation) following attachment of around three to four water molecules. Our ab initio calculations indicate that water attachment onto CO2, N2O, and H2O is a thermodynamically favorable process, such that hydrated CO2·(H2O)n, N2O·(H2O)n, and H2O·(H2O)n clusters would form a significant atmospheric repository of these species.
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
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.
Almond, David; Cardozo, Timothy
2010-01-01
The antigenic diversity of HIV-1 has long been an obstacle to vaccine design, and this variability is especially pronounced in the V3 loop of the virus' surface envelope glycoprotein. We previously proposed that the crown of the V3 loop, although dynamic and sequence variable, is constrained throughout the population of HIV-1 viruses to an immunologically relevant β-hairpin tertiary structure. Importantly, there are thousands of different V3 loop crown sequences in circulating HIV-1 viruses, making 3D structural characterization of trends across the diversity of viruses difficult or impossible by crystallography or NMR. Our previous successful studies with folding of the V3 crown1, 2 used the ab initio algorithm 3 accessible in the ICM-Pro molecular modeling software package (Molsoft LLC, La Jolla, CA) and suggested that the crown of the V3 loop, specifically from positions 10 to 22, benefits sufficiently from the flexibility and length of its flanking stems to behave to a large degree as if it were an unconstrained peptide freely folding in solution. As such, rapid ab initio folding of just this portion of the V3 loop of any individual strain of the 60,000+ circulating HIV-1 strains can be informative. Here, we folded the V3 loop of the R2 strain to gain insight into the structural basis of its unique properties. R2 bears a rare V3 loop sequence thought to be responsible for the exquisite sensitivity of this strain to neutralization by patient sera and monoclonal antibodies4, 5. The strain mediates CD4-independent infection and appears to elicit broadly neutralizing antibodies. We demonstrate how evaluation of the results of the folding can be informative for associating observed structures in the folding with the immunological activities observed for R2. PMID:20864931
Structural determinants of hospital closure.
Longo, D R; Chase, G A
1984-05-01
In a retrospective case-control study, structural characteristics of hospitals that closed during the years 1976-1980 were contrasted with three comparison groups: hospitals that were acquired in a merger; hospitals that joined a multihospital system; and hospitals that remained autonomously opened, to investigate these characteristics as predictors of closure. Characteristics investigated included environmental, structural, and process variables. The independent variables were measured 5 years prior to outcome. Findings indicate that closed hospitals resemble hospitals acquired in a merger ("failure"), and likewise autonomous hospitals resemble hospitals that join a multihospital system ("success"). The most important predictors of hospital failure were the physician-to-population ratio, the East North Central and West North Central census regions, the level of diversification, low occupancy rate, location in a standard metropolitan statistical area, the chief executive officer's lack of affiliation in the American College of Hospital Administrators, profit status, bed size of less than 50, and presence in a state with a rate-setting agency. Surprisingly, this study shows the bed-to-population ratio to be unrelated to closure. In addition, the findings strongly support the open-system perspective, which, unlike the closed-system perspective, is concerned with the vulnerability of the organization to the uncontrollable and often unpredictable influences of the environment.
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
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.
Surface structure determines dynamic wetting
NASA Astrophysics Data System (ADS)
Shiomi, Junichiro; Wang, Jiayu; Do-Quang, Minh; Cannon, James; Yue, Feng; Suzuki, Yuji; Amberg, Gustav
2014-11-01
Dynamic wetting, the spontaneous spreading process after droplet contacts a solid surface, is important in various engineering processes, such as in printing, coating, and lubrication. In the recent years, experiments and numerical simulations have greatly progressed the understanding in the dynamic wetting particularly on ``flat'' substrates. To gain further insight into the governing physics of the dynamic wetting, we perform droplet-wetting experiments on microstructured surfaces, just a few micrometers in size, with complementary numerical simulations, and investigate the dependence of the spreading rate on the microstructure geometries and fluid properties. We reveal that the influence of microstructures 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. The systematic study is also of practical importance since structures and roughness are omnipresent and their influence on spreading rate would give us additional degrees of freedom to control the dynamic wetting. This work was financially supported in part by, the Japan Society for the Promotion of Science (J.W., J.C., and J.S) and Swedish Governmental Agency for Innovation Systems (M.D.-Q. and G.A.).
An ab initio MO study of butalene
NASA Astrophysics Data System (ADS)
Ohta, Katsuhisa; Shima, Toru
1994-01-01
Butalene as a structural isomer of p-benzyne has been studied by using an ab initio GVB wavefunction. The geometry of butalene, which is shown to be almost rectangular, is first optimized as a local minimum on the energy surface at the ab initio level. However, the energy barrier of conversion to p-benzyne is as small as 1.6 kcal/mol, and experimental isolation of butalene is predicted to be difficult from a force-constant analysis.
Gounev, T K; Guirgis, G A; Zhen, P; Durig, J R
2000-11-15
The infrared (3,200-30 cm(-1) spectra of gaseous and solid 1-bromosilacyclobutane, c-C3H6SiBrH, have been recorded. Additionally, the Raman spectra of the liquid (3,200- 30 cm(-1) with quantitative depolarization values and the solid have been recorded. Both the equatorial and the axial conformers have been identified in the fluid phases, Variable temperature ( - 105 to - 150 degrees C) studies of the infrared spectra of the sample dissolved in liquid krypton have been carried out. From these data the enthalpy difference has been determined to be 182 +/- 18 cm(-1) (2.18 +/- 0.22 kJ/mol) with the equatorial conformer the more stable rotamer and only conformer remaining in the annealing solid. At ambient temperature there is approximately 22% of the axial conformer present in the vapor phase. A complete vibrational assignment is proposed for both conformers based on infrared contours, relative intensities, depolarization values and group frequencies. The vibrational assignments are supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G(d) calculations. From the frequencies of the Si-H stretch, the Si-H bond distance of 1.483 A has been determined for both the equatorial and the axial conformers. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing the 6-31G(d) and 6-311 +/- G(d,p) basis sets at levels of Hartree Fock (RHF) and/or Moller- Plesset with full electron correlation by the perturbation method to the second order (MP2). The results are discussed and compared to those obtained for some similar molecules.
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.
Sládek, Vladimír; Lukeš, Vladimír; Ilčin, Michal; Biskupič, Stanislav
2012-03-15
The ground state ab initio CCSD(T) potential curves using various basis sets (aug-cc-pVXZ-PP (X = D, T, Q, 5)) is obtained for the dimers of helium with IIb group metals. The effect of the position of the (mid) bond-functions on the interaction energy is discussed. A Symmetry Adapted Perturbation Theory decomposition of the interaction energy is provided and the trends in the dimer stabilizing and destabilizing contributions are depicted. The spline fitted potential curves are applied together with rigorous statistical formulae in order to obtain the transport coefficients (viscosity coefficients, diffusion coefficients) and the second virial coefficient both for pure constituents and mixtures. The obtained theoretical results are compared with available experimental data. Molecular dynamics is used to obtain reliable values of the diffusion coefficients for all the systems under study.
NASA Astrophysics Data System (ADS)
Aghabozorg, Hossein; Manteghi, Faranak; Ghadermazi, Mohammad; Mirzaei, Masoud; Salimi, Ali R.; Shokrollahi, Ardeshir; Derki, Somayyeh; Eshtiagh-Hosseini, Hossein
2009-02-01
A novel compound with formula unit (pipzH 2)[Cd(pydc) 2]·6H 2O, was synthesized and characterized by IR, 1H NMR and 13C NMR spectroscopy, elemental analysis, single crystal X-ray diffractometry. Moreover, the solution behavior was studied, and ab initio HF, DFT calculations were carried out. The compound belongs to a great family of supramolecular metal complexes derived from a proton transfer ion pair i.e. (pipzH 2)(pydc), where pipz is piperazine and pydcH 2 is pyridine-2,6-dicarboxylic acid. The compound shows a distorted octahedral geometry around the six-coordinated Cd II atom. A variety of intermolecular O sbnd H···O, N sbnd H···O and C sbnd H···O hydrogen bonds are responsible to extend the supramolecular network of the compound. The geometry parameters of [Cd(pydc) 2] 2- complex and free (pydc) 2- ligand have been optimized with the B3LYP method of density functional theory (DFT) and ab initio Hartree-Fock (HF) methods for comparison. The effect of basis sets has been investigated using four combination basis sets. The electronic properties of the Cd II compound and free (pydc) 2- ligand have been investigated based on the natural bond orbital (NBO) analysis at the B3LYP/A level of theory which verifies that the synergistic effect have been occurred in the compound. In solution study, the protonation constants of pipz and pydc, the equilibrium constants for pydc/pipz proton transfer system and the stoichiometry and stability of the system with Cd 2+ ion in aqueous solution were investigated by potentiometric pH titrations. The stoichiometry of one of the most abundant complexed species in solution was found to be the same as that of the crystalline cadmium complex.
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.
Structural determinants of Tau aggregation inhibitor potency.
Schafer, Kelsey N; Cisek, Katryna; Huseby, Carol J; Chang, Edward; Kuret, Jeff
2013-11-01
Small-molecule Tau aggregation inhibitors are under investigation as potential therapeutic agents against Alzheimer disease. Many such inhibitors have been identified in vitro, but their potency-driving features, and their molecular targets in the Tau aggregation pathway, have resisted identification. Previously we proposed ligand polarizability, a measure of electron delocalization, as a candidate descriptor of inhibitor potency. Here we tested this hypothesis by correlating the ground state polarizabilities of cyanine, phenothiazine, and arylmethine derivatives calculated using ab initio quantum methods with inhibitory potency values determined in the presence of octadecyl sulfate inducer under reducing conditions. A series of rhodanine analogs was analyzed as well using potency values disclosed in the literature. Results showed that polarizability and inhibitory potency directly correlated within all four series. To identify putative binding targets, representative members of the four chemotypes were added to aggregation reactions, where they were found to stabilize soluble, but SDS-resistant Tau species at the expense of filamentous aggregates. Using SDS resistance as a secondary assay, and a library of Tau deletion and missense mutants as targets, interaction with cyanine was localized to the microtubule binding repeat region. Moreover, the SDS-resistant phenotype was completely dependent on the presence of octadecyl sulfate inducer, but not intact PHF6/PH6* hexapeptide motifs, indicating that cyanine interacted with a species in the aggregation pathway prior to nucleus formation. Together the data suggest that flat, highly polarizable ligands inhibit Tau aggregation by interacting with folded species in the aggregation pathway and driving their assembly into soluble but highly stable Tau oligomers.
Structural Determinants of Tau Aggregation Inhibitor Potency*
Schafer, Kelsey N.; Cisek, Katryna; Huseby, Carol J.; Chang, Edward; Kuret, Jeff
2013-01-01
Small-molecule Tau aggregation inhibitors are under investigation as potential therapeutic agents against Alzheimer disease. Many such inhibitors have been identified in vitro, but their potency-driving features, and their molecular targets in the Tau aggregation pathway, have resisted identification. Previously we proposed ligand polarizability, a measure of electron delocalization, as a candidate descriptor of inhibitor potency. Here we tested this hypothesis by correlating the ground state polarizabilities of cyanine, phenothiazine, and arylmethine derivatives calculated using ab initio quantum methods with inhibitory potency values determined in the presence of octadecyl sulfate inducer under reducing conditions. A series of rhodanine analogs was analyzed as well using potency values disclosed in the literature. Results showed that polarizability and inhibitory potency directly correlated within all four series. To identify putative binding targets, representative members of the four chemotypes were added to aggregation reactions, where they were found to stabilize soluble, but SDS-resistant Tau species at the expense of filamentous aggregates. Using SDS resistance as a secondary assay, and a library of Tau deletion and missense mutants as targets, interaction with cyanine was localized to the microtubule binding repeat region. Moreover, the SDS-resistant phenotype was completely dependent on the presence of octadecyl sulfate inducer, but not intact PHF6/PH6* hexapeptide motifs, indicating that cyanine interacted with a species in the aggregation pathway prior to nucleus formation. Together the data suggest that flat, highly polarizable ligands inhibit Tau aggregation by interacting with folded species in the aggregation pathway and driving their assembly into soluble but highly stable Tau oligomers. PMID:24072703
NASA Astrophysics Data System (ADS)
Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique
We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface of Sn at 1000 K. A key ingredient in the OF-AIMD method is the local ionic pseudopotential describing the ions-valence electrons interaction. We have developed a force-matching method to derive a local ionic pseudopotential suitable to account for a rapidly varying density system, such as in a free liquid surface. We obtain very good results for several structural properties. We have also studied the evolution of some dynamical properties when going from the central region (where the system behaves like the bulk liquid) towards the free liquid surface. We aknowledge the spanish MSI (Project FIS2012-33126) and the University of Valladolid for the provision of a PhD grant.
NASA Astrophysics Data System (ADS)
Kilin, Dimitri; Micha, David; Ramirez, Jessica
2011-03-01
The optical absorbance and surface photovoltage of slabs of Si with varying number of layers have been calculated starting from their atomic structure. Results have been obtained for nanostructured surfaces with adsorbed metal clusters and for group III and V dopants, from ab initio DFT with periodic boundary conditions for extended systems, and from time-dependent DFT for supercells. Density matrix equations of motion (EOM) have been parametrized in a basis set of Kohn-Sham orbitals, for both crystalline and amorphous Si slabs. Results for properties and from electronic charge distributions provide insight on slab confinement effects for electronically excited states and for particle-hole creation. In addition, the integrodifferential EOMs have been solved for an initial femtosecond pulse excitation to analyze the nature of electron transfer at the surfaces, relevant to photovoltaics. Work supported by the NSF and by the Dreyfus Foundation to DM.
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.
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
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…
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.
NASA Astrophysics Data System (ADS)
Gaudry, É.; Chatelier, C.; McGuirk, G. M.; Serkovic Loli, L. N.; de Weerd, M.-C.; Ledieu, J.; Fournée, V.; Felici, R.; Drnec, J.; Beutier, G.; de Boissieu, M.
2016-10-01
The structure of the quasicrystalline approximant Al13Co4 (100) has been determined by surface x-ray diffraction (SXRD) and complementary density-functional-theory (DFT) calculations. Thanks to the use of a two-dimensional pixel detector, which speeds up the data acquisition enormously, an exceptionally large set of experimental data, consisting of 124 crystal truncation rods, has been collected and used to refine this complex structure of large unit cell and low symmetry. Various models were considered for the SXRD analysis. The best fit is consistent with a surface termination at the puckered type of planes but with a depletion of the protruding Co atoms. The surface energy of the determined surface model was calculated using DFT, and it takes a rather low value of 1.09 J/m 2 . The results for the atomic relaxation of surface planes found by SXRD or DFT were in excellent agreement. This work opens up additional perspectives for the comprehension of related quasicrystalline surfaces.
NASA Astrophysics Data System (ADS)
Hayashi, S.; Léonard, C.; Chambaud, G.
2009-11-01
On the basis of highly correlated ab initio calculations, an accurate determination of the electronic structure and of the rovibrational spectroscopy has been performed for the electronic ground state of the HZnF system. Using effective core pseudopotentials for the Zn and F atoms and associated aug-cc-pVQZ basis sets, we have calculated, at the multireference configuration interaction level including the Davidson correction, the three-dimensional potential energy surface of the X1Σ+ ground state. The rovibrational energy levels have been obtained variationally, and the results have been discussed and compared with existing experimental data on the ground state of the close system HZnCl, which exhibits a complicated vibration-rotation spectrum. Our analysis shows that the nature of the H-ZnF bond is quite similar to that of the H-ZnCl bond, according to their bond lengths, harmonic frequencies of the H-Zn stretching mode, and dissociation energies into H and ZnF/ZnCl. The ab initio study of the electronic ground and excited states of ZnH and ZnH+ are also presented using similar level of calculations. Characteristic constants are given for the first bounded electronic states correlating to the first two dissociation asymptotes of the neutral and ionic diatomics.
First-principles determination of the structure of magnesium borohydride.
Zhou, Xiang-Feng; Oganov, Artem R; Qian, Guang-Rui; Zhu, Qiang
2012-12-14
The energy landscape of Mg(BH(4))(2) under pressure is explored by ab initio evolutionary calculations. Two new tetragonal structures, with space groups P4 and I4(1)/acd, are predicted to be lower in enthalpy by 15.4 and 21.2 kJ/mol, respectively, than the earlier proposed P4(2)nm phase. We have simulated x-ray diffraction spectra, lattice dynamics, and equations of state of these phases. The density, volume contraction, bulk modulus, and simulated x-ray diffraction patterns of I4(1)/acd and P4 structures are in excellent agreement with the experimental results.
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.
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
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.
Tocci, Gabriele; Joly, Laurent; Michaelides, Angelos
2014-12-10
Friction is one of the main sources of dissipation at liquid water/solid interfaces. Despite recent progress, a detailed understanding of water/solid friction in connection with the structure and energetics of the solid surface is lacking. Here, we show for the first time that ab initio molecular dynamics can be used to unravel the connection between the structure of nanoscale water and friction for liquid water in contact with graphene and with hexagonal boron nitride. We find that although the interface presents a very similar structure between the two sheets, the friction coefficient on boron nitride is ≈ 3 times larger than that on graphene. This comes about because of the greater corrugation of the energy landscape on boron nitride arising from specific electronic structure effects. We discuss how a subtle dependence of the friction on the atomistic details of a surface, which is not related to its wetting properties, may have a significant impact on the transport of water at the nanoscale, with implications for the development of membranes for desalination and for osmotic power harvesting.
Direct atomic structure determination by the inspection of structural phase.
Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne
2013-08-27
A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.
Latha, B; Gunasekaran, S; Srinivasan, S; Ramkumaar, G R
2014-11-11
The solid phase FTIR and FT-Raman spectra of Losartan have been recorded in the region 400-4000 cm(-1). The spectra were interpreted in terms of fundamental modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by Quantum chemical methods. The vibrational frequencies yield good agreement between observed and calculated values. The infrared and Raman spectra were also predicted from the calculated intensities. 1H and 13C NMR spectra were recorded and resonance chemical shifts of the molecule were calculated. UV-Visible spectrum of the compound was recorded in the region 200-600 nm and the electronic properties HOMO and LUMO energies calculated by TD-HF approach. NBO atomic charges of the molecules and second order perturbation theory analysis of Fock matrix also calculated and interpreted. The geometrical parameters, energies, harmonic vibrational frequencies, IR intensities, Raman intensities, and absorption wavelengths were compared with experimental and theoretical data of the molecule.
NASA Astrophysics Data System (ADS)
Latha, B.; Gunasekaran, S.; Srinivasan, S.; Ramkumaar, G. R.
2014-11-01
The solid phase FTIR and FT-Raman spectra of Losartan have been recorded in the region 400-4000 cm-1. The spectra were interpreted in terms of fundamental modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by Quantum chemical methods. The vibrational frequencies yield good agreement between observed and calculated values. The infrared and Raman spectra were also predicted from the calculated intensities. (1)H and (13)C NMR spectra were recorded and resonance chemical shifts of the molecule were calculated. UV-Visible spectrum of the compound was recorded in the region 200-600 nm and the electronic properties HOMO and LUMO energies calculated by TD-HF approach. NBO atomic charges of the molecules and second order perturbation theory analysis of Fock matrix also calculated and interpreted. The geometrical parameters, energies, harmonic vibrational frequencies, IR intensities, Raman intensities, and absorption wavelengths were compared with experimental and theoretical data of the molecule.
RNA Secondary Structure Determination by NMR.
Chen, Jonathan L; Bellaousov, Stanislav; Turner, Douglas H
2016-01-01
Dynamic programming methods for predicting RNA secondary structure often use thermodynamics and experimental restraints and/or constraints to limit folding space. Chemical mapping results typically restrain certain nucleotides not to be in AU or GC pairs. Two-dimensional nuclear magnetic resonance (NMR) spectra can reveal the order of AU, GC, and GU pairs in double helixes. This chapter describes a program, NMR-assisted prediction of secondary structure and chemical shifts (NAPSS-CS), that constrains possible secondary structures on the basis of the NMR determined order and 5'-3' direction of AU, GC, and GU pairs in helixes. NAPSS-CS minimally requires input of the order of base pairs as determined from nuclear Overhauser effect spectroscopy (NOESY) of imino protons. The program deduces the 5'-3' direction of the base pairs if certain chemical shifts are also input. Secondary structures predicted by the program provide assignments of input chemical shifts to particular nucleotides in the sequence, thus facilitating an important step for determination of the three dimensional structure by NMR. The method is particularly useful for revealing pseudoknots and an example is provided. The method may also allow determination of secondary structures when a sequence folds into two structures that exchange slowly. PMID:27665599
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.
Schroeder, Sven L M; Weiher, Norbert
2006-04-21
The X-ray absorption near-edge structures (XANES) at the F K-edge of alpha-AlF(3), beta-AlF(3) and a tetragonal AlF(3) phase are analysed by a combination of ab initio calculations with the FEFF8 code and a phenomenological discussion of local molecular orbital (MO) symmetries at the absorbing fluorine atoms. By means of a Walsh correlation diagram it is shown that the two intense absorption bands observed at the F K-edges of the AlF(3) polymorphs can be interpreted as transitions to anti-bonding MOs in [Al-F-Al]-units that have C(2v) and D(infinity h) point group symmetries. The energies of both anti-bonding orbitals are very insensitive to the angle between the Al-F bonds, which explains the close similarity of the XANES signatures from the three polymorphs. The FEFF8 analysis shows that the increased broadening of the XANES structure for beta-AlF(3) and the tetragonal AlF(3) phase is due to the superposition of the individual absorption spectra from the crystallographically distinct F species. The interpretation in terms of local MOs provides for the first time a "chemically intuitive" approach to investigations of solid fluorides by XANES spectroscopy and provides a simple conceptual framework for the discussion of the electronic structure in AlF(3) materials.
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
NASA Astrophysics Data System (ADS)
Li, Hongtao; Feng, Jiwei; Zhang, Wenqing; Jiang, Wan; Gu, Hui; Smith, John R.
2009-11-01
The properties of an interface between a metallic alloy and an oxide are computed by combining ab initio quantum mechanics with thermodynamics. Results for the stability, structures, and chemical compositions of the β-Ni1-xAlx/α-Al2O3 interface are presented. We found that there are two types of stable structures for the interface. Type I is characterized by joining an Al-rich Ni-Al alloy with an Al-rich Al2O3 surface (terminated by two Al atomic layers). Type II is a junction of a Ni-rich Ni-Al alloy with an Al2O3 surface terminated by an oxygen atomic layer and with atomic migrations and interchanges within the interfacial region. Both types of interfaces exhibit Al accumulation on top of the oxide scale while an adjacent Ni-rich layer is found at the type-II interfaces. The atomic geometries, electronic structures, and chemical bonds of the two types of interfacial systems were analyzed. The calculated interfacial works of separation Wsep agree reasonably well with experimental data and earlier calculations.
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)
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].
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.
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
A fragmentation and reassembly method for ab initio phasing.
Shrestha, Rojan; Zhang, Kam Y J
2015-02-01
Ab initio phasing with de novo models has become a viable approach for structural solution from protein crystallographic diffraction data. This approach takes advantage of the known protein sequence information, predicts de novo models and uses them for structure determination by molecular replacement. However, even the current state-of-the-art de novo modelling method has a limit as to the accuracy of the model predicted, which is sometimes insufficient to be used as a template for successful molecular replacement. A fragment-assembly phasing method has been developed that starts from an ensemble of low-accuracy de novo models, disassembles them into fragments, places them independently in the crystallographic unit cell by molecular replacement and then reassembles them into a whole structure that can provide sufficient phase information to enable complete structure determination by automated model building. Tests on ten protein targets showed that the method could solve structures for eight of these targets, although the predicted de novo models cannot be used as templates for successful molecular replacement since the best model for each target is on average more than 4.0 Å away from the native structure. The method has extended the applicability of the ab initio phasing by de novo models approach. The method can be used to solve structures when the best de novo models are still of low accuracy. PMID:25664740
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.
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.
Schnoeckel, H.; Mehner, T.; Plitt, H.S.; Schunck, S. )
1989-06-21
The structure of dimeric SiO is reexamined by a study of the IR spectra of the matrix-isolated species. Spectra of isotopomers from experiments with {sup 29}Si- and {sup 18}O-enriched samples are discussed with the help of normal-coordinate analysis. The results are in line with data of the geometrical and electronic structure obtained by ab initio SCF calculations. The dimerization energy calculated by quantum chemical methods agrees well with experimental data, which have been recalculated. With the help of additional ab initio calculations on the isoelectronic species PN and AlF, interesting correlations between their tendency toward dimerization can be obtained. Structural data of SiO are compared with the analogous ones of similar molecules (e.g., BF).
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)
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.
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.
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.
Mishra, S K; Mishra, P C
2001-10-01
Ground state geometries of the four tautomeric forms keto-N9H, keto-N7H, enol-N9H and enol-N7H of 8-bromoguanine (8BG) were optimized using the ab initio RHF procedure employing a mixed basis set consisting of the 6-311 + G* basis set for the nitrogen atom of the amino group and the bromine atom, and the 4-31G basis set for all other atoms. These calculations were followed by correlation correction of the total energy at the MP2 level using the same basis set. The different tautomeric forms of 8BG in the ground state were solvated using the isodensity surface polarized continuum model (IPCM) of the SCRF theory both at the RHF and MP2 levels. Excited states were generated employing configuration interaction among singly excited configurations (CIS) obtained using a limited window of filled and empty molecular orbitals. Formation of hydrogen-bonded complexes between 8BG and three water molecules in the ground and excited states was considered in order to account for solvent effects approximately. Excited state geometry was optimized in each case for the lowest singlet excited state which was found to be of pi-pi* type. Vibrational frequency analysis was performed in order to ensure that the stationary points located on the potential energy surfaces by geometry optimization were minima. It is found that 8BG would occur in the ground state dominantly in the keto-N7H form both at the aqueous solution-air interface and inside the bulk liquid. The observed absorption and fluorescence spectra of 8BG can be explained satisfactorily considering only the keto-N7H form of the molecule. The enol tautomers of 8BG do not appear to be important from the point of view of ground state properties or electronic spectra. The observed differences between the behaviors of guanine and 8BG can be easily explained on the basis of the results obtained.
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
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.
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)
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).
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)
Lemke, K. H.; Seward, T. M.
2007-12-01
We present results from ab initio calculations for the structures, energetics and atmospheric abundances of neutral clusters containing water, carbon dioxide and nitrous oxide up to 45km altitude using the complete basis set CBS-Q and G3 multi-level procedures. Gas phase hydration energies, enthalpies and entropies for the stepwise attachment of water onto clusters according to X(H2O)n + H2O = X(H2O)n+1 (where X = H2O, CO2 and N2O) are reported for up to n=5. In particular, our results demonstrate that values for the incremental hydration enthalpies and entropies of all three gases H2O, CO2 and N2O asymptotically approach values characteristic of bulk liquid water (i.e. -44.0 kJ/mol for the enthalpy and -118.8 J/Kmol for the entropy of condensation) following attachment of around 3-4 water molecules. Interestingly, our calculated number densities for the water dimer at 292Kelvin are in excellent agreement with recent values obtained from IR measurements of atmospheric media (Pfeilsticker et al., 2003, Science). Our quantum chemical calculations indicate that water attachment onto H2O, CO2 and N2O is a thermodynamically favorable process, such that hydrated clusters would form a significant atmospheric repository of these species.
Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou
2014-01-24
Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G(*) basis set. The -311++G(**) basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of C-H bond length and the elongation of N-H bond length suggest the existence of weak C-H⋯O and N-H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P2(1) space group, with lattice parameters Z=4, a=14.9989 Å, b=4.0367 Å, c=12.9913 Å, ρ=0.998 g cm(-3).
NASA Astrophysics Data System (ADS)
Zijlstra, E. S.; Kortus, J.; Krajčí, M.; Stadnik, Z. M.; Bose, S. K.
2004-03-01
We present a detailed analysis of electronic properties of the Cockayne model of icosahedral AlCuFe, both in its original form and after a structural relaxation using the ab initio density functional approach. The electronic density of states (DOS) and electric field gradients (EFG’s) of the Al and Fe atoms in the original and the relaxed Cockayne models were calculated and compared with available photoemission, Mössbauer, and nuclear quadrupole resonance spectroscopy data. The relaxed and the original models show significantly different electronic properties. Both models are deficient in describing the available experimental data. The DOS’s show two Fe-d peaks, where there is only one such peak in the photoemission spectroscopy data. These models also cannot account for the shape of the Mössbauer spectra. We show that the interchange between 12 Cu and 12 Fe atoms, each belonging to a single symmetry class, results in a smaller number of Cu-Fe nearest-neighbor pairs and a lowering of the total energy by an amount of ΔE˜50 meV/atom. This “modified” version of the Cockayne model was further relaxed for the final comparison between the calculation and experimental results. The modified model shows a considerable improvement: The DOS has only one Fe-d peak, in agreement with photoemission spectroscopy data, and the calculated EFG’s account very well for the experimental Mössbauer spectra.
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.
Accurate SHAPE-directed RNA structure determination
Deigan, Katherine E.; Li, Tian W.; Mathews, David H.; Weeks, Kevin M.
2009-01-01
Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis. PMID:19109441
Precise equilibrium structure determination of hydrazoic acid (HN3) by millimeter-wave spectroscopy.
Amberger, Brent K; Esselman, Brian J; Stanton, John F; Woods, R Claude; McMahon, Robert J
2015-09-14
The millimeter-wave spectrum of hydrazoic acid (HN3) 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 (Ae, Be, and Ce). These equilibrium rotational constants were then used to obtain an equilibrium (Re) structure using a least-squares fitting routine. The Re structural parameters are consistent with a previously published Rs structure, largely falling within the uncertainty limits of that Rs structure. The present Re geometric parameters of HN3 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 Re 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.
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.
Conformational properties of molecules by ab initio quantum mechanical energy minimization.
Pedersen, L
1985-01-01
The recent literature on the determination of minimum energy conformations by ab initio quantum mechanical techniques is reviewed. The availability of computer-coded analytical first and second derivatives of the Hartree-Fock energy makes possible calculations that will be of significant assistance in structure determination of molecules. A short review of recent progress in empirical energy minimization and molecular dynamics is provided. PMID:3905373
NASA Astrophysics Data System (ADS)
Zhou, X.; Roehl, J. L.; Lind, C.; Khare, S. V.
2013-02-01
We have studied the pressure-induced phase transitions from NaCl-type (B1) to CsCl-type (B2) structure in BaS, BaSe and BaTe by using ab initio density functional theory computations in the local density approximation. The Buerger and WTM mechanisms were explored by mapping the enthalpy contours in two- and four-dimensional configuration space for the two mechanisms, respectively. Transition pressures for BaS, BaSe and BaTe were determined to be 5.5 GPa, 4.9 GPa and 3.4 GPa, respectively. From these configuration space landscapes, a low enthalpy barrier path was constructed for the transitions to proceed at three different pressures. We obtained barriers of 0.18, 0.16 and 0.15 eV/pair (17.4, 15.4 and 14.5 kJ mol-1) for the Buerger mechanism and 0.13, 0.13 and 0.12 eV/pair (12.5, 12.5 and 11.6 kJ mol-1) for the WTM mechanism at the transition pressures for BaS, BaSe and BaTe, respectively, indicating that the WTM mechanism is slightly more favorable in these compounds. We describe the difference between the two mechanisms by differences in their symmetry and atomic coordination.
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.
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.
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.
Vincent, Mark A; Hillier, Ian H; Morgado, Claudio A; Burton, Neil A; Shan, Xiao
2008-01-28
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, pi 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 N(2) 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.
NASA Astrophysics Data System (ADS)
Schäfer, Lothar; Van Alsenoy, C.; Scarsdale, J. N.
1982-02-01
The molecular structures of four conformations of N-acetyl-N'-methyl glycyl amide were refined by geometrically unconstrained ab initio gradient relaxation on the 4-21G level. The most stable form I contains a seven-membered ring closed by hydrogen bonding. A second local minimum II is less than 1 kcal/mol above I and represents the fully extended form with a five-membered hydrogen bonded ring. The two other minima refined, III and IV, are open forms which are 4-5 kcal/mol less stable than I. The refined geometries make it possible to estimate the significance of local geometries, in contrast to standard geometry, in the various conformations. It is found that bond distances in different conformations can vary by up to 0.02 Å, and important backbone bond angles can vary by up to 7°. Except for the symmetrical form II, small deviations from amide planarity (H-N-C = 0 angles of 3-10°) are the rule, even though the equilibrium structure of the unperturbed amide group in 4-21G space is planar. It can be concluded that local geometry relaxations at different points of the potential energy surface of a peptide system can amount to several Kcal/mol per residue and should be an important aspect of protein conformational analysis.
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.
Membrane protein structure determination - the next generation.
Moraes, Isabel; Evans, Gwyndaf; Sanchez-Weatherby, Juan; Newstead, Simon; Stewart, Patrick D Shaw
2014-01-01
The field of Membrane Protein Structural Biology has grown significantly since its first landmark in 1985 with the first three-dimensional atomic resolution structure of a membrane protein. Nearly twenty-six years later, the crystal structure of the beta2 adrenergic receptor in complex with G protein has contributed to another landmark in the field leading to the 2012 Nobel Prize in Chemistry. At present, more than 350 unique membrane protein structures solved by X-ray crystallography (http://blanco.biomol.uci.edu/mpstruc/exp/list, Stephen White Lab at UC Irvine) are available in the Protein Data Bank. The advent of genomics and proteomics initiatives combined with high-throughput technologies, such as automation, miniaturization, integration and third-generation synchrotrons, has enhanced membrane protein structure determination rate. X-ray crystallography is still the only method capable of providing detailed information on how ligands, cofactors, and ions interact with proteins, and is therefore a powerful tool in biochemistry and drug discovery. Yet the growth of membrane protein crystals suitable for X-ray diffraction studies amazingly remains a fine art and a major bottleneck in the field. It is often necessary to apply as many innovative approaches as possible. In this review we draw attention to the latest methods and strategies for the production of suitable crystals for membrane protein structure determination. In addition we also highlight the impact that third-generation synchrotron radiation has made in the field, summarizing the latest strategies used at synchrotron beamlines for screening and data collection from such demanding crystals. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
Sai, Linwei; Zhao, Jijun; Huang, Xiaoming; Wang, Jun
2012-01-01
Using genetic algorithm incorporated with density functional theory, we have explored the size evolution of structural and electronic properties of neutral gallium clusters of 20-40 atoms in terms of their ground state structures, binding energies, second differences of energy, HOMO-LUMO gaps, distributions of bond length and bond angle, and electron density of states. In the size range studied, the Ga(n) clusters exhibit several growth patterns, and the core-shell structures become dominant from Ga31. With high point group symmetries, Ga23 and Ga36 show particularly high stability and Ga36 owns a large HOMO-LUMO gap. The atomic structures and electronic states of Ga(n) clusters significantly differ from the a solid but resemble beta solid and liquid to certain extent.
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.
Liebschner, Dorothee; Brzezinski, Krzysztof; Dauter, Miroslawa; Dauter, Zbigniew; Nowak, Marta; Kur, Józef; Olszewski, Marcin
2012-12-01
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.
Liebschner, Dorothee; Brzezinski, Krzysztof; Dauter, Miroslawa; Dauter, Zbigniew; Nowak, Marta; Kur, Józef; Olszewski, Marcin
2012-01-01
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. PMID:23151633
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.
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.
Choudhuri, Jyoti Roy; Chandra, Amalendu
2014-10-01
We have performed ab initio molecular dynamics simulations of a liquid-vapor interfacial system consisting of a mixture of water and methanol molecules. Detailed results are obtained for the structural and dynamical properties of the bulk and interfacial regions of the mixture. Among structural properties, we have looked at the inhomogeneous density profiles of water and methanol molecules, hydrogen bond distributions and also the orientational profiles of bulk and interfacial molecules. The methanol molecules are found to have a higher propensity to be at the interface than water molecules. It is found that the interfacial molecules show preference for specific orientations so as to form water-methanol hydrogen bonds at the interface with the hydrophobic methyl group pointing towards the vapor side. It is also found that for both types of molecules, the dipole moment decreases at the interface. It is also found that the local electric field of water influences the dipole moment of methanol molecules. Among the dynamical properties, we have calculated the diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational frequency fluctuations in bulk and interfacial regions. It is found that the diffusion and orientation relaxation of the interfacial molecules are faster than those of the bulk. However, the hydrogen bond lifetimes are longer at the interface which can be correlated with the time scales found from the decay of frequency time correlations. The slower hydrogen bond dynamics for the interfacial molecules with respect to bulk can be attributed to diminished cooperative effects at the interface due to reduced density and number of hydrogen bonds.
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.
Durig, James R; Zheng, Chao; Williams, Michael J; Stidham, Howard D; Guirgis, Gamil A
2004-06-01
The infrared spectra (3200-400 cm(-1)) of krypton solutions of 1,3-difluoropropane, FCH2CH2CH2F, at variable temperatures (-105 to -150 degrees C) have been recorded. Additionally, the infrared spectra (3200-50 cm(-1)) of the gas and solid have been recorded as well as the Raman spectrum of the liquid. From a comparison of the spectra of the fluid phases with that in the solid, all of the fundamental vibrations of the C2 conformer (gauche-gauche) where the first gauche indicates the form for one of the CH2F groups and the second gauche the other CH2F, and many of those for the C1 form (trans-gauche) have been identified. Tentative assignments have been made for a few of the fundamentals of the other two conformers, i.e. C2v (trans-trans) and Cs (gauche-gauche'). By utilizing six pairs of fundamentals for these two conformers in the krypton solutions, an enthalpy difference of 277 +/- 28 cm(-1) (3.31 +/- 0.33 kJ mol(-1)) has been obtained for the C2 versus C1 conformer with the C2 conformer the more stable form. For the C2v conformer, the enthalpy difference has been determined to be 716 +/- 72 cm(-1) (8.57 +/- 0.86 kJ mol(-1)) and for the Cs form 971 +/- 115 cm(-1) (11.6 +/- 1.4 kJ mol(-1)). It is estimated that there is 64 +/- 3% of the C2 form, 34 +/-3% of the C1 form, 1% of the C2v form and 0.6% of the Cs conformer present at ambient temperature. Equilibrium geometries and total energies of the four stable conformers have been determined from ab initio calculations with full electron correlation by the perturbation method to second order as well as by hybrid density functional theory calculations with the B3LYP method using a number of basis sets. The MP2 calculations predict the C1 conformer stability to be slightly higher than the experimentally determined value whereas for the C2v and Cs conformers the predicted energy difference is much larger than the experimental value. The B3LYP calculations predict a better energy difference for both the C1 and C2v as
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.
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.
NASA Astrophysics Data System (ADS)
Königstein, Markus; Catlow, C. Richard A.
1998-10-01
We report a detailed computationally study of the stability of the alkaline earth metal peroxidesMO2(M=Ba, Sr, Ca, Mg, Be) with respect to decomposition into the corresponding oxidesMOand molecular oxygen using Hartree-Fock and density functional theory (DFT) techniques. A comparison between calculated and experimental binding energies indicates that the DFT method is most suitable for a correct description of the peroxide bond. The DFT reaction energies for the peroxide decompositionMO2→MO+{1}/{2}O2show that only BaO2and SrO2are thermodynamically stable compounds, while CaO2(in the calcium carbide structure), MgO2, and BeO2(in the pyrite structure) are energetically unstable with reaction energies of -24.7, -26.8, and -128.7kJ/mol, respectively, and are therefore unlikely to exist as pure compounds. The published calcium carbide structure for CaO2is probably incorrect, at least for pure calcium peroxide, since apart from the thermodynamical instability the compound is more stable in the pyrite structure by 25.5 kJ/mol. Our analysis suggests that the water and/or hydrogen peroxide content of experimentally prepared MgO2samples is necessary for the stabilization of the structure, while BeO2is clearly unstable under ambient conditions. We studied also the effect of the zero point energies and the entropies on the decomposition free energies and, for this purpose, performed atomistic lattice simulations based on interatomic potentials, which we derived from ourab initiodata; the results indicate a negligible effect of the zero point energies, while the entropy terms favor the decomposition reaction by ca. 20 kJ/mol at 298.15 K.
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.
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.
Influence of the sequence on the ab initio band structures of single and double stranded DNA models
NASA Astrophysics Data System (ADS)
Bogár, Ferenc; Bende, Attila; Ladik, János
2014-06-01
The solid state physical approach is widely used for the characterization of electronic properties of DNA. In the simplest case the helical symmetry is explicitly utilized with a repeat unit containing only a single nucleotide or nucleotide pair. This model provides a band structure that is easily interpretable and reflects the main characteristic features of the single nucleotide or a nucleotide pair chain, respectively. The chemical variability of the different DNA chains is, however, almost completely neglected in this way. In the present work we have investigated the effect of the different sequences on the band structure of periodic DNA models. For this purpose we have applied the Hartree-Fock crystal orbital method for single and double stranded DNA chains with two different subsequent nucleotides in the repeat unit of former and two different nucleotide pairs in the latter case, respectively. These results are compared to simple helical models with uniform sequences. The valence and conduction bands related to the stacked nucleotide bases of single stranded DNA built up only from guanidine as well as of double stranded DNA built up only from guanidine-cytidine pairs showed special properties different from the other cases. Namely, they had higher conduction and lower valence band positions and this way larger band gaps and smaller widths of these bands. With the introduction of non-uniform guanidine containing sequences band structures became more similar to each other and to the band structures of other sequences without guanidine. The maximal bandwidths of the non-uniform sequences are considerably smaller than in the case of uniform sequences implying smaller charge carrier mobilities both in the conduction and valence bands.
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.
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.
Trachtman, Mendel; Markham, George D.; Glusker, Jenny P.; George, Philip; Bock, Charles W.
1998-08-24
The formation and properties of a wide range of metal ion monohydrates, M(n)()(+)-OH(2), where n = 1 and 2, have been studied by ab initio molecular orbital calculations at the MP2(FULL)/6-311++G//MP2(FULL)/6-311++G and CCSD(T)(FULL)/6-311++G//MP2(FULL)/6-311++G computational levels. The ions M are from groups 1A, 2A, 3A, and 4A in the second, third, and fourth periods of the periodic table and the first transition series. Structural parameters, vibrational frequencies, bonding enthalpies, orbital occupancies and energies, and atomic charge distributions are reported. Trends in these properties are correlated with the progressive occupancy of the s, p, and d orbitals. Except for K(+)-OH(2) and Ca(2+)-OH(2), the O-H bond lengths and HOH angles are greater in the hydrates than in unbound water. The M-O bond lengths decrease proceeding from group 1A --> 4A but become larger in proceeding from the second --> fourth period. The bonding enthalpies, are found to be inversely linearly dependent on the M-O bond length M(n)()(+) according to equations of the form = A + B(1/M-O) for n = 1 and n = 2. Within each monohydrate the distribution of atomic charge reveals a small but definite transfer of charge from water to the metal ion. Compared to unbound water there is, in a metal-ion-bound water complex, an increase in the electronic (negative) charge on the oxygen atom, accompanied by a (significantly) larger decrease in the electronic charge on the hydrogen atoms. The bonding of the water molecule, although electrostatic in origin, is thus more complex than a simple interaction between a point charge on the metal ion, and the water dipole.
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.
Brameld, K.A.; Goddard, W.A. III
1999-02-10
The authors have used ab initio quantum mechanical (QM) methods to determine the potential energy of pseudorotation for 3,4-dihydroxy-5-methyl-2-(1-pyrollyl)tetrahydrofuran and 4-hydroxy-5-methyl-2-(1-pyrollyl)-tetrahydrofuran, close analogues of 2{prime}-deoxyribose and ribose sugars. The pyrrole is a substitute for the naturally occurring nucleic acid bases: adenine, thymine, guanine, cytosine, and uracil. At the highest calculation level (LMP2/cc-pVTZ(-f)//HF/6-31G**) for 2{prime}-deoxyribose, they find the C2{prime}-endo conformation is the global minimum. The C3{prime}-endo conformation is a local minimum 0.6 kcal/mol higher in energy, and an eastern barrier of 1.6 kcal/mol separates the two minima. Pseudorotation energies of ribose are quite complex and are strongly affected by local orientations of the 2{prime} and 3{prime} hydroxyl groups. When the hydroxyl groups are allowed to assume any conformation, the global minimum remains the C2{prime}-endo conformation. The eastern barrier increases slightly to 1.8 kcal/mol, and the C3{prime}-endo local minimum lies 0.6 kcal/mol above the global minimum. Constraining the torsion angle of the C3{prime} hydroxyl group to {minus}146{degree}, as is found in RNA polymers, results in the C3{prime}-endo conformation becoming the only energy minimum with a C2{prime}-endo conformation 1.9 kcal/mol higher in energy. Bond angles within the pentofuranose ring are correlated to the pseudorotational phase, as is observed by X-ray crystallography and is predicted by pseudorotation theory. Finally, a force field for use in molecular mechanics and dynamics simulations is presented which reproduces the QM potential energies for the 2{prime}-deoxyribose and ribose sugars.
NASA Astrophysics Data System (ADS)
Bahloul, B.; Bentabet, A.; Amirouche, L.; Bouhadda, Y.; Bounab, S.; Deghfel, B.; Fenineche, N.
2014-03-01
Structural, electronic and thermodynamic properties of SrTe and BaTe compounds and their ternary mixed crystals BaxSr1-xTe in the rock-salt structure have been studied with density functional theory (DFT), whereas the optical properties have been obtained by using empirical methods such as the modified Moss relation. The exchange-correlation potential was calculated using the generalized gradient approximation (GGA) of Perdew-Burke-Ernzerhof (PBE) and the local density approximation (LDA) of Teter-Pade (TP). In the present work, we used the virtual-crystal approximation (VCA) to study the effect of composition (x). The calculated lattice parameters at equilibrium volume and the bulk modulus for x=0 and x=1 are in good agreement with the literature data. Furthermore, the BaxSr1-xTe alloys are found to be an indirect band gap semiconductor. In addition, we have also predicted the heat capacities (CV), the entropy(S), the internal energy (U) and the Helmholtz free energy (F) of the parent compounds SrTe and BaTe.
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.
Christie, Jamieson K; Ainsworth, Richard I; de Leeuw, Nora H
2014-08-01
Phosphate-based bioactive glasses containing fluoride ions offer the potential of a biomaterial which combines the bioactive properties of the phosphate glass and the protection from dental caries by fluoride. We conduct accurate first-principles molecular dynamics simulations of two compositions of fluorinated phosphate-based glass to assess its suitability as a biomaterial. There is a substantial amount of F-P bonding and as a result the glass network will be structurally homogeneous on medium-range length scales, without the inhomogeneities which reduce the bioactivity of other fluorinated bioactive glasses. We observe a decrease in the network connectivity with increasing F content, caused by the replacement of bridging oxygen atoms by non-bridging fluorine atoms, but this decrease is small and can be opposed by an increase in the phosphate content. We conclude that the structural changes caused by the incorporation of fluoride into phosphate-based glasses will not adversely affect their bioactivity, suggesting that fluorinated phosphate glasses offer a superior alternative to their silicate-based counterparts.
Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki -Alexandra
2015-10-12
Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivitymore » and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences
Ab initio study on structural, electronic properties, and hardness of re-doped W2B5
NASA Astrophysics Data System (ADS)
Feng, ShiQuan; Li, XiaoDong; Su, Lei; Li, HaiNing; Yang, Hongyan; Cheng, Xinlu
2016-11-01
Using first principle calculations method, we calculated the structural stability, electronic properties and hardness for three Re-doped hexagonal W2B5 compounds. The electronic properties were carried out to discuss the effect of doped Re on the conductivity, chemical bonding components and orbital hybridization of W2B5. What is more, the hardness of these three doped crystals was calculated by a semiempirical method considering the role of metallic components. A Re-doped W2B5 compound with a greater hardness value than that of pure W2B5 was obtained. And the effect of doping on the hardness of hexagonal W2B5was discussed.
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.
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.
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.
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
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.
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.
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
Shields, Ashley E; van Mourik, Tanja
2007-12-20
We establish that routine B3LYP and MP2 methods give qualitatively wrong conformations for flexible organic systems containing pi systems and that recently developed methods can overcome the known inadequacies of these methods. This is illustrated for a molecule (a conformer of the Tyr-Gly dipeptide) for which B3LYP/6-31+G(d) and MP2/6-31+G(d) geometry optimizations yield strikingly different structures [Mol. Phys. 2006, 104, 559-570]: MP2 predicts a folded "closed-book" conformer with the glycine residue located above the tyrosine ring, whereas B3LYP predicts a more open conformation. By employing different levels of theory, including the local electron correlation methods LMP2 (local MP2) and LCCSD(T0) (local coupled cluster with single, double, and noniterative local triple excitations) and large basis sets (aug-cc-pVnZ, n=D, T, Q), it is shown that the folded MP2 minimum is an artifact caused by large intramolecular BSSE (basis set superposition error) effects in the MP2/6-31+G(d) calculations. The B3LYP functional gives the correct minimum, but the potential energy apparently rises too steeply when the glycine and tyrosine residues approach each other, presumably due to missing dispersion effects in the B3LYP calculations. The PWB6K and M05-2X functionals, designed to give good results for weak interactions, remedy this to some extent. The reduced BSSE in the LMP2 calculations leads to faster convergence with increasing basis set quality, and accurate results can be obtained with smaller basis sets as compared to canonical MP2. We propose LMP2 as a suitable method to study interactions with pi-electron clouds.
An ab initio potential function for the ν13 vibrational mode of 1,3-butadiene
NASA Astrophysics Data System (ADS)
Senent, M. L.
1995-06-01
The restricted potential of the ν13 torsional mode of 1,3-butadiene has been determined from ab initio calculations. The relative energy and geometry of the second rotamer were calculated with the optimized couple cluster method with double substitutions. This ab initio level provides that the second stable structure attaches to a gauche form situated at 140.8°. The potential energy function was obtained by fitting to a symmetry-adapted Fourier series the total electronic energies of several selected conformations. These energies were calculated by the Möller-Plesset perturbation theory up to the second order (MP2) with full and partial optimization of the geometry. Torsional Raman band positions and fundamental frequencies were determined from the periodic potentials with a good agreement with experimental data. The convenience of performing fully optimized calculations to determine the restricted function is also refuted.
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
NASA Astrophysics Data System (ADS)
Ventura, Oscar N.; Segovia, Marc
2005-02-01
The experimental enthalpy of formation of perfluoropropane (C 3F 8), reported originally as -1729 kJ/mol and latter corrected to -1784.7 kJ/mol, is reexamined at the light of density functional and model chemistry (G3, CBS-4, CBS-Q) calculations of several isodesmic reactions relating C 3F 8 to smaller fluoroalkanes. The average enthalpy of formation of C 3F 8 obtained from all reactions studied was -1739 ± 12 kJ/mol at the DFT level and -1748 ± 12 kJ/mol at the ab initio level, thus ruling out the larger experimental value. A value of -1732 ± 5 kJ/mol is recommended from careful analysis of the theoretical results.
Laasonen, Kari
2013-01-01
In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth.
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.
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 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.
Howell, Sarah L; Matthewson, Benjamin J; Polson, Matthew I J; Burrell, Anthony K; Gordon, Keith C
2004-05-01
A series of bridging ligands, dipyrido[2,3-a:3',2'-c]phenazine (ppb), dipyrido[2,3-a:3',2'-c]-6,7-dichlorophenazine (ppbCl2), and dipyrido[2,3-a:3',2'-c]-6,7-dimethylphenazine (ppbMe2), and their binuclear copper(I) complexes have been synthesized, and their spectral properties were measured. The single-crystal structure of the complex, [(PPh3)2Cu(mu-ppbCl2)Cu(PPh3)2](BF4)2 in the monoclinic space group P21/c, 18.2590(1), 21.1833(3), 23.2960(3) A with Z = 4 is reported. The copper(I) complexes are deeply colored through MLCT transitions in the visible region. The vibrational spectra of the ligands have been modeled using ab initio hybrid density functional theory (DFT) methods (B3LYP/6-31G(d)) and compared to experimental FT-Raman and IR data. The DFT calculations are used to interpret the resonance Raman spectra, and thus the electronic spectra, of the complexes. The preferential enhancement of modes associated with the phenanthroline section of the ligands with blue excitation (lambda(exc) = 457.9 nm) over phenazine-based modes with redder excitation (lambda(exc) = 514.5 and 632.8 nm) suggests the 2 MLCT transitions terminated on different unoccupied MOs are present under the visible absorption envelope. The radical anion species of the ligands are prepared by the electrochemical reduction of the binuclear copper(I) complexes; no evidence of dechelation prevalent in other copper(I) complexes is observed. The resonance Raman spectra of the reduced complexes are dramatically different from those of the parent species. Across the series common bands are observed at about 1590 and 1570 cm(-1) which do not shift with reduction but are altered in intensity. The normal-mode analysis of the radical anion species suggests that these normal modes primarily involve bond length distortions that are unaffected by reduction.
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.
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
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.
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.
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.
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.
Wu, Chengyin Liu, Yunquan; Gong, Qihuang; Wu, Cong; Xie, Xiguo; Li, Min; Deng, Yongkai; Song, Di; Su, Hongmei
2014-04-14
We experimentally reconstructed the structure of the N{sub 2}Ar van der Waals complex with the technique of laser-based channel-selected Coulomb explosion imaging. The internuclear distance between the N{sub 2} center of mass and the Ar atom, i.e., the length of the van der Waals bond, was determined to be 3.88 Å from the two-body explosion channels. The angle between the van der Waals bond and the N{sub 2} principal axis was determined to be 90° from the three-body explosion channels. The reconstructed structure was contrasted with our high level ab initio calculations. The agreement demonstrated the potential application of laser-based Coulomb explosion in imaging transient molecular structure, particularly for floppy van der Waals complexes, whose structures remain difficult to be determined by conventional spectroscopic methods.
NASA Astrophysics Data System (ADS)
Muhammad, Rashid; Fayyaz, Hussain; Muhammad, Imran; A. Ahmad, S.; A. Noor, N.
2014-01-01
The structural, electronic, and optical properties of binary CdO, CdSe, and their ternary CdO1-xSex alloys (0 <= x <= 1) in the rock salt and zinc blend phases have been studied by the special quasi-random structure (SQS) method. All the calculations are performed using full-potential linearized augmented plane wave plus local orbital's (FP-LAPW+lo) method within the framework of density function theory (DFT). We use Wu—Cohen (WC) generalized gradient approximation (GGA) to calculate structural parameters, whereas both Wu—Cohen and Engel—Vosko (EV) GGA have been applied to calculate electronic structure of the materials. Our predicted results of lattice constant and bulk modulus show only a slight deviation from Vegard's law for the whole concentrations. The obtained band structure indicates that for the rock-salt phase, the ternary alloys present semi-metallic behavior, while for the zinc blend phase, semiconductor behavior with direct bandgap is observed with decreasing order of x except for CdSe. Finally, by incorporating the basic optical properties, we discuss the dielectric function, refractive index, optical reflectivity, the absorption coefficient, and optical conductivity in terms of incident photon energy up to 14 eV. The calculated results of both binaries are in agreement with existing experimental and theoretical values.
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.
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.
NASA Astrophysics Data System (ADS)
Hong, Qi-Jun; van de Walle, Axel
2015-07-01
Using electronic structure calculations, we conduct an extensive investigation into the Hf-Ta-C system, which includes the compounds that have the highest melting points known to date. We identify three major chemical factors that contribute to the high melting temperatures. Based on these factors, we propose a class of materials that may possess even higher melting temperatures and explore it via efficient ab initio molecular dynamics calculations in order to identify the composition maximizing the melting point. This study demonstrates the feasibility of automated and high-throughput materials screening and discovery via ab initio calculations for the optimization of "higher-level" properties, such as melting points, whose determination requires extensive sampling of atomic configuration space.
Determining crystal structures through crowdsourcing and coursework
NASA Astrophysics Data System (ADS)
2016-09-01
We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.
Determining crystal structures through crowdsourcing and coursework.
Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A
2016-09-16
We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.
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)
Determining crystal structures through crowdsourcing and coursework.
Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A
2016-01-01
We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552
Determining crystal structures through crowdsourcing and coursework
Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.
2016-01-01
We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552
NASA Astrophysics Data System (ADS)
Dahlqvist, Martti; Hotokka, Matti; Räsänen, Markku
1998-04-01
The infrared spectra of monomeric pinacol molecules (2,3-dimethyl-2,3-butanediol; (CH 3) 2C(OH)C(OH)(CH 3) 2) have been recorded in the gas phase and dilute nonpolar solutions, and in an argon matrix. The vibrational data are consistent with the intramolecularly hydrogen-bonded G-type (gauche with respect to the central C-C bond) conformers and there is no evidence for the T-type (trans with respect to the central C-C bond) conformers, which have been observed in the condensed phases. This was confirmed by studying the infrared region 835-815 cm -1, which was found to be the most indicative to show spectral changes within the type of the conformers. In this region the band of the T-type conformers (assigned to the hybridized asymmetric vibration of the central CC and CO stretching modes) disappears when going from the condensed phases to phases, where pinacol molecules are monomeric. Ab initio HF/6-311G** (MP2/6-311G**) calculations support the experimental findings; the calculated relative energies for the tGg', gGg', g'Gg', tTt, and gTg' conformers are 0.0 (0.0), 3.4 (3.4), 5.1 (5.9), 7.9 (11.3), and 12.0 (14.0) kJ mol -1, respectively. Consequently, only the G-type conformers are sufficiently populated to give rise to observable spectral lines. Both experimental findings and theoretical calculations demonstrated that the bands in the argon matrix spectrum of pinacol are due to the most stable tGg' conformer. Although the ab initio calculations predict that also the gGg' and g'Gg' conformers are present in the gas phase and in dilute nonpolar solutions their existence could not be confirmed experimentally. Hence, we conclude that the conformation sensitive bands may coincide in the spectra. The HF/6-311G** ab initio calculations for vibrational frequencies of pinacol are consistent with this conclusion, suggesting only small differences between the wavenumbers of the G-type conformers. Pinacol does not show infrared-induced photorotamerization in the low
NASA Astrophysics Data System (ADS)
Potter, Brian S.; Palmer, Rex A.; Withnall, Robert; Chowdhry, Babur Z.; Price, Sarah L.
1999-08-01
The crystal and molecular structure of 5-azauracil, C 3H 3O 2N 3, Mr=113.07 Da, was determined from X-ray diffraction data. The material crystallizes in the orthorhombic space group Pbca with eight molecules of 5-azauracil in a cell of dimensions a=6.5135(3), b=13.5217(4), c=6.5824(4) Å, crystal density Dc=1.779 g cm -3. The structure was determined using direct methods and refined by full-matrix least-squares to a conventional R index of 0.0337 for 763 observed reflections and 86 parameters. Two strong hydrogen bonds, N1H1…O4 and N3H3…N5, and several weaker intermolecular interactions produce a crinkled sheet structure. This crystal structure was independently predicted by a search for minima in the lattice energy, as calculated using an ab initio optimised molecular structure and a distributed multipole model for the electrostatic interactions. Indeed, the global minimum in the search corresponded to the same Pbca space group, with rms errors in the cell lengths of 3.7%. There is a larger energy gap separating the observed hydrogen bonding motif structure from alternative structures, with different hydrogen bonds and connectivity, for 5-azauracil than for 6-azauracil and uracil.
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.
Photochemical determination of different DNA structures.
Xu, Yan; Tashiro, Ryu; Sugiyama, Hiroshi
2007-01-01
The various conformations of DNA are thought to have important biological roles. Investigation of the local DNA conformational changes associated with biological events is therefore essential to an understanding of the functions of DNA. We have reported the photoreactivities of 5-halouracil in the five characteristic local DNA structures: the A, B and Z forms, protein-induced DNA kinks and the G-quadruplex form. These studies demonstrate the detailed relationships between the local DNA structures and the photochemical products of photoinduced hydrogen abstraction by the resulting uracil-5-yl radicals, and show that this photochemical method can be used to detect DNA structures. Here, we describe in detail procedures that have been developed in our laboratory for probing DNA conformations by product analysis of photoirradiated 5-halouracil-containing DNA. The protocol includes the preparation of 5-halouracil-containing DNA and the characterization of the photoproducts, and it can be completed in 2 weeks.
Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.
Martí-Rujas, Javier; Kawano, Masaki
2013-02-19
Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific
Determination of hair structure and shape.
Schlake, Thomas
2007-04-01
The hair follicle attracted significant attention as a model for the investigation of diverse biological problems. Whereas its morphology and the structure of the hair shaft are known in detail, the molecular biology of this miniorgan is significantly less characterised. Many efforts focussed on the development of the hair follicle and its stem cell reservoir; by contrast, the follicular product, the hair, which is interesting not only in terms of cosmetics was neglected. This review highlights our current knowledge of the control of hair structure and shape with emphasis on mouse hair follicle biology and discusses continuing problems.
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…
Vascular structure determines pulmonary blood flow distribution.
Hlastala, M P; Glenny, R W
1999-10-01
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…
Structure determination of {alpha}-La{sub 6}W{sub 2}O{sub 15}
Chambrier, M-H.; Ibberson, R.M.; Goutenoire, F.
2010-06-15
The structure of the high temperature alpha form of La{sub 6}W{sub 2}O{sub 15} has been determined ab-initio from high temperature laboratory X-ray and neutron time-of-flight data. This tungstate crystallizes in the non-centrosymmetric orthorhombic space group (No. 20) C222{sub 1}, with Z=2, a=12.6250(2) A, b=9.1875(1) A, c=5.9688(1) A. The structure comprises [O{sub 2}La{sub 3}] infinite ribbons and is better described by the structural formula [O{sub 2}La{sub 3}]{sub 2}[WO{sub 5.5}]{sub 2}. Using this description we can understand the strong structural similarity of the present compound with compounds of the general composition BiM{sub 2}AO{sub 6} (M=Cu, Mg, Zn, Mn, Cd, Ca, Pb; A=P, As, V) described as [O{sub 2}M{sub 2}Bi][AO{sub 4}]. The [WO{sub 5.5}] entity implies oxygen disorder in the material. - Graphical abstract: Projection of the polyhedra around the tungsten atom. Atoms labelled in grey are occupied at 50%. Short oxygen-oxygen distances are marked. The polyhedra represents WO{sub 5.5} that is related to the structural unit W{sub 2}O{sub 11} unit. Alpha-La{sub 6}W{sub 2}O{sub 15} could be described as [O{sub 2}La{sub 3}]{sub 2}[WO{sub 5.5}]{sub 2}.
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.
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.
NASA Astrophysics Data System (ADS)
Carmichael, Ian
1987-09-01
The structures, characteristic vibrations and magnetic properties of two isoelectronic series of radicals and radical ions derived from group 13-15 trihydrides have been investigated by post-Hartree-Fock theoretical techniques. Møller-Plesset perturbation theory based on an unrestricted Hartree-Fock determinant has been employed to determine the structures and vibrational frequencies in the 9-electron series, BH -3, CH 3, and NH +3. These species are found to be planar. Spin density distributions and ionization energetics have been estimated using a variational configuration interaction procedure. A positive electron affinity for BH 3 has not been demonstrated. The effect of out-of-plane vibrations on the hyperfine coupling constants is determined at a similar level of theory. In the 17-electron series AlH -3, SiH 3, and PH +3, pyramidal structures are found by using and extended split-valence basis at the SCF level. The computed harmonic force field suggests that a tentative assignment of a matrix isolated infrared spectrum to SiH 3 is incorrect. This conclusion is reinforced by calculation of the vibrational intensity patterns. Hyperfine interaction tensors computed at the optimized geometries from the UHF wavefunction with a more complete polarized double-zeta basis set are in accord with experiment. Vibrational effects are estimated by averaging the UHF spin density over an energy surface determined by second-order perturbation theory. Corrections due to vibrations are smaller than in the carbon series and single-point configuration interaction calculations confirm the reliability of the UHF spin densities.
Ab Initio Force Fields for Imidazolium-Based Ionic Liquids.
McDaniel, Jesse G; Choi, Eunsong; Son, Chang Yun; Schmidt, J R; Yethiraj, Arun
2016-07-21
We develop ab initio force fields for alkylimidazolium-based ionic liquids (ILs) that predict the density, heats of vaporization, diffusion, and conductivity that are in semiquantitative agreement with experimental data. These predictions are useful in light of the scarcity of and sometimes inconsistency in experimental heats of vaporization and diffusion coefficients. We illuminate physical trends in the liquid cohesive energy with cation chain length and anion. These trends are different than those based on the experimental heats of vaporization. Molecular dynamics prediction of the room temperature dynamics of such ILs is more difficult than is generally realized in the literature due to large statistical uncertainties and sensitivity to subtle force field details. We believe that our developed force fields will be useful for correctly determining the physics responsible for the structure/property relationships in neat ILs.
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).
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
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. PMID:27500056
Ab initio phonon limited transport
NASA Astrophysics Data System (ADS)
Verstraete, Matthieu
We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)
Serianni, A.S.; Chipman, D.M.
1987-09-02
Ab initiao molecular orbital calculations have been conducted on four tetrofuranose anomers, ..cap alpha..- and ..beta..-D-erythrofuranose and ..cap alpha..- and ..beta..-D-threofuranose, to study the effect of ring conformation on molecular parameters (bond lengths, bond angles, bond torsions) and on total energies. Geometric optimizations of envelope and planar conformers were conducted using the STO-3G basis set; single-point calculations were also performed with the 3-21G basis set. Preferred solution conformations deduced from previous NMR studies are in good agreement with those predicted by calculation, indicating that the intrinsic structures of these furanoses dictate their preferred geometries, and that solvation by water (/sup 2/H/sub 2/O) does not appear to be a major conformational determinant. The ..beta..-D-erythro configuration, which is structurally related to the ..beta..-D-ribo configuration found in RNA, was found to have significantly different conformational behavior from the other three configurations.
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.
Determining building interior structures using compressive sensing
NASA Astrophysics Data System (ADS)
Lagunas, Eva; Amin, Moeness G.; Ahmad, Fauzia; Nájar, Montse
2013-04-01
We consider imaging of the building interior structures using compressive sensing (CS) with applications to through-the-wall imaging and urban sensing. We consider a monostatic synthetic aperture radar imaging system employing stepped frequency waveform. The proposed approach exploits prior information of building construction practices to form an appropriate sparse representation of the building interior layout. We devise a dictionary of possible wall locations, which is consistent with the fact that interior walls are typically parallel or perpendicular to the front wall. The dictionary accounts for the dominant normal angle reflections from exterior and interior walls for the monostatic imaging system. CS is applied to a reduced set of observations to recover the true positions of the walls. Additional information about interior walls can be obtained using a dictionary of possible corner reflectors, which is the response of the junction of two walls. Supporting results based on simulation and laboratory experiments are provided. It is shown that the proposed sparsifying basis outperforms the conventional through-the-wall CS model, the wavelet sparsifying basis, and the block sparse model for building interior layout detection.
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
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.
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. DOI: http://dx.doi.org/10.7554/eLife.03600.001 PMID:25303172
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
Language Structure Is Partly Determined by Social Structure
Lupyan, Gary; Dale, Rick
2010-01-01
Background Languages differ greatly both in their syntactic and morphological systems and in the social environments in which they exist. We challenge the view that language grammars are unrelated to social environments in which they are learned and used. Methodology/Principal Findings We conducted a statistical analysis of >2,000 languages using a combination of demographic sources and the World Atlas of Language Structures— a database of structural language properties. We found strong relationships between linguistic factors related to morphological complexity, and demographic/socio-historical factors such as the number of language users, geographic spread, and degree of language contact. The analyses suggest that languages spoken by large groups have simpler inflectional morphology than languages spoken by smaller groups as measured on a variety of factors such as case systems and complexity of conjugations. Additionally, languages spoken by large groups are much more likely to use lexical strategies in place of inflectional morphology to encode evidentiality, negation, aspect, and possession. Our findings indicate that just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in which they are being learned and used. As adults learn a language, features that are difficult for them to acquire, are less likely to be passed on to subsequent learners. Languages used for communication in large groups that include adult learners appear to have been subjected to such selection. Conversely, the morphological complexity common to languages used in small groups increases redundancy which may facilitate language learning by infants. Conclusions/Significance We hypothesize that language structures are subjected to different evolutionary pressures in different social environments. Just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche) in
THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY
Turchi, P A
2004-09-24
Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. 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. Finally, comments will be made on challenges and future prospects.
Eremeev, S V; Chukurov, E N; Gruznev, D V; Zotov, A V; Saranin, A A
2015-08-01
Using ab initio calculations, atomic structure and electronic properties of Si(1 1 1)[Formula: see text]-Bi surface modified by adsorption of 1/3 monolayer of alkali metals, Li, Na, K, Rb and Cs, have been explored. Upon adsorption of all metals, a similar atomic structure develops at the surface where twisted chained Bi trimers are arranged into a honeycomb network and alkali metal atoms occupy the [Formula: see text] sites in the center of each honeycomb unit. Among other structural characteristics, the greatest variation concerns the relative heights at which alkali metals reside with respect to Bi-trimer layer. Except for Li, the other metals reside higher than Bi layer and their heights increase with atomic number. All adsorbed surface structures display similar electron band structures of which the most essential feature is metallic surface-state band with a giant spin splitting. This electronic property allows one to consider the Si(1 1 1)[Formula: see text]-Bi surfaces modified by alkali metal adsorption as a set of material systems showing promise for spintronic applications.
NASA Astrophysics Data System (ADS)
Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.
2015-05-01
The ab initio calculation has been performed for the crystal structure and the phonon spectrum of titanates with the structure of pyrochlore R 2Ti2O7 ( R = Gd-Lu). The frequencies and types of fundamental vibrations have been found. For R = Tb, Tm, and Yb, this calculation has been carried out for the first time; furthermore, there is no available information on experimental studies of the phonon spectrum for Tm and Yb. The influence of hydrostatic pressure to 35 GPa on the structure, dynamics, and elastic properties of the Gd2Ti2O7 lattice has been investigated. The dependence of the phonon frequencies on the pressure has been obtained. The calculations have predicted that the relative change in the pyrochlore structure volume during compression at pressures to 35 GPa is well described by the third-order Birch-Murnaghan equation of states. The results of the calculations agree with the available experimental data. It has been shown that the structural, dynamic, and elastic properties of the R 2Ti2O7 crystal lattice can be adequately described in the case where the inner shells of the RE ion up to 4 f are replaced by the pseudopotential.
Hou, Gao-Lei; Feng, Gang; Zhao, Li-Juan; Xu, Hong-Guang; Zheng, Wei-Jun
2015-11-12
The (KI)n(-) (n = 1-4) and K(KI)n(-) (n = 1-3) clusters were studied by negative ion photoelectron spectroscopy and ab initio calculations. Comparison between the theoretical vertical detachment energies and the experimental values revealed that multiple isomers may coexist in the experiments. The existence of two isomers for K(KI)(-) and K(KI)2(-) were confirmed directly by isomer-depletion experiments, in which the low adiabatic detachment energy isomers were depleted by a 1064 nm laser beam before the anions were photodetached by a 532 nm laser beam. Our results show that the most stable structures of the K(KI)(-), (KI)2(-), and K(KI)2(-) anions are chain structures, while those of their neutral counterparts are planar. Three-dimensional structures start to appear at n = 3 for (KI)n(-/0) and K(KI)n(-/0). In the K(KI)n(-) cluster anions, the excess electron is localized on the extra K atom and forms an electron pair with the existing s electron of the K atom; the resulting negatively charged K prefers to interact with the other positively charged K atoms rather than with the I atoms. Both the anionic and neutral (KI)4 clusters have cuboid structures, which may be regarded as the smallest structural motif of KI crystal. PMID:26473992
Ab initio Ti-Zr-Ni phase diagram predicts stability of icosahedral TiZrNi quasicrystals
NASA Astrophysics Data System (ADS)
Hennig, R. G.; Carlsson, A. E.; Kelton, K. F.; Henley, C. L.
2005-04-01
The ab initio phase diagram determines the energetic stability of the icosahedral TiZrNi quasicrystal. The complete ab initio zero-temperature ternary phase diagram is constructed from the calculated energies of the elemental, binary and ternary Ti-Zr-Ni phases. For this, the icosahedral i -TiZrNi quasicrystal is approximated by periodic structures of up to 123 atoms/unit cell, based on a decorated-tiling model [R. G. Hennig, K. F. Kelton, A. E. Carlsson, and C. L. Henley, Phys. Rev. B 67, 134202 (2003)]. The approximant structures containing the 45-atom Bergman cluster are nearly degenerate in energy, and are all energetically stable against the competing phases. It is concluded that i -TiZrNi is a ground-state quasicrystal, as it is experimentally the low-temperature phase for its composition.
Hickel, Tilmann; Uijttewaal, Matthé; Grabowski, Blazej; Neugebauer, Jörg
2008-02-13
Ni(2)MnGa is a typical example of a Heusler alloy that undergoes a martensitic transformation. In the high temperature austenitic phase it has a cubic L2(1) structure, whereas below 200 K the symmetry is reduced by an orthorhombic distortion. Despite lattice deformations of more than 6% and large strains connected to this change, it is completely reversible. Therefore, Ni(2)MnGa serves as a shape memory compound. The fact that Ni(2)MnGa additionally orders ferromagnetically below 360 K makes the material particularly attractive for applications in actuators and sensors. Nevertheless, its structural details in the martensitic phase are still a subject of much debate. Several shuffling structures have been observed experimentally. The temperature and magnetic field dependent transformations between these structures need to be understood for improvement of the magnetic switching (e.g. operation with higher reliability and smaller magnetic fields). Our tool for identifying the stable structures and the low energy transition paths is the calculation of free energy surfaces as functions of key reaction coordinates (e.g. the ratio c/a) in density functional theory. (The generalized gradient approximation to the exchange-correlation functional and the projector augmented wave approach implemented in VASP (Vienna Ab initio Simulation Package) were used in these investigations.) The different variants of the low symmetry orthorhombic structures lead to characteristic minima on this surface. However, the ab initio determination of the experimentally observed shuffling structures is challenging, due to the large phase space of possible atomic positions and the small shuffling formation energies of only a few meV per unit cell. Hence, we used the quasiharmonic approximation in order to compute and analyze phonon spectra. Starting with the symmetric structure of the austenite, the TA(2) (TA standing for transverse acoustic) phonon dispersion shows a phonon softening along
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.
Algorithms for Determining Physical Responses of Structures Under Load
NASA Technical Reports Server (NTRS)
Richards, W. Lance; Ko, William L.
2012-01-01
Ultra-efficient real-time structural monitoring algorithms have been developed to provide extensive information about the physical response of structures under load. These algorithms are driven by actual strain data to measure accurately local strains at multiple locations on the surface of a structure. Through a single point load calibration test, these structural strains are then used to calculate key physical properties of the structure at each measurement location. Such properties include the structure s flexural rigidity (the product of the structure's modulus of elasticity, and its moment of inertia) and the section modulus (the moment of inertia divided by the structure s half-depth). The resulting structural properties at each location can be used to determine the structure s bending moment, shear, and structural loads in real time while the structure is in service. The amount of structural information can be maximized through the use of highly multiplexed fiber Bragg grating technology using optical time domain reflectometry and optical frequency domain reflectometry, which can provide a local strain measurement every 10 mm on a single hair-sized optical fiber. Since local strain is used as input to the algorithms, this system serves multiple purposes of measuring strains and displacements, as well as determining structural bending moment, shear, and loads for assessing real-time structural health. The first step is to install a series of strain sensors on the structure s surface in such a way as to measure bending strains at desired locations. The next step is to perform a simple ground test calibration. For a beam of length l (see example), discretized into n sections and subjected to a tip load of P that places the beam in bending, the flexural rigidity of the beam can be experimentally determined at each measurement location x. The bending moment at each station can then be determined for any general set of loads applied during operation.
First fully ab initio potential energy surface of methane with a spectroscopic accuracy
NASA Astrophysics Data System (ADS)
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2016-09-01
Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.
Al-Douri, Y.; Ahmad, S.; Hashim, U.; Reshak, Ali Hussain; Baaziz, H.; Charifi, Z.; Khenata, R.
2010-12-15
The structural, electronic and optical properties of cubic CdS{sub 1-x}Te{sub x} alloys, with Te-concentrations varying from 0% up to 100% are investigated. The calculations are based on the total-energy calculations using the full potential-linearized augmented plane wave (FP-LAPW) method. The exchange and correlation potential is treated by the generalized-gradient approximation (GGA) for the total-energy calculations, while for electronic properties in addition to that the Engel-Vosko (EV-GGA) formalism was also applied. The ground state properties for all Te-concentrations are presented. The optical dielectric constant is also determined for both the binary and their related ternary alloys. (author)
Cadoni, Enzo; Ferino, Giulio; Pitzanti, Patrizia; Secci, Francesco; Fattuoni, Claudia; Nicolò, Francesco; Bruno, Giuseppe
2015-01-01
The aim of this study is to describe and compare the supramolecular interactions, in the solid state, of chloro-, bromo-, and iodobenzothiophene diols. The compounds were obtained through organo-catalyzed reactions starting from 3-substituted halobenzothiophene carbaldehydes. Energies of the noncovalent interactions were obtained by density functional theory calculations. Bond distances and angles were found to be in accordance with those determined by X-ray structure analysis. anti-Bromobenzothiophene derivatives showed strong halogen⋅⋅⋅π interactions between bromine and the heterocyclic phenyl ring, corresponding to an energy of 7.5 kcal mol−1. syn-Bromo and syn-iodo derivatives appeared to be isostructural, showing X⋅⋅⋅O (carbonyl) interactions, π stacking, and formation of extended hydrogen bonding networks. In contrast, the chloro derivatives displayed no halogen bonding interactions. PMID:25969814
Ab Initio Studies of Stratospheric Ozone Depletion Chemistry
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.
a Microwave and AB Initio Study of the Nitric Acid - Trimethylamine Complex
NASA Astrophysics Data System (ADS)
Sedo, Galen; Leopold, Kenneth R.
2009-06-01
The microwave spectrum of the gas phase nitric acid - trimethylamine complex has been observed using Fourier transform microwave spectroscopy. The experimental rotational constants and (CH{_3}){_3}{^1}{^5}N-HNO{_3} isotope shifts are consistent with a complex in which the nitric acid proton forms a hydrogen bond to the nitrogen of the amine, similar to the experimentally determined structure of H{_3}N-HNO{_3} Analysis of the hyperfine structure in both the parent and (CH{_3}){_3}{^1}{^5}N-HNO{_3} spectra made it possible to determine, unambiguously, the quadrupole coupling constants of the {^1}{^5}N nuclei in both the nitric acid and trimethylamine moieties. Ab initio calculations, using the MP2/6-311++G(2df,2pd) level of theory and basis set, have been performed and are in quantitative agreement with the available experimental data. Both the experimentally determined quadrupole coupling constants and the ab initio structure have been used to assess the degree of proton transfer occurring in the nitric acid - trimethylamine complex. These results will be compared to those obtained for the H{_3}N-HNO{_3} and HNO{_3}-(H{_2}O){_n} [n = 0 - 3] complexes and discussed in terms of how binding partner basicity and the number of solvent molecules influence the incipient ionization of nitric acid moiety. M. E. Ott, and K. R. Leopold, J. Phys. Chem. A 1999, 103,1322-1328.
NASA Astrophysics Data System (ADS)
Kumar, J. Sharmi; Devi, T. S. Renuga; Ramkumaar, G. R.; Bright, A.
2016-01-01
The FTIR and FT-Raman spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid were recorded and the structural and spectroscopic data of the molecule in the ground state were calculated using Hartree-Fock and Density Functional Method (B3LYP). The most stable conformer was optimized and the structural and vibrational parameters were determined. With the observed FTIR and FT-Raman data, a complete vibrational band assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties, Mulliken and natural atomic charge distribution were calculated using both Hartree-Fock and Density Functional Method and compared. UV-Visible and HOMO-LUMO analysis were carried out. 1H and 13C NMR chemical shifts of the molecule were calculated using gauge including atomic orbital method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. The first order hyperpolarizability (β) and molecular electrostatic potential of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemically reactive site in the molecule.
Kumar, J Sharmi; Devi, T S Renuga; Ramkumaar, G R; Bright, A
2016-01-01
The FTIR and FT-Raman spectra of 4-(2-Hydroxyethyl) piperazine-1-ethanesulfonic acid were recorded and the structural and spectroscopic data of the molecule in the ground state were calculated using Hartree-Fock and Density Functional Method (B3LYP). The most stable conformer was optimized and the structural and vibrational parameters were determined. With the observed FTIR and FT-Raman data, a complete vibrational band assignment and analysis of the fundamental modes of the compound were carried out. Thermodynamic properties, Mulliken and natural atomic charge distribution were calculated using both Hartree-Fock and Density Functional Method and compared. UV-Visible and HOMO-LUMO analysis were carried out. (1)H and (13)C NMR chemical shifts of the molecule were calculated using gauge including atomic orbital method and were compared with experimental results. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital analysis. The first order hyperpolarizability (β) and molecular electrostatic potential of the molecule was computed using DFT calculations. The electron density based local reactivity descriptor such as Fukui functions were calculated to explain the chemically reactive site in the molecule.
Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.
Fromm, S A; Sachse, C
2016-01-01
Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method.
Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction.
Fromm, S A; Sachse, C
2016-01-01
Treating helices as single-particle-like segments followed by helical image reconstruction has become the method of choice for high-resolution structure determination of well-ordered helical viruses as well as flexible filaments. In this review, we will illustrate how the combination of latest hardware developments with optimized image processing routines have led to a series of near-atomic resolution structures of helical assemblies. Originally, the treatment of helices as a sequence of segments followed by Fourier-Bessel reconstruction revealed the potential to determine near-atomic resolution structures from helical specimens. In the meantime, real-space image processing of helices in a stack of single particles was developed and enabled the structure determination of specimens that resisted classical Fourier helical reconstruction and also facilitated high-resolution structure determination. Despite the progress in real-space analysis, the combination of Fourier and real-space processing is still commonly used to better estimate the symmetry parameters as the imposition of the correct helical symmetry is essential for high-resolution structure determination. Recent hardware advancement by the introduction of direct electron detectors has significantly enhanced the image quality and together with improved image processing procedures has made segmented helical reconstruction a very productive cryo-EM structure determination method. PMID:27572732
NASA Astrophysics Data System (ADS)
Tossell, J. A.
2005-12-01
B(OH) 3 and CO 2 are acidic species of considerable geochemical importance, yet the microscopic nature of the acid dissociation reactions for these B and C species is not well understood. Quantum mechanical methods have recently been applied to the direct ab initio calculation of p Ka values for many organic and inorganic weak acids, but the B and C acids have not yet been considered in detail. In the present study, p Ka values are calculated quantum mechanically for the oxyacids B(OH) 3, H 2CO 3 and HNO 3, which have experimental first p Ka values of 9.2, 6.4 and -1.3, respectively. We calculate the gas-phase reaction free energies at the highly accurate CBS-QB3 ab initio quantum mechanical level and reaction free energies of hydration using a polarizable continuum method. Using a thermodynamic cycle corresponding to the simple dissociation process HA A - + H +, in aqueous solution, we calculate p Ka values of 21.6, 3.8 to 2.2 and -0.8 for the three oxyacids mentioned above, closely matching experiment only for HNO 3. The discrepancies with experiment arise from the more complex nature of the acid dissociation process for B(OH) 3, which involves the addition of H 2O to B(OH) 3 and formation of the B(OH) 4- anion, and from the instability of hypothetical H 2CO 3 compared to the proper hydrated reactant complex CO 2. . . H 2O. When the proper microscopic description of the reactants and products is used the calculated p Ka values for the three acids become 11.1, 7.2 and -0.8, in considerably better agreement with experiment for B(OH) 3 and CO 2. . . H 2O. Thus p Ka calculations using this approach are accurate enough to give information on the actual acid species present in solution and the details of their acid dissociation processes at the microscopic level. 11B and 13C-NMR chemical shifts are also calculated for the various species and compared to experiment. By comparison of our calculations with experiment it is apparent that the 13C-NMR chemical shift has
NASA Astrophysics Data System (ADS)
Yu, H. L.; Jiang, X. F.; Zheng, Y.; Yang, G. W.
2012-08-01
The formation of MgO epitaxial layers on a Co2MnSi (0 0 1) surface was studied using the ab initio electronic structure calculations based on the density functional theory. The free energy calculations showed that the O-rich, O-top and Mg-rich configurations in the CoCo termination case, and the O-rich and O-top configurations in the MnSi termination case were thermodynamically stable. The magnetic and electronic properties of these stable configurations were investigated in detail, and the results indicated that only the Mg-rich configuration with CoCo termination exhibited near half-metallic properties at the interface. The influence of the interfacial structure on the tunnelling conductance of the Co2MnSi/MgO/Co2MnSi magnetic tunnel junctions (MTJs) was also discussed using the nonequilibrium Green's function method. The attained conductance showed that a large difference of up to 104 was observed in the magnitude of parallel conductance, which means that the interface structure plays a crucial role in the electronic transport of the MTJ. These findings are useful in designing MTJs with high performance.
Protein Structure Determination Using Protein Threading and Sparse NMR Data
Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.
1999-11-14
It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.
NASA Astrophysics Data System (ADS)
Feller, D. F.
1993-07-01
This collection of benchmark timings represents a snapshot of the hardware and software capabilities available for ab initio quantum chemical calculations at Pacific Northwest Laboratory's Molecular Science Research Center in late 1992 and early 1993. The 'snapshot' nature of these results should not be underestimated, because of the speed with which both hardware and software are changing. Even during the brief period of this study, we were presented with newer, faster versions of several of the codes. However, the deadline for completing this edition of the benchmarks precluded updating all the relevant entries in the tables. As will be discussed below, a similar situation occurred with the hardware. The timing data included in this report are subject to all the normal failures, omissions, and errors that accompany any human activity. In an attempt to mimic the manner in which calculations are typically performed, we have run the calculations with the maximum number of defaults provided by each program and a near minimum amount of memory. This approach may not produce the fastest performance that a particular code can deliver. It is not known to what extent improved timings could be obtained for each code by varying the run parameters. If sufficient interest exists, it might be possible to compile a second list of timing data corresponding to the fastest observed performance from each application, using an unrestricted set of input parameters. Improvements in I/O might have been possible by fine tuning the Unix kernel, but we resisted the temptation to make changes to the operating system. Due to the large number of possible variations in levels of operating system, compilers, speed of disks and memory, versions of applications, etc., readers of this report may not be able to exactly reproduce the times indicated. Copies of the output files from individual runs are available if questions arise about a particular set of timings.
Feller, D.F.
1993-07-01
This collection of benchmark timings represents a snapshot of the hardware and software capabilities available for ab initio quantum chemical calculations at Pacific Northwest Laboratory`s Molecular Science Research Center in late 1992 and early 1993. The ``snapshot`` nature of these results should not be underestimated, because of the speed with which both hardware and software are changing. Even during the brief period of this study, we were presented with newer, faster versions of several of the codes. However, the deadline for completing this edition of the benchmarks precluded updating all the relevant entries in the tables. As will be discussed below, a similar situation occurred with the hardware. The timing data included in this report are subject to all the normal failures, omissions, and errors that accompany any human activity. In an attempt to mimic the manner in which calculations are typically performed, we have run the calculations with the maximum number of defaults provided by each program and a near minimum amount of memory. This approach may not produce the fastest performance that a particular code can deliver. It is not known to what extent improved timings could be obtained for each code by varying the run parameters. If sufficient interest exists, it might be possible to compile a second list of timing data corresponding to the fastest observed performance from each application, using an unrestricted set of input parameters. Improvements in I/O might have been possible by fine tuning the Unix kernel, but we resisted the temptation to make changes to the operating system. Due to the large number of possible variations in levels of operating system, compilers, speed of disks and memory, versions of applications, etc., readers of this report may not be able to exactly reproduce the times indicated. Copies of the output files from individual runs are available if questions arise about a particular set of timings.
Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density
Baker, Matthew L; Jiang, Wen; Wedemeyer, William J; Rixon, Frazer J; Baker, David; Chiu, Wah
2006-01-01
Efforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy (cryoEM) has assumed an increasingly important role in determining the structures of these large macromolecular assemblies to intermediate resolutions (6–10 Å). While these structures provide a snapshot of the assembly and its components in well-defined functional states, the resolution limits the ability to build accurate structural models. In contrast, sequence-based modeling techniques are capable of producing relatively robust structural models for isolated proteins or domains. In this work, we developed and applied a hybrid modeling approach, utilizing cryoEM density and ab initio modeling to produce a structural model for the core domain of a herpesvirus structural protein, VP26. Specifically, this method, first tested on simulated data, utilizes the cryoEM density map as a geometrical constraint in identifying the most native-like models from a gallery of models generated by ab initio modeling. The resulting model for the core domain of VP26, based on the 8.5-Å resolution herpes simplex virus type 1 (HSV-1) capsid cryoEM structure and mutational data, exhibited a novel fold. Additionally, the core domain of VP26 appeared to have a complementary interface to the known upper-domain structure of VP5, its cognate binding partner. While this new model provides for a better understanding of the assembly and interactions of VP26 in HSV-1, the approach itself may have broader applications in modeling the components of large macromolecular assemblies. PMID:17069457
Ambiguity of structure determination from a minimum of diffraction intensities.
Al-Asadi, Ahmed; Leggas, Dimitri; Tsodikov, Oleg V
2014-07-01
Although the ambiguity of the crystal structures determined directly from diffraction intensities has been historically recognized, it is not well understood in quantitative terms. Bernstein's theorem has recently been used to obtain the number of one-dimensional crystal structures of equal point atoms, given a minimum set of diffraction intensities. By a similar approach, the number of two- and three-dimensional crystal structures that can be determined from a minimum intensity data set is estimated herein. The ambiguity of structure determination from the algebraic minimum of data increases at least exponentially fast with the increasing structure size. Substituting lower-resolution intensities by higher-resolution ones in the minimum data set has little or no effect on this ambiguity if the number of such substitutions is relatively small. PMID:25970192
Crystallization and Structure Determination of Superantigens and Immune Receptor Complexes.
Rödström, Karin E J; Lindkvist-Petersson, Karin
2016-01-01
Structure determination of superantigens and the complexes they form with immune receptors have over the years provided insight in their modes of action. This technique requires growing large and highly ordered crystals of the superantigen or receptor-superantigen complex, followed by exposure to X-ray radiation and data collection. Here, we describe methods for crystallizing superantigens and superantigen-receptor complexes using the vapor diffusion technique, how the crystals may be optimized, and lastly data collection and structure determination.
NMRFAM-SDF: a protein structure determination framework.
Dashti, Hesam; Lee, Woonghee; Tonelli, Marco; Cornilescu, Claudia C; Cornilescu, Gabriel; Assadi-Porter, Fariba M; Westler, William M; Eghbalnia, Hamid R; Markley, John L
2015-08-01
The computationally demanding nature of automated NMR structure determination necessitates a delicate balancing of factors that include the time complexity of data collection, the computational complexity of chemical shift assignments, and selection of proper optimization steps. During the past two decades the computational and algorithmic aspects of several discrete steps of the process have been addressed. Although no single comprehensive solution has emerged, the incorporation of a validation protocol has gained recognition as a necessary step for a robust automated approach. The need for validation becomes even more pronounced in cases of proteins with higher structural complexity, where potentially larger errors generated at each step can propagate and accumulate in the process of structure calculation, thereby significantly degrading the efficacy of any software framework. This paper introduces a complete framework for protein structure determination with NMR--from data acquisition to the structure determination. The aim is twofold: to simplify the structure determination process for non-NMR experts whenever feasible, while maintaining flexibility by providing a set of modules that validate each step, and to enable the assessment of error propagations. This framework, called NMRFAM-SDF (NMRFAM-Structure Determination Framework), and its various components are available for download from the NMRFAM website (http://nmrfam.wisc.edu/software.htm).
Introducing Chemists to X-Ray Structure Determination.
ERIC Educational Resources Information Center
Enemark, John H.
1988-01-01
Presents the organization of a one-semester graduate course in structural chemistry including lectures and problems. Discusses the coverage of diffraction from real crystals and structure determination. Summarizes experiments on real crystals conducted by students in the X-ray laboratory. (CW)
Labor Market Structure and Salary Determination among Professional Basketball Players.
ERIC Educational Resources Information Center
Wallace, Michael
1988-01-01
The author investigates the labor market structure and determinants of salaries for professional basketball players. An expanded version of the resource perspective is used. A three-tiered model of labor market segmentation is revealed for professional basketball players, but other variables also are important in salary determination. (Author/CH)
Curtiss, L.A.
1993-04-01
The structures and energies of the molten salt vapor complexes LiAlF{sub 4} and NaAlF{sub 4} are studied using new high level ab initio molecular orbital methods. The structures are determined using Moller-Plesset perturbation theory to second-order and the total energies are determined using a recently introduced modification of Gaussian-2 (G2) theory. The total energies are used to determine relative energies of the corner-, edge-, and face-bridged structures and accurate reaction energies. The results are compared to previous theoretical and experimental studies.
Curtiss, L.A.
1993-01-01
The structures and energies of the molten salt vapor complexes LiAlF[sub 4] and NaAlF[sub 4] are studied using new high level ab initio molecular orbital methods. The structures are determined using Moller-Plesset perturbation theory to second-order and the total energies are determined using a recently introduced modification of Gaussian-2 (G2) theory. The total energies are used to determine relative energies of the corner-, edge-, and face-bridged structures and accurate reaction energies. The results are compared to previous theoretical and experimental studies.
Ab initio non-relativistic spin dynamics
Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong; Frisch, Michael J.
2014-12-07
Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.
Ab initio non-relativistic spin dynamics
NASA Astrophysics Data System (ADS)
Ding, Feizhi; Goings, Joshua J.; Frisch, Michael J.; Li, Xiaosong
2014-12-01
Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li3 molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.
NASA Astrophysics Data System (ADS)
Hatch, Richard C.; Seo, Hosung; Ponath, Patrick; Choi, Miri; Posadas, Agham B.; Demkov, Alexander A.
2014-03-01
Using high-resolution angle-resolved photoemission spectroscopy (ARPES) we compare the surface electronic structure of both Ge(001) and Si(001) surfaces. Unlike previous ARPES experiments, where the Ge(001) surfaces were prepared using cycles of ion sputtering and annealing, our Ge(001) surfaces were prepared using a combination of wet etching and oxygen plasma cleaning. This new technique has the advantage that it avoids the incomplete healing of surface roughening associated with sputtering and annealing cycles. The ARPES data show that the dimer-derived surface state that determines the charge neutrality level, and thus the Schottky barrier height in Si, is actually a surface resonance in Ge, and the highest occupied state is a bulk state. In order to avoid theory predicting an overlap of the valence and conduction bands, we employed first-principles, hybrid density functional theory (DFT). This theory effectively explains the presence of a number of photoemission features in both Si and Ge. We found it is necessary to incorporate spin-orbit interaction in the hybrid DFT calculations for Ge in order to model ARPES data, and we found a spin-orbit splitting of 0.28 eV both experimentally and theoretically.
Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M; Ben Altabef, Aída
2015-02-01
The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34°C and decomposes at temperatures higher than 193°C.
NASA Astrophysics Data System (ADS)
Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M.; Altabef, Aída Ben
2015-02-01
The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34 °C and decomposes at temperatures higher than 193 °C.
Sridevi, C; Velraj, G
2013-04-15
This study represents the vibrational, electronic, NMR, NLO, reactivity and structural aspects of (3Z)-3-(2-oxo-2-phenylethylidene)-1,3-dihydro-2H-indol-2-one (OPEDI). A detailed interpretation of the FT-IR, FT-Raman, UV and NMR spectra were reported. Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. The most preferred Z isomer (cis-configuration) was confirmed through PES scan studies. The vibrational wavenumbers and potential energy distribution (PED) of various normal modes were calculated. The lower frontier orbital energy gap and high dipole moment of OPEDI illustrates the high reactivity. The stability and charge delocalization of the molecule was studied by natural bond orbital (NBO) analysis. OPEDI exhibited good nonlinear optical activity and was 13 times greater than that of urea. Molecular electrostatic potential (MEP) was carried out for predicting the reactive sites. The NMR results indicated that the observed chemical shifts depend not only on the structure of the molecule being studied, but also on the solvent used.
Ab initio studies of anisotropic magnetism in uranium and cerium monopnictides and monochalcogenides
NASA Astrophysics Data System (ADS)
Collins, Eric Mason
We have applied two ab initio based methods to investigate the origin in the electronic structure of the unusual magnetic behavior of the cerium and uranium monopnictides and monochalcogenides. First, we have carried out spin-polarized electronic structure calculations, based on the full potential linear muffin tin (FPLMTO) method, with spin polarization (orbital polarization only via spin-orbit coupling) and also with orbital polarization correction. Second, we have carried out ab initio based calculations synthesizing (1) a phenomenological theory of orbitally driven magnetism based on the Anderson and Kondo, lattice model which incorporates explicitly the hybridization induced and the Coulomb exchange interactions on an equal footing, and (2) FPLMTO electronic structure calculations allowing a first principles evaluation of all the parameters entering the model Hamiltonian. For the cerium compounds, we also include the crystal field interactions on an equal footing with the hybridization and Coulomb exchange interactions with a scaling determined by experiment. The results for the uranium compound calculations show that both methods are limited to the extremes to which they are best suited. The pure band structure calculations provide the best agreement for the lighter uranium compounds, while the model hamiltonian approach provides better agreement for the heavier uranium compounds. In the case of the cerium compounds, while the pure FPLMTO calculations yield values for the magnetic moment in agreement with experiment for the lighter cerium chalcogenides, they fail to give, even qualitatively, the magnetic properties for all other systems. On the other hand, the ab initio based model Hamiltonian calculations reveal for the first time the interplay of hybridization, Coulomb exchange, and crystal field interactions across the cerium series, and give results for the low-temperature moment and ordering temperature in excellent agreement with experiment, for the
Zhang, Yi-Quan; Luo, Cheng-Lin; Wu, Xin-Bao; Wang, Bing-Wu; Gao, Song
2014-04-01
Until now, the expressions of the anisotropic energy barriers Δξ and ΔA, using the uniaxial magnetic anisotropy D, the intrachain coupling strength J, and the high-spin ground state S for single-chain magnets (SCMs) in the intermediate region between the Ising and the Heisenberg limits, were unknown. To explore this relationship, we used density functional theory and ab initio methods to obtain expressions of Δξ and ΔA in terms of D, J, and S of six R4Fe(II)-Re(IV)Cl4(CN)2 (R = diethylformamide (1), dibutylformamide (2), dimethylformamide (3), dimethylbutyramide (4), dimethylpropionamide (5), and diethylacetamide (6)) SCMs in the intermediate region. The ΔA value for compounds 1-3 was very similar to the magnetic anisotropic energy of a single Fe(II), while the value of Δξ was predicted using the exchange interaction of Fe(II) with the neighboring Re(IV), which could be expressed as 2JSReSFe. Similar to compounds 1-3, the anisotropy energy barrier ΔA of compounds 4 and 5 was also equal to (Di - Ei)SFe(2), but the correlation energy Δξ was closely equal to 2JSReSFe(cos 98.4 - cos 180) due to the reversal of the spins on the opposite Fe(II). For compound 6, one unit cell of Re(IV)Fe(II) was regarded as a domain wall since it had two different Re(IV)-Fe(II) couplings. Thus, the Δξ of compound 6 was expressed as 4J″SRe1Fe1SRe2Fe2, where J″ was the coupling constant of the neighboring unit cells of Re1Fe1 and Re2Fe2, and ΔA was equal to the anisotropic energy barrier of one domain wall given by DRe1Fe1(S(2)Re1Fe1 - 1/4). PMID:24673387
Structure Determination of Natural Products by Mass Spectrometry.
Biemann, Klaus
2015-01-01
I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts. PMID:26161970
Structural determination of intact proteins using mass spectrometry
Kruppa, Gary; Schoeniger, Joseph S.; Young, Malin M.
2008-05-06
The present invention relates to novel methods of determining the sequence and structure of proteins. Specifically, the present invention allows for the analysis of intact proteins within a mass spectrometer. Therefore, preparatory separations need not be performed prior to introducing a protein sample into the mass spectrometer. Also disclosed herein are new instrumental developments for enhancing the signal from the desired modified proteins, methods for producing controlled protein fragments in the mass spectrometer, eliminating complex microseparations, and protein preparatory chemical steps necessary for cross-linking based protein structure determination.Additionally, the preferred method of the present invention involves the determination of protein structures utilizing a top-down analysis of protein structures to search for covalent modifications. In the preferred method, intact proteins are ionized and fragmented within the mass spectrometer.
Structure Determination of Natural Products by Mass Spectrometry
NASA Astrophysics Data System (ADS)
Biemann, Klaus
2015-07-01
I review laboratory research on the development of mass spectrometric methodology for the determination of the structure of natural products of biological and medical interest, which I conducted from 1958 to the end of the twentieth century. The methodology was developed by converting small peptides to their corresponding polyamino alcohols to make them amenable to mass spectrometry, thereby making it applicable to whole proteins. The structures of alkaloids were determined by analyzing the fragmentation of a known alkaloid and then using the results to deduce the structures of related compounds. Heparin-like structures were investigated by determining their molecular weights from the mass of protonated molecular ions of complexes with highly basic, synthetic peptides. Mass spectrometry was also employed in the analysis of lunar material returned by the Apollo missions. A miniaturized gas chromatograph mass spectrometer was sent to Mars on board of the two Viking 1976 spacecrafts.
The progress made in determining the Mycobacterium tuberculosis structural proteome
Hecker, Michael
2011-01-01
Mycobacterium tuberculosis is a highly infectious pathogen that is still responsible for millions of deaths annually. Effectively treating this disease typically requires a course of antibiotics, most of which were developed decades ago. These drugs are, however, not effective against persistent tubercle bacilli and the emergence of drug-resistant stains threatens to make many of them obsolete. The identification of new drug targets, allowing the development of new potential drugs, is therefore imperative. Both proteomics and structural biology have important roles to play in this process, the former as a means of identifying promising drug targets and the latter allowing understanding of protein function and protein–drug interactions at atomic resolution. The determination of M. tuberculosis protein structures has been a goal of the scientific community for the last decade, who have aimed to supply a large amount of structural data that can be used in structure-based approaches for drug discovery and design. Only since the genome sequence of M. tuberculosis has been available has the determination of large numbers of tuberculosis protein structures been possible. Currently, the molecular structures of 8.5% of all the pathogen's protein-encoding ORFs have been determined. In this review, we look at the progress made in determining the M. tuberculosis structural proteome and the impact this has had on the development of potential new drugs, as well as the discovery of the function of crucial mycobaterial proteins. PMID:21674801
NASA Astrophysics Data System (ADS)
Tossell, J. A.
2006-10-01
Boric acid, B(OH) 3, forms complexes in aqueous solution with a number of bidentate O-containing ligands, HL -, where H 2L is C 2O 4H 2 (oxalic acid), C 3O 4H 4 (malonic acid), C 2H 6O 2 (ethylene glycol), C 6H 6O 2 (catechol), C 10H 8O 2 (dioxynaphthalene) and C 2O 3H 4 (glycolic acid). McElligott and Byrne [McElligott, S., Byrne, R.H., 1998. Interaction of B(OH)30 and HCO3- in seawater: Formation of B(OH)CO3-. Aquat. Geochem.3, 345-356.] have also found B(OH) 3 to form an aqueous complex with HCO3-1. Recently Lemarchand et al. [Lemarchand, E., Schott, J., Gaillardeet, J., 2005. Boron isotopic fractionation related to boron sorption on humic acid and the structure of surface complexes formed. Geochim. Cosmochim. Acta69, 3519-3533] have studied the formation of surface complexes of B(OH) 3 on humic acid, determining 11B NMR shifts and fitted values of formation constants, and 11B, 10B isotope fractionations for a number of surface complexation models. Their work helps to clarify both the nature of the interaction of boric acid with the functional groups in humic acid and the nature of some of these coordinating sites on the humic acid. The determination of isotope fractionations may be seen as a form of vibrational spectroscopy, using the fractionating element as a local probe of the vibrational spectrum. We have calculated quantum mechanically the structures, stabilities, vibrational spectra, 11B NMR spectra and 11B, 10B isotope fractionations of a number of complexes B(OH) 2L - formed by reactions of the type: B(OH)3+HL-⇒B(OH)2L+HO using a 6-311G(d,p) basis set and the B3LYP method for determination of structures, vibrational frequencies and isotopic fractionations, the highly accurate Complete Basis Set-QB3 method for calculating the free energies and the GIAO HF method with a 6-311+G(2d,p) basis for the NMR shieldings. The calculations indicate that oxalic acid, malonic acid, catechol and glycolic acid all form stable complexes (Δ G < 0 for Reaction (1
Barrett, B R; Navratil, P; Vary, J P
2011-04-11
A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN
Determination of surface structure of cleaved (001) USb2 single crystal
Chen, Shao-ping; Hawley, Marilyn; Bauer, Eric D; Stockum, Phil B; Manoharan, Hari C
2009-01-01
We have achieved what we believe to be the first atomic resolution STM images for a uranium compound taken at room temperature. The a, b, and c lattice parameters in the images confirm that the USb{sub 2} crystals cleave on the (001) basal plane as expected. The a and b dimensions were equal, with the atoms arranged in a cubic pattern. Our calculations indicate a symmetric cut between Sb planes to be the most favorable cleavage plane and U atoms to be responsible for most of the DOS measured by STM. Some strange features associated with vacancies were observed in the STM win be discussed in conjunction with ab initio calculations. The purpose of this work is to demonstrate the power of scanning tunneling microscopy (STM) techniques combined with a theoretical underpinning to determine the surface atomic structure and properties of actinide materials, such as the quasi 2-dimensional uranium dipnictide USb{sub 2} single crystal, thereby contributing to the understanding of their surface structural and electronic properties. The members of this interesting UX{sub 2} (X=P, As, Sb, Bi) series of compounds display dual localized and itinerant 5f electron behavior within the same compound due to the hybridization of the 5f orbitals with the conduction band. With the exception of UO{sub 2}, which has to be studied at elevated temperature to generate enough carriers for STM imaging, STM techniques have not been applied successfully to the characterization of the surface atomic structure of any other single crystal actinide compound, to the best of our knowledge. However, STM has been used to a limited extent for the study of some cerium compounds. STM probes electronic properties at the atomic level and can directly provide information about the local density of filled and empty states (LDOS) states simultaneously. A STM topograph provides the local atomic arrangement and spacing of the atoms on the surface, local defect structures (e.g. steps, vacancies, and kink sites