Ab initio solution of macromolecular crystal structures without direct methods.

PubMed

McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

2017-04-04

The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

Atomistic insights into the nanosecond long amorphization and crystallization cycle of nanoscale G e2S b2T e5 : An ab initio molecular dynamics study

NASA Astrophysics Data System (ADS)

Branicio, Paulo S.; Bai, Kewu; Ramanarayan, H.; Wu, David T.; Sullivan, Michael B.; Srolovitz, David J.

2018-04-01

The complete process of amorphization and crystallization of the phase-change material G e2S b2T e5 is investigated using nanosecond ab initio molecular dynamics simulations. Varying the quench rate during the amorphization phase of the cycle results in the generation of a variety of structures from entirely crystallized (-0.45 K/ps) to entirely amorphized (-16 K/ps). The 1.5-ns annealing simulations indicate that the crystallization process depends strongly on both the annealing temperature and the initial amorphous structure. The presence of crystal precursors (square rings) in the amorphous matrix enhances nucleation/crystallization kinetics. The simulation data are used to construct a combined continuous-cooling-transformation (CCT) and temperature-time-transformation (TTT) diagram. The nose of the CCT-TTT diagram corresponds to the minimum time for the onset of homogenous crystallization and is located at 600 K and 70 ps. That corresponds to a critical cooling rate for amorphization of -4.5 K/ps. The results, in excellent agreement with experimental observations, suggest that a strategy that utilizes multiple quench rates and annealing temperatures may be used to effectively optimize the reversible switching speed and enable fast and energy-efficient phase-change memories.

Ab initio study of energy transfer rates and impact sensitivities of crystalline explosives.

PubMed

Bernstein, Jonathan

2018-02-28

Impact sensitivities of various crystalline explosives were predicted by means of plane wave-density functional theory calculations. Crystal structures and complete vibrational spectra of TATB, PETN, FOX7, TEX, 14DNI, and β-HMX molecular crystals were calculated. A correlation between the phonon-vibron coupling (which is proportionally related to the energy transfer rate between the phonon manifold and the intramolecular vibrational modes) and impact sensitivities of secondary explosives was found. We propose a method, based on ab initio calculations, for the evaluation of impact sensitivities, which consequently can assist in screening candidates for chemical synthesis of high energetic materials.

Ab initio study of energy transfer rates and impact sensitivities of crystalline explosives

NASA Astrophysics Data System (ADS)

Bernstein, Jonathan

2018-02-01

Impact sensitivities of various crystalline explosives were predicted by means of plane wave-density functional theory calculations. Crystal structures and complete vibrational spectra of TATB, PETN, FOX7, TEX, 14DNI, and β-HMX molecular crystals were calculated. A correlation between the phonon-vibron coupling (which is proportionally related to the energy transfer rate between the phonon manifold and the intramolecular vibrational modes) and impact sensitivities of secondary explosives was found. We propose a method, based on ab initio calculations, for the evaluation of impact sensitivities, which consequently can assist in screening candidates for chemical synthesis of high energetic materials.

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

PubMed Central

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 molecular crystal structures, spectra, and phase diagrams.

PubMed

Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

2014-09-16

Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher.

Structural, spectroscopic and electronic properties of hydrogen-bonded water molecules in crystals. Ab initio calculations and experimental data of MC1 2· n(H,D) 2O, M = Sr or Ba

NASA Astrophysics Data System (ADS)

Möller, H.; Niu, J. E.; Lutz, H. D.; Schwarz, W. H. E.

1997-12-01

Structural, spectroscopic and electronic properties of (more or less deuterated) water molecules in the crystal fields of SrCl 2·2H 2O, SrCl 2·H 2O and BaCl 2·H 2O, previously investigated by experimental techniques, were calculated by ab initio SCF-MP methods. The H 2O molecules of each compound are asymmetrically surrounded by three adjacent chloride ions, one hydrogen atom being attached to a nearby Cl -, the other less perturbed hydrogen atom bridging the two less near Cl -. The diversity of structural and spectroscopic features found experimentally, for instance the trends from free H 2O to H 2O in BaCl 2·H 2OSrCl 2·H 2OSrCl 2·2H 2O, are well reproduced by the model calculations, which provide the correct assignment and physical interpretation. The differences between the compounds and the asymmetry of the hydrate water molecules can be rationalized with the help of crystal fields. The crystal environment expands the internuclear distances of H 2O by up to 3 pm. The change of vibrational frequencies can be explained qualitatively by only taking the coupling and anharmonicity of the free water molecule and its modified structure in the crystals into account. The infra-red intensities, however, are strongly influenced by the electronic polarization.

Insights into water-mediated ion clustering in aqueous CaSO4 solutions: pre-nucleation cluster characteristics studied by ab initio calculations and molecular dynamics simulations.

PubMed

Li, Hui-Ji; Yan, Dan; Cai, Hou-Qin; Yi, Hai-Bo; Min, Xiao-Bo; Xia, Fei-Fei

2017-05-10

The molecular structure of growth units building crystals is a fundamental issue in the crystallization processes from aqueous solutions. In this work, a systematic investigation of pre-nucleation clusters and their hydration characteristics in aqueous CaSO 4 solutions was performed using ab initio calculations and molecular dynamics (MD) simulations. The results of ab initio calculations and MD simulations indicate that the dominant species in aqueous CaSO 4 solutions are monodentate ion-associated structures. Compared with charged ion clusters, neutral clusters are more likely to be present in an aqueous CaSO 4 solution. Neutral (CaSO 4 ) m clusters are probably the growth units involved in the pre-nucleation or crystallization processes. Meanwhile, hydration behavior around ion associated species in aqueous CaSO 4 solutions plays an important role in related phase/polymorphism selections. Upon ion clustering, the residence of some water molecules around Ca 2+ in ion-associated species is weakened while that of some bridging waters is enhanced due to dual interaction by Ca 2+ and SO 4 2- . Some phase/polymorphism selections can be achieved in aqueous CaSO 4 solutions by controlling the hydration around pre-nucleation clusters. Moreover, the association trend between calcium and sulfate is found to be relatively strong, which hints at the low solubility of calcium sulfate in water.

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

DOE PAGES

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; ...

2016-09-19

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 obstaclemore » 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 showwith 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.« less

Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

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

Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio

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 obstaclemore » 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 showwith 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.« less

Integrative interactive visualization of crystal structure, band structure, and Brillouin zone

NASA Astrophysics Data System (ADS)

Hanson, Robert; Hinke, Ben; van Koevering, Matthew; Oses, Corey; Toher, Cormac; Hicks, David; Gossett, Eric; Plata Ramos, Jose; Curtarolo, Stefano; Aflow Collaboration

The AFLOW library is an open-access database for high throughput ab-initio calculations that serves as a resource for the dissemination of computational results in the area of materials science. Our project aims to create an interactive web-based visualization of any structure in the AFLOW database that has associate band structure data in a way that allows novel simultaneous exploration of the crystal structure, band structure, and Brillouin zone. Interactivity is obtained using two synchronized JSmol implementations, one for the crystal structure and one for the Brillouin zone, along with a D3-based band-structure diagram produced on the fly from data obtained from the AFLOW database. The current website portal (http://aflowlib.mems.duke.edu/users/jmolers/matt/website) allows interactive access and visualization of crystal structure, Brillouin zone and band structure for more than 55,000 inorganic crystal structures. This work was supported by the US Navy Office of Naval Research through a Broad Area Announcement administered by Duke University.

Microscopic Mechanism of Doping-Induced Kinetically Constrained Crystallization in Phase-Change Materials.

PubMed

Lee, Tae Hoon; Loke, Desmond; Elliott, Stephen R

2015-10-07

A comprehensive microscopic mechanism of doping-induced kinetically constrained crystallization in phase-change materials is provided by investigating structural and dynamical dopant characteristics via ab initio molecular dynamics simulations. The information gained from this study may provide a basis for a fast screening of dopant species for electronic memory devices, or for understanding the general physics involved in the crystallization of doped glasses. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio elastic properties and tensile strength of crystalline hydroxyapatite.

PubMed

Ching, W Y; Rulis, Paul; Misra, A

2009-10-01

We report elastic constant calculation and a "theoretical" tensile experiment on stoichiometric hydroxyapatite (HAP) crystal using an ab initio technique. These results compare favorably with a variety of measured data. Theoretical tensile experiments are performed on the orthorhombic cell of HAP for both uniaxial and biaxial loading. The results show considerable anisotropy in the stress-strain behavior. It is shown that the failure behavior of the perfect HAP crystal is brittle for tension along the z-axis with a maximum stress of 9.6 GPa at 10% strain. Biaxial failure envelopes from six "theoretical" loading tests show a highly anisotropic pattern. Structural analysis of the crystal under various stages of tensile strain reveals that the deformation behavior manifests itself mainly in the rotation of the PO(4) tetrahedron with concomitant movements of both the columnar and axial Ca ions. These results are discussed in the context of mechanical properties of bioceramic composites relevant to mineralized tissues.

Ab initio simulations of iron-nickel alloys at Earth's core conditions

NASA Astrophysics Data System (ADS)

Côté, Alexander S.; Vočadlo, Lidunka; Brodholt, John P.

2012-09-01

We report ab initio density functional theory calculations on iron-nickel (FeNi) alloys at conditions representative of the Earth's inner core. We test different concentrations of Ni, up to ∼39 wt% using ab initio lattice dynamics, and investigate the thermodynamic and vibrational stability of the three candidate crystal structures (bcc, hcp and fcc). First of all, at inner core pressures, we find that pure Fe transforms from the hcp to the fcc phase at around 6000 K. Secondly, in agreement with low pressure experiments on Fe-Ni alloys, we find the fcc structure is stabilised by the incorporation of Ni under core pressures and temperatures. Our results show that the fcc structure may, therefore, be stable under core conditions depending on the temperature in the inner core and the Ni content. Lastly, we find that within the quasi-harmonic approximation, there is no stability field for FeNi alloys in the bcc structure under core conditions.

Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations.

PubMed

Aalbergsjø, Siv G; Pauwels, Ewald; Van Yperen-De Deyne, Andy; Van Speybroeck, Veronique; Sagstuen, Einar

2014-08-28

As the chemical structures of radiation damaged molecules may differ greatly from their undamaged counterparts, investigation and description of radiation damaged structures is commonly biased by the researcher. Radical formation from ionizing radiation in crystalline α-l-rhamnose monohydrate has been investigated using a new method where the selection of radical structures is unbiased by the researcher. The method is based on using ab initio molecular dynamics (MD) studies to investigate how ionization damage can form, change and move. Diversity in the radical production is gained by using different points on the potential energy surface of the intact crystal as starting points for the ionizations and letting the initial velocities of the nuclei after ionization be generated randomly. 160 ab initio MD runs produced 12 unique radical structures for investigation. Out of these, 7 of the potential products have never previously been discussed, and 3 products are found to match with radicals previously observed by electron magnetic resonance experiments.

Crossover of cation partitioning in olivines: a combination of ab initio and Monte Carlo study

NASA Astrophysics Data System (ADS)

Chatterjee, Swastika; Bhattacharyya, Sirshendu; Sengupta, Surajit; Saha-Dasgupta, Tanusri

2011-04-01

We report studies based on a combination of ab initio electronic structure and Monte Carlo (MC) technique on the problem of cation partitioning among inequivalent octahedral sites, M1 and M2 in mixed olivines containing Mg2+ and Fe2+ ions. Our MC scheme uses interactions derived out of ab initio, density functional calculations carried out on measured crystal structure data. Our results show that there is no reversal of the preference of Fe for M1 over M2 as a function of temperature. Our findings do not agree with the experimental findings of Redfern et al. (Phys Chem Miner 27:630-637, 2000), but are in agreement with those of Heinemann et al. (Eur J Mineral 18:673-689, 2006) and Morozov et al. (Eur J Mineral 17:495-500, 2005).

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

PubMed

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

2018-01-18

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

Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

PubMed

Iuzzolino, Luca; Reilly, Anthony M; McCabe, Patrick; Price, Sarah L

2017-10-10

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

Electronic structure and pair potential energy analysis of 4-n-methoxy-4′-cyanobiphenyl: A nematic liquid crystal

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

Sharma, Dipendra, E-mail: d-11sharma@rediffmail.com; Tiwari, S. N., E-mail: sntiwari123@rediffmail.com; Dwivedi, M. K., E-mail: dwivedi-ji@gmail.com

2016-05-06

Electronic structure properties of 4-n-methoxy-4′-cyanobiphenyl, a pure nematic liquid crystal have been examined using an ab‒initio, HF/6‒31G(d,p) technique with GAMESS program. Conformational and charge distribution analysis have been carried out. MEP, HOMO and LUMO surfaces have been scanned. Ionization potential, electron affinity, electronegativity, global hardness and softness of the liquid crystal molecule have been calculated. Further, stacking, side by side and end to end interactions between a molecular pair have been evaluated. Results have been used to elucidate the physico-chemical and liquid crystalline properties of the system.

Local Atomic Arrangements and Band Structure of Boron Carbide.

PubMed

Rasim, Karsten; Ramlau, Reiner; Leithe-Jasper, Andreas; Mori, Takao; Burkhardt, Ulrich; Borrmann, Horst; Schnelle, Walter; Carbogno, Christian; Scheffler, Matthias; Grin, Yuri

2018-05-22

Boron carbide, the simple chemical combination of boron and carbon, is one of the best-known binary ceramic materials. Despite that, a coherent description of its crystal structure and physical properties resembles one of the most challenging problems in materials science. By combining ab initio computational studies, precise crystal structure determination from diffraction experiments, and state-of-the-art high-resolution transmission electron microscopy imaging, this concerted investigation reveals hitherto unknown local structure modifications together with the known structural alterations. The mixture of different local atomic arrangements within the real crystal structure reduces the electron deficiency of the pristine structure CBC+B 12 , answering the question about electron precise character of boron carbide and introducing new electronic states within the band gap, which allow a better understanding of physical properties. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

CERES: An ab initio code dedicated to the calculation of the electronic structure and magnetic properties of lanthanide complexes.

PubMed

Calvello, Simone; Piccardo, Matteo; Rao, Shashank Vittal; Soncini, Alessandro

2018-03-05

We have developed and implemented a new ab initio code, Ceres (Computational Emulator of Rare Earth Systems), completely written in C++11, which is dedicated to the efficient calculation of the electronic structure and magnetic properties of the crystal field states arising from the splitting of the ground state spin-orbit multiplet in lanthanide complexes. The new code gains efficiency via an optimized implementation of a direct configurational averaged Hartree-Fock (CAHF) algorithm for the determination of 4f quasi-atomic active orbitals common to all multi-electron spin manifolds contributing to the ground spin-orbit multiplet of the lanthanide ion. The new CAHF implementation is based on quasi-Newton convergence acceleration techniques coupled to an efficient library for the direct evaluation of molecular integrals, and problem-specific density matrix guess strategies. After describing the main features of the new code, we compare its efficiency with the current state-of-the-art ab initio strategy to determine crystal field levels and properties, and show that our methodology, as implemented in Ceres, represents a more time-efficient computational strategy for the evaluation of the magnetic properties of lanthanide complexes, also allowing a full representation of non-perturbative spin-orbit coupling effects. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Comparative study of crystallization process in metallic melts using ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Debela, Tekalign T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

2017-05-01

The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.

Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis.

PubMed

Schmidt, Andrea; Gruber, Karl; Kratky, Christoph; Lamzin, Victor S

2008-08-01

Hydroxynitrile lyases are versatile enzymes that enantiospecifically cope with cyanohydrins, important intermediates in the production of various agrochemicals or pharmaceuticals. We determined four atomic resolution crystal structures of hydroxynitrile lyase from Hevea brasiliensis: one native and three complexes with acetone, isopropyl alcohol, and thiocyanate. We observed distinct distance changes among the active site residues related to proton shifts upon substrate binding. The combined use of crystallography and ab initio quantum chemical calculations allowed the determination of the protonation states in the enzyme active site. We show that His(235) of the catalytic triad must be protonated in order for catalysis to proceed, and we could reproduce the cyanohydrin synthesis in ab initio calculations. We also found evidence for the considerable pK(a) shifts that had been hypothesized earlier. We envision that this knowledge can be used to enhance the catalytic properties and the stability of the enzyme for industrial production of enantiomerically pure cyanohydrins.

Atomic and electronic structure of exfoliated black phosphorus

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

Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok

2015-11-15

Black phosphorus, a layered two-dimensional crystal with tunable electronic properties and high hole mobility, is quickly emerging as a promising candidate for future electronic and photonic devices. Although theoretical studies using ab initio calculations have tried to predict its atomic and electronic structure, uncertainty in its fundamental properties due to a lack of clear experimental evidence continues to stymie our full understanding and application of this novel material. In this work, aberration-corrected scanning transmission electron microscopy and ab initio calculations are used to study the crystal structure of few-layer black phosphorus. Directly interpretable annular dark-field images provide a three-dimensional atomic-resolutionmore » view of this layered material in which its stacking order and all three lattice parameters can be unambiguously identified. In addition, electron energy-loss spectroscopy (EELS) is used to measure the conduction band density of states of black phosphorus, which agrees well with the results of density functional theory calculations performed for the experimentally determined crystal. Furthermore, experimental EELS measurements of interband transitions and surface plasmon excitations are also consistent with simulated results. Finally, the effects of oxidation on both the atomic and electronic structure of black phosphorus are analyzed to explain observed device degradation. The transformation of black phosphorus into amorphous PO{sub 3} or H{sub 3}PO{sub 3} during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time.« less

Dynamical spin structure factors of α-RuCl3

NASA Astrophysics Data System (ADS)

Suzuki, Takafumi; Suga, Sei-ichiro

2018-03-01

Honeycomb-lattice magnet α-RuCl3 is considered to be a potential candidate of realizing Kitaev spin liquid, although this material undergoes a phase transition to the zigzag magnetically ordered state at T N ∼ 7 K. Quite recently, inelastic neutron-scattering experiments using single crystal α-RuCl3 have unveiled characteristic dynamical properties. We calculate dynamical spin structure factors of three ab-initio models for α-RuCl3 with an exact numerical diagonalization method. We also calculate temperature dependences of the specific heat by employing thermal pure quantum states. We compare our numerical results with the experiments and discuss characteristics obtained by using three ab-initio models.

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

Manikandan, M.; Santhosh, M.; Rajeswarapalanichamy, R., E-mail: rrpalanichamy@gmail.com

Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of actinide carbides AnC (An=U, Np) for three different crystal structures, namely NaCl, CsCl and ZnS. Among the considered structures, NaCl structure is found to be the most stable structure for these carbides at normal pressure. A pressure induced structural phase transition from NaCl to ZnS is observed. The electronic structure reveals that these carbides are metals. The calculated elastic constants indicate that these carbides are mechanically stable at normal pressure.

Cracking a chemical conundrum

NASA Astrophysics Data System (ADS)

Adams, James M.; Ivanov, Alexandre S.; Johnson, Mark R.; Stride, John A.

2004-07-01

An everyday laboratory chemical, hexamethylbenzene (HMB) has assumed an important role in the history of molecular structure and crystallography. It was one of the first organic crystal structures to be solved and provided direct experimental proof for the hypothesis of planarity in aromatic systems. Very soon after this, HMB was found to undergo a phase transition at 117K, resulting in crystal shattering. Since then, many attempts have been made to obtain the low-temperature structure, but none have succeeded until now. Making use of the unique properties of the neutron, we have performed powder diffraction measurements to obtain the low-temperature crystal structure and inelastic measurements to determine the dynamics of the system. These experiments have been augmented by the use of ab initio calculations and molecular modelling to obtain a complete picture of HMB in the solid state.

A functional role of Rv1738 in Mycobacterium tuberculosis persistence suggested by racemic protein crystallography.

PubMed

Bunker, Richard D; Mandal, Kalyaneswar; Bashiri, Ghader; Chaston, Jessica J; Pentelute, Bradley L; Lott, J Shaun; Kent, Stephen B H; Baker, Edward N

2015-04-07

Protein 3D structure can be a powerful predictor of function, but it often faces a critical roadblock at the crystallization step. Rv1738, a protein from Mycobacterium tuberculosis that is strongly implicated in the onset of nonreplicating persistence, and thereby latent tuberculosis, resisted extensive attempts at crystallization. Chemical synthesis of the L- and D-enantiomeric forms of Rv1738 enabled facile crystallization of the D/L-racemic mixture. The structure was solved by an ab initio approach that took advantage of the quantized phases characteristic of diffraction by centrosymmetric crystals. The structure, containing L- and D-dimers in a centrosymmetric space group, revealed unexpected homology with bacterial hibernation-promoting factors that bind to ribosomes and suppress translation. This suggests that the functional role of Rv1738 is to contribute to the shutdown of ribosomal protein synthesis during the onset of nonreplicating persistence of M. tuberculosis.

Analysis of the local structure around Cr3+ centers in perovskite KMgF3 using both ab initio (DFT) and semi-empirical (SPM) calculations

NASA Astrophysics Data System (ADS)

Emül, Y.; Erbahar, D.; Açıkgöz, M.

2014-11-01

The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.

Ab initio electronic structure calculations for metallic intermediate band formation in photovoltaic materials

NASA Astrophysics Data System (ADS)

Wahnón, P.; Tablero, C.

2002-04-01

A metallic isolated band in the middle of the band gap of several III-V semiconductors has been predicted as photovoltaic materials with the possibility of providing substantially enhanced efficiencies. We have investigated the electronic band structures and lattice constants of GanAsmM and GanPmM with M=Sc, Ti, V, and Cr, to identify whether this isolated band is likely to exist by means of accurate calculations. For this task, we use the SIESTA program, an ab initio periodic density-functional method, fully self consistent in the local-density approximation. Norm-conserving, nonlocal pseudopotentials and confined linear combination of atomic orbitals have been used. We have carried out a case study of GanAsmTi and GanPmTi energy-band structure including analyses of the effect of the basis set, fine k-point mesh to ensure numerical convergence, structural parameters, and generalized gradient approximation for exchange and correlation corrections. We find the isolated intermediate band when one Ti atom replaces the position of one As (or P) atom in the crystal structure. For this kind of compound we show that the intermediate band relative position inside the band gap and width are sensitive to the dynamic relaxation of the crystal and the size of the basis set.

Decohesion models informed by first-principles calculations: The ab initio tensile test

NASA Astrophysics Data System (ADS)

Enrique, Raúl A.; Van der Ven, Anton

2017-10-01

Extreme deformation and homogeneous fracture can be readily studied via ab initio methods by subjecting crystals to numerical "tensile tests", where the energy of locally stable crystal configurations corresponding to elongated and fractured states are evaluated by means of density functional method calculations. The information obtained can then be used to construct traction curves of cohesive zone models in order to address fracture at the macroscopic scale. In this work, we perform an in depth analysis of traction curves and how ab initio calculations must be interpreted to rigorously parameterize an atomic scale cohesive zone model, using crystalline Ag as an example. Our analysis of traction curves reveal the existence of two qualitatively distinct decohesion criteria: (i) an energy criterion whereby the released elastic energy equals the energy cost of creating two new surfaces and (ii) an instability criterion that occurs at a higher and size independent stress than that of the energy criterion. We find that increasing the size of the simulation cell renders parts of the traction curve inaccessible to ab initio calculations involving the uniform decohesion of the crystal. We also find that the separation distance below which a crack heals is not a material parameter as has been proposed in the past. Finally, we show that a large energy barrier separates the uniformly stressed crystal from the decohered crystal, resolving a paradox predicted by a scaling law based on the energy criterion that implies that large crystals will decohere under vanishingly small stresses. This work clarifies confusion in the literature as to how a cohesive zone model is to be parameterized with ab initio "tensile tests" in the presence of internal relaxations.

Molecular Modeling and Experimental Investigations of Nonlinear Optical Compounds Monosubstituted Derivatives of Dicyanovinylbenzene

NASA Technical Reports Server (NTRS)

Timofeeva, Tatiana V.; Nesterov, Vladimir N.; Antipin, Mikhail Yu.; Clark, Ronald D.; Sanghadasa, Mohan; Cardelino, Beatriz H.; Moore, Craig E.; Frazier, Donald O.

1999-01-01

A search for potential nonlinear optical compounds was performed using the Cambridge Structure Database and molecular modeling. We investigated a series of monosubstituted derivatives of dicyanovinylbenzene, since the nonlinear optical (NLO) properties of such derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were studied earlier. The molecular geometry of these compounds was investigated with x-ray analysis and discussed along with the results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the planarity of the molecules of this series has been revealed. Two new compounds from the series studied, ortho-F and para-Cl-dicyanovinylbenzene, according to powder measurements, were found to be NLO compounds in the crystal state about 10 times more active than urea. The peculiarities of crystal structure formation in the framework of balance between van der Waals and electrostatic interactions have been discussed. The crystal shape of DIVA and two new NLO compounds have been calculated on the basis of the known crystal structure.

Structural phase transition of gold under uniaxial, tensile, and triaxial stresses: An ab initio study

NASA Astrophysics Data System (ADS)

Durandurdu, Murat

2007-07-01

The behavior of gold crystal under uniaxial, tensile, and three different triaxial stresses is studied using an ab initio constant pressure technique within a generalized gradient approximation. Gold undergoes a phase transformation from the face-centered-cubic structure (fcc) to a body-centered-tetragonal (bct) structure having the space group of I4/mmm with the application of uniaxial stress, while it transforms to a face-centered-tetragonal (fct) phase within I4/mmm symmetry under uniaxial tensile loading. Further uniaxial compression of the bct phase results in a symmetry change from I4/mmm to P1 at high stresses and ultimately structural failure around 200.0GPa . For the case of triaxial stresses, gold also converts into a bct state. The critical stress for the fcc-to-bct transformation increases as the ratio of the triaxial stress increases. Both fct and bct phases are elastically unstable.

Does the thermal evolution of molecular structures critically affect the magnetic anisotropy?† †Electronic supplementary information (ESI) available. CCDC 1045631–1045633. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc01245g

PubMed Central

Qian, Kang; Baldoví, José J.; Zhang, Yi-Quan; Overgaard, Jacob; Wang, Bing-Wu

2015-01-01

A dysprosium based single-ion magnet is synthesized and characterized by the angular dependence of the single-crystal magnetic susceptibility. Ab initio and effective electrostatic analyses are performed using the molecular structures determined from single crystal X-ray diffraction at 20 K, 100 K and 300 K. Contrary to the common assumption, the results reveal that the structural thermal effects that may affect the energy level scheme and magnetic anisotropy below 100 K are negligible. PMID:29568416

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

PubMed

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

Thermal, spectroscopic, and ab initio structural characterization of carprofen polymorphs.

PubMed

Bruni, Giovanna; Gozzo, Fabia; Capsoni, Doretta; Bini, Marcella; Macchi, Piero; Simoncic, Petra; Berbenni, Vittorio; Milanese, Chiara; Girella, Alessandro; Ferrari, Stefania; Marini, Amedeo

2011-06-01

Commercial and recrystallized polycrystalline samples of carprofen, a nonsteroidal anti-inflammatory drug, were studied by thermal, spectroscopic, and structural techniques. Our investigations demonstrated that recrystallized sample, stable at room temperature (RT), is a single polymorphic form of carprofen (polymorph I) that undergoes an isostructural polymorphic transformation by heating (polymorph II). Polymorph II remains then metastable at ambient conditions. Commercial sample is instead a mixture of polymorphs I and II. The thermodynamic relationships between the two polymorphs were determined through the construction of an energy/temperature diagram. The ab initio structural determination performed on synchrotron X-Ray powder diffraction patterns recorded at RT on both polymorphs allowed us to elucidate, for the first time, their crystal structure. Both crystallize in the monoclinic space group type P2(1) /c, and the unit cell similarity index and the volumetric isostructurality index indicate that the temperature-induced polymorphic transformation I → II is isostructural. Polymorphs I and II are conformational polymorphs, sharing a very similar hydrogen bond network, but with different conformation of the propanoic skeleton, which produces two different packing. The small conformational change agrees with the low value of transition enthalpy obtained by differential scanning calorimetry measurements and the small internal energy computed with density functional methods. Copyright © 2011 Wiley-Liss, Inc.

Ab-initio calculations of the Ruddlesden Popper phases CaMnO3, CaO(CaMnO3) and CaO(CaMnO3)2

NASA Astrophysics Data System (ADS)

Cardoso, C.; Borges, R. P.; Gasche, T.; Godinho, M.

2008-01-01

The present work reports ab-initio density functional theory calculations for the Ruddlesden-Popper phase CaO(CaMnO3)n compounds. In order to study the evolution of the properties with the number of perovskite layers, a detailed analysis of the densities of states calculated for each compound and for several magnetic configurations was performed. The effect of distortions of the crystal structure on the magnetic ground state is also analysed and the exchange constants and transition temperatures are calculated for the three compounds using a mean field model. The calculated magnetic ground state structures and magnetic moments are in good agreement with experimental results and previous calculations.

Optical properties of B12P2 crystals: Ab initio calculation and EELS

NASA Astrophysics Data System (ADS)

Reshetniak, V. V.; Mavrin, B. N.; Medvedev, V. V.; Perezhogin, I. A.; Kulnitskiy, B. A.

2018-05-01

We report an experimental and theoretical investigation of the electronic structure and optical properties of B12P2 crystals in the energy range up to 60 eV. Experimental studies are performed by the method of electron energy loss spectroscopy, and theoretical studies are carried out using density functional theory and the GW approximation. The calculated dependence of the energy loss function is in agreement with the experiment. Based on the results of the calculations, we determine the optical properties of B12P2 crystals and investigate their anisotropy. The dispersion and density of electronic states are calculated and analyzed.

Formation of superconducting platinum hydride under pressure: an ab initio approach

NASA Astrophysics Data System (ADS)

Kim, Duck Young; Scheicher, Ralph; Pickard, Chris; Needs, Richard; Ahuja, Rajeev

2012-02-01

Noble metals such as Pt, Au, or Re are commonly used for electrodes and gaskets in diamond anvil cells for high-pressure research because they are expected to rarely undergo structural transformation and possess simple equation of states. Specifically Pt has been used widely for high-pressure experiments and has been considered to resist hydride formation under pressure. Pressure-induced reactions of metals with hydrogen are in fact quite likely because hydrogen atoms can occupy interstitial positions in the metal lattice, which can lead to unexpected effects in experiments. In our study, PRL 107 117002 (2011), we investigated crystal structures using ab initio random structure searching (AIRSS) and predicted the formation of platinum mono-hydride above 22 GPa and superconductivity Tc was estimated to be 10 -- 25 K above around 80 GPa. Furthermore, we showed that the formation of fcc noble metal hydrides under pressure is common and examined the possibility of superconductivity in these materials.

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

NASA Astrophysics Data System (ADS)

Bano, Amreen; Gaur, N. K.

2018-05-01

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

An ab initio density functional study of the optical functions of 9-Methyl-3-Thiophen-2-YI-Thieno [3,2e] [1,2,4] Thriazolo [4,3c] Pyrimidine-8-Carboxylic Acid Ethyl Ester crystals.

PubMed

Reshak, Ali H; Kityk, I V; Khenata, R; Al-Douri, Y; Auluck, S

2012-09-01

An ab initio investigation of the optical constants of 9-Methyl-3-Thiophen-2-YI-Thieno [3,2e] [1,2,4] Thriazolo [4,3c] Pyrimidine-8-Carboxylic Acid Ethyl Ester crystal is performed within a framework of local density approximation (LDA), and the Engel-Vosko generalized gradient approximation (EV-GGA) exchange correlation potentials. It is established that there are two independent molecules (A and B) exhibiting different intra-molecular interactions: C-H⋯O (A) and C-H⋯N (B). These intra-molecular interactions favor stabilization of the crystal structure for molecules A and B. It should be emphasized that there exist remarkable π-π interactions between the pyrimidine rings of the two neighbors B molecules giving extra strengths and stabilizations to the superamolecular structure. These different intra-molecular interactions C-H⋯O (A) and C-H⋯N (B) and the π-π interaction between the pyrimidine rings of the two neighbors B molecules give principal contribution to dispersion of optical properties. With a view to seek deeper insight into the electronic structure, the optical properties were investigated. Our calculations show that the optical constants are very anisotropic. The EVGGA calculation shows a blue spectral shift of around 0.024 eV with significant changes in the spectra compared to the LDA calculation. The observed spectral shifts are in agreement with the calculated band structure and corresponding electron density of states. Copyright © 2012 Elsevier B.V. All rights reserved.

Phonon conductivity metrics for compact, linked-cage, layered, and filled-cage crystals, using ab initio, molecular dynamics and Boltzmann transport treatments

NASA Astrophysics Data System (ADS)

Huang, Baoling

Atomic-level thermal transport in compact, layered, linked-cage, and filled-cage crystals is investigated using a multiscale approach, combines the ab initio calculation, molecular dynamics (MD), Boltzman transport equations (BTE), and the kinetic theory. These materials are of great interests in energy storage, transport, and conversion. The structural metrics of phonon conductivity of these crystals are then explored. An atomic structure-based model is developed for the understanding the relationship between the atomic structure and phonon transport in compact crystals at high temperatures. The elemental electronegativity, element mass, and the arrangement of bonds are found to be the dominant factors to determine the phonon conductivity. As an example of linked-cage crystals, the phonon conductivity of MOF-5 is investigated over a wide temperature range using MD simulations and the Green-Kubo method. The temperature dependence of the thermal conductivity of MOF-5 is found to be weak at high temperatures, which results from the suppression of the long-range acoustic phonon transport by the special linked-cage structure. The mean free path of the majority of phonons in MOF-5 is limited by the cage size. The phonon and electron transport in layered Bi2Te3 structure are investigated using the first-principle calculations, MD, and BTE. Strong anisotropy has been found for both phonon and electron transport due to the special layered structure. The long-range acoustic phonons dominate the phonon transport with a strong temperature and direction dependence. Temperature dependence of the energy gap and appropriate modelling of relaxation times are found to be important for the prediction of the electrical transport in the intrinsic regime. The scattering by the acoustic, optical, and polar-optical phonons are found to dominate the electron transport. For filled skutterudite structure, strong coupling between the filler and the host is found, which contradicts the traditional "rattler" concept. The interatomic bonds of the host are significantly affected by the filler. It is shown that without changing the interatomic potentials for the host, the filler itself can not result in a lower phonon conductivity for the filled structure. It is also found that the behavior of partially-filled skutterudites can be better understood by treating the partially-filled structure as a solid solution of the empty structure and fully-filled structure. The combination of theoretical-analysis methods used in this work, provides for comparative insight into the role of atomic structure on the phonon transport in a variety of crystals used in energy storage, transport, and conversion.

New phases of osmium carbide from evolutionary algorithm and ab initio computations

NASA Astrophysics Data System (ADS)

Fadda, Alessandro; Fadda, Giuseppe

2017-09-01

New crystal phases of osmium carbide are presented in this work. These results were found with the CA code, an evolutionary algorithm (EA) presented in a previous paper which takes full advantage of crystal symmetry by using an ad hoc search space and genetic operators. The new OsC2 and Os2C structures have a lower enthalpy than any known so far. Moreover, the layered pattern of OsC2 serves as a blueprint for building new crystals by adding or removing layers of carbon and/or osmium and generating many other Os  +  C structures like Os2C, OsC, OsC2 and OsC4. These again have a lower enthalpy than all the investigated structures, including those of the present work. The mechanical, vibrational and electronic properties are discussed as well.

Electronic Structure of Energetic Molecules and Crystals Under Compression

NASA Astrophysics Data System (ADS)

Kay, Jeffrey

Understanding how the electronic structure of energetic materials change under compression is important to elucidating mechanisms of shock-induced reactions and detonation. In this presentation, the electronic structure of prototypical energetic crystals are examined under high degrees of compression using ab initio quantum chemical calculations. The effects of compression on and interactions between the constituent molecules are examined in particular. The insights these results provide into previous experimental observations and theoretical predictions of energetic materials under high pressure are discussed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.

The electronic structure of RbTiOPO4 and the effects of the A-site cation substitution in KTiOPO4-family crystals

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Kesler, V. G.; Meng, Guangsi; Lin, Z. S.

2012-10-01

The electronic structure of RbTiOPO4 has been investigated with x-ray photoemission spectroscopy. Detailed photoemission spectra of the element core levels have been recorded under excitation by nonmonochromatic Al Kα radiation (1486.6 eV). The chemical bonding parameters are compared to those reported for complex titanates and phosphates. The band structures of KTiOPO4, RbTiOPO4, K0.535R0.465TiOPO4 and TlTiOPO4 have been calculated by ab initio methods and compared to available experimental results. It is found that the band structure of KTP-type phosphate crystals is weakly dependent on the nature of the A-site (A=K, Rb, Tl) element.

The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates.

PubMed

Dureckova, Hana; Woo, Tom K; Udachin, Konstantin A; Ripmeester, John A; Alavi, Saman

2017-10-13

Clathrate hydrate phases of Cl 2 and Br 2 guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen-halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen-halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme-substrate compounds. The nature of the halogen-water interactions for the Cl 2 and Br 2 molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl 2 and Br 2 guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.

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

NASA Astrophysics Data System (ADS)

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

2018-07-01

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

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

Development of interatomic potentials appropriate for simulation of devitrification of Al 90Sm 10 alloy

DOE PAGES

Mendelev, M. I.; Zhang, F.; Ye, Z.; ...

2015-04-23

In this study, a semi-empirical potential for the Al 90Sm 10 alloy is presented. The potential provides satisfactory reproduction of pure Al properties, the formation energies of a set of Al–Sm crystal phases with Sm content about 10%, and the structure of the liquid Al 90Sm 10 alloy. During molecular dynamics simulation in which the liquid alloy is cooled at a rate of 10 10 K/s, the developed potential produces a glass structure with lower ab initio energy than that produced by ab initio molecular dynamics (AIMD) itself using a typical AIMD cooling rate of 8 ∙10 13 K/s. Basedmore » on these facts the developed potential should be suitable for simulations of phase transformations in the Al 90Sm 10 alloy.« less

Ab initio calculations of the electron spectrum and density of states of TlFeS{sub 2} and TlFeSe{sub 2} crystals

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

Ismayilova, N. A., E-mail: ismayilova-narmin-84@mail.ru; Orudjev, H. S.; Jabarov, S. H.

2017-04-15

The results of ab initio calculations of the electron spectrum of TlFeS{sub 2} and TlFeSe{sub 2} crystals in the antiferromagnetic phase are reported. Calculations are carried out in the context of the density functional theory. The origin of the bands of s, p, and d electron states of Tl, Fe, S, and Se atoms is studied. It is established that, in the antiferromagnetic phase, the crystals possess semiconductor properties. The band gaps are found to be 0.05 and 0.34 eV for TlFeS{sub 2} and TlFeSe{sub 2} crystals, respectively.

Iterative projection algorithms for ab initio phasing in virus crystallography.

PubMed

Lo, Victor L; Kingston, Richard L; Millane, Rick P

2016-12-01

Iterative projection algorithms are proposed as a tool for ab initio phasing in virus crystallography. The good global convergence properties of these algorithms, coupled with the spherical shape and high structural redundancy of icosahedral viruses, allows high resolution phases to be determined with no initial phase information. This approach is demonstrated by determining the electron density of a virus crystal with 5-fold non-crystallographic symmetry, starting with only a spherical shell envelope. The electron density obtained is sufficiently accurate for model building. The results indicate that iterative projection algorithms should be routinely applicable in virus crystallography, without the need for ancillary phase information. Copyright © 2016 Elsevier Inc. All rights reserved.

Enhanced angular overlap model for nonmetallic f -electron systems

NASA Astrophysics Data System (ADS)

Gajek, Z.

2005-07-01

An efficient method of interpretation of the crystal field effect in nonmetallic f -electron systems, the enhanced angular overlap model (EAOM), is presented. The method is established on the ground of perturbation expansion of the effective Hamiltonian for localized electrons and first-principles calculations related to available experimental data. The series of actinide compounds AO2 , oxychalcogenides AOX , and dichalcogenides UX2 where X=S ,Se,Te and A=U ,Np serve as probes of the effectiveness of the proposed method. An idea is to enhance the usual angular overlap model with ab initio calculations of those contributions to the crystal field potential, which cannot be represented by the usual angular overlap model (AOM). The enhancement leads to an improved fitting and makes the approach intrinsically coherent. In addition, the ab initio calculations of the main, AOM-consistent part of the crystal field potential allows one to fix the material-specific relations for the EAOM parameters in the effective Hamiltonian. Consequently, the electronic structure interpretation based on EAOM can be extended to systems of the lowest point symmetries or/and deficient experimental data. Several examples illustrating the promising capabilities of EAOM are given.

Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

PubMed

Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

2015-12-01

A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

Prediction of possible CaMnO3 modifications using an ab initio minimization data-mining approach.

PubMed

Zagorac, Jelena; Zagorac, Dejan; Zarubica, Aleksandra; Schön, J Christian; Djuris, Katarina; Matovic, Branko

2014-10-01

We have performed a crystal structure prediction study of CaMnO3 focusing on structures generated by octahedral tilting according to group-subgroup relations from the ideal perovskite type (Pm\\overline 3 m), which is the aristotype of the experimentally known CaMnO3 compound in the Pnma space group. Furthermore, additional structure candidates have been obtained using data mining. For each of the structure candidates, a local optimization on the ab initio level using density-functional theory (LDA, hybrid B3LYP) and the Hartree--Fock (HF) method was performed, and we find that several of the modifications may be experimentally accessible. In the high-pressure regime, we identify a post-perovskite phase in the CaIrO3 type, not previously observed in CaMnO3. Similarly, calculations at effective negative pressure predict a phase transition from the orthorhombic perovskite to an ilmenite-type (FeTiO3) modification of CaMnO3.

Luminescence of BaBrI and SrBrI single crystals doped with Eu2+

NASA Astrophysics Data System (ADS)

Shalaev, A. A.; Shendrik, R.; Myasnikova, A. S.; Bogdanov, A.; Rusakov, A.; Vasilkovskyi, A.

2018-05-01

The crystal growth procedure and luminescence properties of pure and Eu2+-doped BaBrI and SrBrI crystals are reported. Emission and excitation spectra were recorded under ultraviolet and vacuum ultraviolet excitations. The energy of the first Eu2+ 4f-5d transition and SrBrI band gap are obtained. The electronic structure calculations were performed within GW approximation as implemented in the Vienna Ab Initio Simulation Package. The energy between lowest Eu2+ 5d state and the bottom of conduction band are found based on luminescence quenching parameters. The vacuum referred binding energy diagram of lanthanide levels was constructed using the chemical shift model.

Parametrization of semiempirical models against ab initio crystal data: evaluation of lattice energies of nitrate salts.

PubMed

Beaucamp, Sylvain; Mathieu, Didier; Agafonov, Viatcheslav

2005-09-01

A method to estimate the lattice energies E(latt) of nitrate salts is put forward. First, E(latt) is approximated by its electrostatic component E(elec). Then, E(elec) is correlated with Mulliken atomic charges calculated on the species that make up the crystal, using a simple equation involving two empirical parameters. The latter are fitted against point charge estimates of E(elec) computed on available X-ray structures of nitrate crystals. The correlation thus obtained yields lattice energies within 0.5 kJ/g from point charge values. A further assessment of the method against experimental data suggests that the main source of error arises from the point charge approximation.

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

PubMed

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

2015-12-14

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Conductivity and local structure in LaNiO3

NASA Astrophysics Data System (ADS)

Fowlie, Jennifer; Gibert, Marta; Tieri, Giulio; Gloter, Alexandre; à+/-Iguez, Jorge; Filippetti, Alessio; Catalano, Sara; Gariglio, Stefano; StéPhan, Odile; Triscone, Jean-Marc

In this study we approach the thickness-dependence of the properties of LaNiO3 films along multiple, complementary avenues: sophisticated ab initio calculations, scanning transmission electron microscopy and electronic transport. Specifically, we find an unexpected maximum in conductivity in films of thickness 6 - 10 unit cells (3 nm) for several series of LaNiO3 films. Ab initio transport based on the detailed crystal structure also reveals a maximum in conductivity at the same thickness. In agreement with the structure obtained from scanning transmission electron microscopy (STEM), our simulated structures reveal that the substrate- and surface-induced distortions lead to three types of local structure (heterointerface, interior-layer, surface). Based on this observation, a 3-element parallel conductor model neatly reproduces the trend of conductivity with thickness. This study addresses the question of how structural distortions at the atomic scale evolve in a thin film under the influence of the substrate and the surface. This topic is key to the understanding of the physics of heterostructures and the design of functional oxides.

Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus

PubMed Central

Leyrat, Cedric; Renner, Max; Harlos, Karl; Grimes, Jonathan M.

2013-01-01

Human metapneumovirus (HMPV) of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P) from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs). We located the central region of HMPV P (Pced) which is involved in tetramerization using disorder analysis and modeled its 3D structure ab initio using Rosetta fold-and-dock. We characterized the solution-structure of Pced using small angle X-ray scattering (SAXS) and carried out direct fitting to the scattering data to filter out incorrect models. Molecular dynamics simulations (MDS) and ensemble optimization were employed to select correct models and capture the dynamic character of Pced. Our analysis revealed that oligomerization involves a compact central core located between residues 169-194 (Pcore), that is surrounded by flexible regions with α-helical propensity. We crystallized this fragment and solved its structure at 3.1 Å resolution by molecular replacement, using the folded core from our SAXS-validated ab initio model. The RMSD between modeled and experimental tetramers is as low as 0.9 Å, demonstrating the accuracy of the approach. A comparison of the structure of HMPV P to existing mononegavirales Pced structures suggests that Pced evolved under weak selective pressure. Finally, we discuss the advantages of using SAXS in combination with ab initio modeling and MDS to solve the structure of small, homo-oligomeric protein complexes. PMID:24224051

The prediction of crystal structure by merging knowledge methods with first principles quantum mechanics

NASA Astrophysics Data System (ADS)

Ceder, Gerbrand

2007-03-01

The prediction of structure is a key problem in computational materials science that forms the platform on which rational materials design can be performed. Finding structure by traditional optimization methods on quantum mechanical energy models is not possible due to the complexity and high dimensionality of the coordinate space. An unusual, but efficient solution to this problem can be obtained by merging ideas from heuristic and ab initio methods: In the same way that scientist build empirical rules by observation of experimental trends, we have developed machine learning approaches that extract knowledge from a large set of experimental information and a database of over 15,000 first principles computations, and used these to rapidly direct accurate quantum mechanical techniques to the lowest energy crystal structure of a material. Knowledge is captured in a Bayesian probability network that relates the probability to find a particular crystal structure at a given composition to structure and energy information at other compositions. We show that this approach is highly efficient in finding the ground states of binary metallic alloys and can be easily generalized to more complex systems.

Relationship between crystal structure and solid-state properties of pharmaceuticals

NASA Astrophysics Data System (ADS)

Sheth, Agam R.

This thesis strives to understand the structure-property relationships of some pharmaceutical crystals at the molecular level with emphasis on the effect of secondary processing on the solid phase. Using single crystal X-ray diffractometry (SCXRD), the structure of warfarin sodium 2-propanol adduct (W) was established to be a true solvate, contrary to previous reports. Using dynamic water vapor sorption, optical and environmental scanning electron microscopy, SCXRD, powder X-ray diffractometry (PXRD), volume computations and molecular modeling, the effect of relative humidity and temperature on the crystal structure of W was investigated. Ab initio calculations on piroxicam showed that the difference in energy between the two polymorphs, I and II, arises predominantly from the difference between their lattice energies. The detailed hydrogen bonding networks of the two polymorphs are described and compared using graph sets. Despite stabilization of the polymorphs by hydrogen bonds, pair-wise distribution function transforms show a loss of polymorphic memory upon cryogrinding the two polymorphs, leading to a difference in recrystallization behavior between amorphous piroxicam prepared from polymorphs I and II. Structural and solid-state changes of piroxicam polymorphs under mechanical stress were investigated using cryogenic grinding, PXRD, diffuse-reflectance solid-state ultraviolet-visible spectroscopy, 13C solid-state nuclear magnetic resonance spectroscopy, and diffuse-reflectance solid-state Fourier-transform infrared spectroscopy. Intermolecular proton transfer was found to accompany changes in phase and color observed upon cryogrinding the two polymorphs. Model-free and model-fitting studies of the dehydration kinetics of piroxicam monohydrate (PM) showed the dependence of activation energy ( Ea) on both isothermal and non-isothermal heating conditions, and on the fraction of conversion. In the constant-E a region, isothermal dehydration follows the two-dimensional phase boundary model, while non-isothermal dehydration follows a mechanism intermediate between two- and three-dimensional diffusion that cannot be described by any of the common models. Structural studies suggest that the complex hydrogen bond pattern in PM is responsible for the observed dehydration behavior. Ab initio calculations provide an explanation for the changes in the molecular and crystal structures accompanying the reversible change in hydration state between anhydrous piroxicam Form I and PM. The thesis further demonstrates the utility of model-free analysis in describing complex dehydration kinetics.

Band structure and unconventional electronic topology of CoSi

NASA Astrophysics Data System (ADS)

Pshenay-Severin, D. A.; Ivanov, Y. V.; Burkov, A. A.; Burkov, A. T.

2018-04-01

Semimetals with certain crystal symmetries may possess unusual electronic structure topology, distinct from that of the conventional Weyl and Dirac semimetals. Characteristic property of these materials is the existence of band-touching points with multiple (higher than two-fold) degeneracy and nonzero Chern number. CoSi is a representative of this group of materials exhibiting the so-called ‘new fermions’. We report on an ab initio calculation of the electronic structure of CoSi using density functional methods, taking into account the spin-orbit interactions. The linearized \

Report of Research at Technische Universitaet Darmstadt on Ultrahard Materials in the B-C-N-Si System

DTIC Science & Technology

2015-06-01

structure at the micro- and nanoscale. In other words, development of nanocomposites, multilayers, and superlattices via appropriate design and control of...C-B and C-N bonds as C-C and B-N bonds. Later, the same research group , based on first-principles total-energy, and dynamic phonon calculations...Vickers hardness values.7 Another research group employed an ab initio evolutionary algorithm42 to resolve the crystal structure of the observed

Boron monosulfide: Equation of state and pressure-induced phase transition

NASA Astrophysics Data System (ADS)

Cherednichenko, K. A.; Kruglov, I. A.; Oganov, A. R.; Le Godec, Y.; Mezouar, M.; Solozhenko, V. L.

2018-04-01

Quasi-hydrostatic compression of rhombohedral boron monosulfide (r-BS) has been studied up to 50 GPa at room temperature using diamond-anvil cells and angle-dispersive synchrotron X-ray diffraction. A fit of the experimental P-V data to the Vinet equation of state yields the bulk modulus B0 of 42.2(1.4) GPa and its first pressure derivative B0' of 7.6(2) that are in excellent agreement with our ab initio calculations. Formation of a new high-pressure phase of boron monosulfide (hp-BS) has been observed above 35 GPa. According to ab initio evolutionary crystal structure predictions combined with Rietveld refinement of high-pressure X-ray diffraction data, the structure of hp-BS has trigonal symmetry and belongs to the space group P-3m1. As it follows from the electron density of state calculations, the phase transformation is accompanied by an insulator-metal transition.

Molecular Modeling and Experimental Study of Nonlinear Optical Compounds: Mono-Substituted Derivatives of Dicyanovinylbenzene

NASA Technical Reports Server (NTRS)

Timofeeva, Tatyana V.; Nesterov, Vladimir N.; Antipin, Mikhael Y.; Clark, R. D.; Sanghadasa, M.; Cardelino, B. H.; Moore, C. E.; Frazier, Donald O.

2000-01-01

A search for potential nonlinear optical (NLO) compounds has been performed using the Cambridge Structural Database and molecular modeling. We have studied a series of mono-substituted derivatives of dicyanovinylbenzene as the NLO properties of one of its derivatives (o-methoxy-dicyanovinylbenzene, DIVA) were described earlier. The molecular geometry in the series of the compounds studied was investigated with an X- ray analysis and discussed along with results of molecular mechanics and ab initio quantum chemical calculations. The influence of crystal packing on the molecular planarity has been revealed. Two new compounds from the series studied were found to be active for second harmonic generation (SHG) in the powder. The measurements of SHG efficiency have shown that the o-F- and p-Cl-derivatives of dicyanovinylbenzene are about 10 and 20- times more active than urea, respectively. The peculiarities of crystal structure formation in the framework of balance between the van der Waals and electrostatic interactions have been discussed. The crystal morphology of DIVA and two new SHG-active compounds have been calculated on the basis of their known crystal structures.

Ab initio random structure searching of organic molecular solids: assessment and validation against experimental data† †Electronic supplementary information (ESI) available: Results of similarity analysis between the 11 structures of lowest energy obtained in the AIRSS calculations and the reported structures of form III and form IV of m-ABA; unit cell parameters and volumes for all structures considered; comparison of 2θ values derived from the unit cell parameters of different structural models representing form III of m-ABA; Le Bail fitting of the experimental powder XRD pattern of form IV of m-ABA recorded at 70 K using, as the initial structural model, the reported crystal structure following geometry optimization; table of calculated (GIPAW) absolute isotropic NMR shieldings; simulated powder XRD data for the considered structures after precise geometry optimization; experimental 1H MAS NMR spectra of forms III and IV. (pdf) The calculated and experimental data for this study are provided as a supporting dataset from WRAP, the Warwick Research Archive Portal at http://wrap.warwick.ac.uk/91884. See DOI: 10.1039/c7cp04186a

PubMed Central

Zilka, Miri; Dudenko, Dmytro V.; Hughes, Colan E.; Williams, P. Andrew; Sturniolo, Simone; Franks, W. Trent; Pickard, Chris J.

2017-01-01

This paper explores the capability of using the DFT-D ab initio random structure searching (AIRSS) method to generate crystal structures of organic molecular materials, focusing on a system (m-aminobenzoic acid; m-ABA) that is known from experimental studies to exhibit abundant polymorphism. Within the structural constraints selected for the AIRSS calculations (specifically, centrosymmetric structures with Z = 4 for zwitterionic m-ABA molecules), the method is shown to successfully generate the two known polymorphs of m-ABA (form III and form IV) that have these structural features. We highlight various issues that are encountered in comparing crystal structures generated by AIRSS to experimental powder X-ray diffraction (XRD) data and solid-state magic-angle spinning (MAS) NMR data, demonstrating successful fitting for some of the lowest energy structures from the AIRSS calculations against experimental low-temperature powder XRD data for known polymorphs of m-ABA, and showing that comparison of computed and experimental solid-state NMR parameters allows different hydrogen-bonding motifs to be discriminated. PMID:28944393

A new series of two-dimensional silicon crystals with versatile electronic properties

NASA Astrophysics Data System (ADS)

Chae, Kisung; Kim, Duck Young; Son, Young-Woo

2018-04-01

Silicon (Si) is one of the most extensively studied materials owing to its significance to semiconductor science and technology. While efforts to find a new three-dimensional (3D) Si crystal with unusual properties have made some progress, its two-dimensional (2D) phases have not yet been explored as much. Here, based on a newly developed systematic ab initio materials searching strategy, we report a series of novel 2D Si crystals with unprecedented structural and electronic properties. The new structures exhibit perfectly planar outermost surface layers of a distorted hexagonal network with their thicknesses varying with the atomic arrangement inside. Dramatic changes in electronic properties ranging from semimetal to semiconducting with indirect energy gaps and even to one with direct energy gaps are realized by varying thickness as well as by surface oxidation. Our predicted 2D Si crystals with flat surfaces and tunable electronic properties will shed light on the development of silicon-based 2D electronics technology.

Structural phase transition, electronic structure and optical properties of half Heusler alloys LiBeZ (Z = As, Sb)

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

Amudhavalli, A.; Rajeswarapalanichamy, R., E-mail: rajeswarapalanichamy@gmail.com

2016-05-23

Ab initio calculations are performed to investigate the structural stability, electronic structure, mechanical properties and optical properties of half Heusler alloys (LiBeAs and LiBeSb) for three different phases of zinc blende crystal structure. Among the considered phases, α- phase is found to be the most stable phase for these alloys at normal pressure. A pressure induced structural phase transition from α-phase to β- phase is observed for LiBeAs. The electronic structure reveals that these alloys are semiconductors. The optical properties confirm that these alloys are semiconductor in nature.

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

NASA Astrophysics Data System (ADS)

KoleŻyński, Andrzej; Szczypka, Wojciech

2016-03-01

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

An Ab Initio Description of the Excitonic Properties of LH2 and Their Temperature Dependence.

PubMed

Cupellini, Lorenzo; Jurinovich, Sandro; Campetella, Marco; Caprasecca, Stefano; Guido, Ciro A; Kelly, Sharon M; Gardiner, Alastair T; Cogdell, Richard; Mennucci, Benedetta

2016-11-10

The spectroscopic properties of light-harvesting (LH) antennae in photosyntehtic organisms represent a fingerprint that is unique for each specific pigment-protein complex. Because of that, spectroscopic observations are generally combined with structural data from X-ray crystallography to obtain an indirect representation of the excitonic properties of the system. Here, an alternative strategy is presented which goes beyond this empirical approach and introduces an ab initio computational description of both structural and electronic properties and their dependence on the temperature. The strategy is applied to the peripheral light-harvesting antenna complex (LH2) present in purple bacteria. By comparing this model with the one based on the crystal structure, a detailed, molecular level explanation of the absorption and circular dichroism (CD) spectra and their temperature dependence is achieved. The agreement obtained with the experiments at both low and room temperature lays the groundwork for an atomistic understanding of the excitation dynamics in the LH2 system.

Molecular structure and charge density analysis of p-methoxybenzoic acid (anisic acid)

NASA Astrophysics Data System (ADS)

Fausto, R.; Matos-Beja, A.; Paixão, J. A.

1997-12-01

A concerted X-ray and ab initio SCF-MO study of the structure and charge density of p-methoxybenzoic acid (anisic acid) is reported. An extensive X-ray data set (7401 reflections) was measured on a single crystal using Mo K α radiation and the structure refined with 2121 unique reflections, leading to a final R( F)-factor of 0.047 calculated for reflections with I>2 σ. The molecular geometry of crystalline anisic acid, where the molecules dimerize via a moderately strong CO-H⋯O hydrogen bond, is compared with that of the isolated molecule, resulting from SCF-MO ab initio calculations. A topological analysis of the molecular charge density was performed using Bader's method to gain insight into the dominant intra- and intermolecular interactions in this compound. In particular, the effects of the substituents on the observed distortions of the benzene ring were investigated as well as the internal rotation of the methyl group.

Novel high-pressure phase of ZrO{sub 2}: An ab initio prediction

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

Durandurdu, Murat, E-mail: murat.durandurdu@agu.edu.tr

2015-10-15

The high-pressure behavior of the orthorhombic cotunnite type ZrO{sub 2} is explored using an ab initio constant pressure technique. For the first time, a novel hexagonal phase (Ni{sub 2}In type) within P6{sub 3}/mmc symmetry is predicted through the simulation. The Ni{sub 2}In type crystal is the densest high-pressure phase of ZrO{sub 2} proposed so far and has not been observed in other metal dioxides at high pressure before. The phase transformation is accompanied by a small volume drop and likely to occur around 380 GPa in experiment. - Graphical abstract: Post-cotunnite Ni{sub 2}In type hexagonal phase forms in zirconia atmore » high pressure. - Highlights: • A post-cotunnite phase is predicted for ZrO{sub 2} through an ab initio simulation. • Cotunnite ZrO{sub 2} adopts the Ni{sub 2}In type structure at high pressure. • The Ni{sub 2}In type structure is the densest high-pressure phase of ZrO{sub 2} proposed so far. • The preferred mechanism in ZrO{sub 2} differs from the other metal dioxides.« less

Observation of high-spin mixed oxidation state of cobalt in ceramic Co3TeO6

NASA Astrophysics Data System (ADS)

Singh, Harishchandra; Ghosh, Haranath; Chandrasekhar Rao, T. V.; Sinha, A. K.; Rajput, Parasmani

2014-12-01

We report coexistence of high spin Co3+ and Co2+ in ceramic Co3TeO6 using X-ray Absorption Near Edge Structure (XANES), DC magnetization, and first principles ab-initio calculations. The main absorption line of cobalt Co K-edge XANES spectra, along with a linear combination fit, led us to estimate relative concentration of Co2+ and Co3+as 60:40. The pre edge feature of XANES spectrum shows crystal field splitting of ˜1.26 eV between eg and t2g states, suggesting a mixture of high spin states of both Co2+ and Co3+. Temperature dependent high field DC magnetization measurements reveal dominant antiferromagnetic order with two Neel temperatures (TN1 ˜ 29 K and TN2 ˜ 18 K), consistent with single crystal study. A larger effective magnetic moment is observed in comparison to that reported for single crystal (which contains only Co2+), supports our inference that Co3+ exists in high spin state. Furthermore, we show that both Co2+ and Co3+ being in high spin states constitute a favorable ground state through first principles ab-initio calculations, where Rietveld refined synchrotron X-ray diffraction data are used as input.

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

PubMed

Gryaznov, Denis; Heifets, Eugene; Kotomin, Eugene

2009-09-07

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

On Predicting the Crystal Structure of Energetic Materials From Quantum Mechanics

DTIC Science & Technology

2008-12-01

DE ABSTRACT A quantum-mechanically-based potential energy function that describes interactions of dimers of the explosive ...method is capable of producing force fields for interactions of the molecular crystalline explosive RDX, and appears to be suitable to enable reliable...Ridge, TN. Byrd, E.F.C., Scuseria, G.E., Chabalowski, C.F., 2004: “An ab initio study of solid nitromethane , HMX, RDX and CL20: Successes and

Electronic and structural ground state of heavy alkali metals at high pressure

DOE PAGES

Fabbris, G.; Lim, J.; Veiga, L. S. I.; ...

2015-02-17

Here, alkali metals display unexpected properties at high pressure, including emergence of low symmetry crystal structures, that appear to occur due to enhanced electronic correlations among the otherwise nearly-free conduction electrons. We investigate the high pressure electronic and structural ground state of K, Rb, and Cs using x-ray absorption spectroscopy and x-ray diffraction measurements together with ab initio theoretical calculations. The sequence of phase transitions under pressure observed at low temperature is similar in all three heavy alkalis except for the absence of the oC84 phase in Cs. Both the experimental and theoretical results point to pressure-enhanced localization of themore » valence electrons characterized by pseudo-gap formation near the Fermi level and strong spd hybridization. Although the crystal structures predicted to host magnetic order in K are not observed, the localization process appears to drive these alkalis closer to a strongly correlated electron state.« less

Materials Design of the Codoping for the Fabrication of Low-Resistivity p-Type ZnSe and GaN by ab-initio Electronic Structure Calculation

NASA Astrophysics Data System (ADS)

Katayama-Yoshida, H.; Yamamoto, T.

1997-08-01

We propose an effective doping method, the codoping (doping with n- and p-type dopants at the same time) method, for the fabrication of low-resistivity p-type ZnSe and GaN with wide-band-gap based upon ab-initio electronic band structure calculations. p-type doping eminently leads to an increase in the electrostatic energy, called the Madelung energy, which shifts the Se 4p levels for p-type doped ZnSe and the N 2p levels for p-type doped GaN materials towards higher energy regions. This leads to a destabilization of ionic charge distributions in p-type ZnSe and p-type GaN crystals, resulting in the self-compensation of anion intrinsic defects. For ZnSe crystals, we propose the codoping of n-type In donors at Zn sites and p-type N acceptors at Se sites based on the calculation. In addition, we propose the codoping of n-type Si-donors at Ga sites (n-type O donors at N sites) and p-type Be- or Mg acceptors at Ga sites. The codoping decreases the Madelung energy and leads to an increase in the net acceptor carrier density.

Crystal structure and phase stability in Fe{sub 1{minus}x}Co{sub x} from AB initio theory

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

Soederlind, P.; Abrikosov, I.A.; James, P.

1996-06-01

For alloys between Fe and Co, their magnetic properties determine their structure. From the occupation of d states, a phase diagram is expected which depend largely on the spin polarization. A method more elaborate than canonical band models is used to calculate the spin moment and crystal structure energies. This method was the multisublattice generalization of the coherent potential approximation in conjunction with the Linear-Muffin-Tin-Orbital method in the atomic sphere approximation. To treat itinerant magnetism, the Vosko-Wilk-Nusair parameterization was used for the local spin density approximation. The fcc, bcc, and hcp phases were studied as completely random alloys, while themore » {alpha}{prime} phase for off-stoichiometries were considered as partially ordered. Results are compared with experiment and canonical band model.« less

High-pressure structural, elastic, and thermodynamic properties of zircon-type HoPO 4 and TmPO 4

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

Gomis, O.; Lavina, B.; Rodríguez-Hernández, P.

2017-01-20

Zircon-type holmium phosphate (HoPO 4) and thulium phosphate (TmPO 4) have been studied by single-crystal x-ray diffraction and ab initio calculations. We report on the influence of pressure on the crystal structure, and on the elastic and thermodynamic properties. The equation of state for both compounds is accurately determined. We have also obtained information on the polyhedral compressibility which is used to explain the anisotropic axial compressibility and the bulk compressibility. Both compounds are ductile and more resistive to volume compression than to shear deformation at all pressures. Furthermore, the elastic anisotropy is enhanced upon compression. Finally, the calculations indicatemore » that the possible causes that make the zircon structure unstable are mechanical instabilities and the softening of a silent B 1u mode.« less

Ab Initio Crystal Field for Lanthanides.

PubMed

Ungur, Liviu; Chibotaru, Liviu F

2017-03-13

An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc) 2 ] - (Pc=phthalocyanine) and Dy 4 K 2 ([Dy 4 K 2 O(OtBu) 12 ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H 3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of glue type potentials for the Al-Pb system: computer simulation of Pb/Al interfaces and phase diagram calculation

NASA Astrophysics Data System (ADS)

Landa, Alex; Wynblatt, Paul; Siegel, Donald; Adams, Jim; Johnson, Erik; Dahmen, Uli

2000-03-01

Empirical many-body potentials have been constructed for the Al-Pb system using the ``force matching" method. The potentials have been fitted to a set of the ground state physical quantities calculated within ab initio approach and a massive quantum mechanical forces database for samples of bulk Al-Pb liquid alloys generated using ab initio molecular dynamics program VASP. Monte Carlo simulations using these potentials have been employed to compute an Al-Pb phase diagram, which is in fair agreement with experimental data, and to model the structure of (111) and (100) Pb/Al interfaces. The calculated free energy ratios for the Pb/Al 100 and 111 interfaces are in good agreement with recent high-resolution transmission electron microscopy measurements. The constructed glue potentials correctly reflects the large change in anisotropy which is observed experimentally between isolated Pb crystals and Pb crystals embedded in Al. Support by the DOE under grants DE-FG02-99ER45773 and DE-AC03-76SF00098, the NSF under grant DMR9619353 and the Danish Natural Sciences Research Council.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

On the ab initio evaluation of Hubbard parameters. II. The κ-(BEDT-TTF)2Cu[N(CN)2]Br crystal

NASA Astrophysics Data System (ADS)

Fortunelli, Alessandro; Painelli, Anna

1997-05-01

A previously proposed approach for the ab initio evaluation of Hubbard parameters is applied to BEDT-TTF dimers. The dimers are positioned according to four geometries taken as the first neighbors from the experimental data on the κ-(BEDT-TTF)2Cu[N(CN)2]Br crystal. RHF-SCF, CAS-SCF and frozen-orbital calculations using the 6-31G** basis set are performed with different values of the total charge, allowing us to derive all the relevant parameters. It is found that the electronic structure of the BEDT-TTF planes is adequately described by the standard Extended Hubbard Model, with the off-diagonal electron-electron interaction terms (X and W) of negligible size. The derived parameters are in good agreement with available experimental data. Comparison with previous theoretical estimates shows that the t values compare well with those obtained from Extended Hückel Theory (whereas the minimal basis set estimates are completely unreliable). On the other hand, the Uaeff values exhibit an appreciable dependence on the chemical environment.

Magnetocrystalline anisotropy of cementite pseudo single crystal fabricated under a rotating magnetic field

NASA Astrophysics Data System (ADS)

Yamamoto, Sukeyoshi; Terai, Tomoyuki; Fukuda, Takashi; Sato, Kazunori; Kakeshita, Tomoyuki; Horii, Shigeru; Ito, Mikio; Yonemura, Mitsuharu

2018-04-01

We have fabricated a pseudo single crystal of cementite under a rotating magnetic field and investigated its easy and hard axes of magnetization, and determined its magnetocrystalline anisotropy energy. The obtained results are as follows: the hard and easy axes of cementite are the a- and c-axes of the orthorhombic structure with the space group Pnma, respectively. The hard axis observed experimentally was in good agreement with that obtained by an ab initio calculation; however, such consistency was not observed for the easy axis. The magnetocrystalline anisotropy energy was determined as 334 ± 20 kJ/m3 at 5 K.

Structures, phase stabilities, and electrical potentials of Li-Si battery anode materials

NASA Astrophysics Data System (ADS)

Tipton, William W.; Bealing, Clive R.; Mathew, Kiran; Hennig, Richard G.

2013-05-01

The Li-Si materials system holds promise for use as an anode in Li-ion battery applications. For this system, we determine the charge capacity, voltage profiles, and energy storage density solely by ab initio methods without any experimental input. We determine the energetics of the stable and metastable Li-Si phases likely to form during the charging and discharging of a battery. Ab initio molecular dynamics simulations are used to model the structure of amorphous Li-Si as a function of composition, and a genetic algorithm coupled to density-functional theory searches the Li-Si binary phase diagram for small-cell, metastable crystal structures. Calculations of the phonon densities of states using density-functional perturbation theory for selected structures determine the importance of vibrational, including zero-point, contributions to the free energies. The energetics and local structural motifs of these metastable Li-Si phases closely resemble those of the amorphous phases, making these small unit cell crystal phases good approximants of the amorphous phase for use in further studies. The charge capacity is estimated, and the electrical potential profiles and the energy density of Li-Si anodes are predicted. We find, in good agreement with experimental measurements, that the formation of amorphous Li-Si only slightly increases the anode potential. Additionally, the genetic algorithm identifies a previously unreported member of the Li-Si binary phase diagram with composition Li5Si2 which is stable at 0 K with respect to previously known phases. We discuss its relationship to the partially occupied Li7Si3 phase.

Ab initio calculations of the lattice dynamics of silver halides

NASA Astrophysics Data System (ADS)

Gordienko, A. B.; Kravchenko, N. G.; Sedelnikov, A. N.

2010-12-01

Based on ab initio pseudopotential calculations, the results of investigations of the lattice dynamics of silver halides AgHal (Hal = Cl, Br, I) are presented. Equilibrium lattice parameters, phonon spectra, frequency densities and effective atomic-charge values are obtained for all types of crystals under study.

Solid state linear dichroic infrared spectral analysis of benzimidazoles and their N 1-protonated salts

NASA Astrophysics Data System (ADS)

Ivanova, B. B.

2005-11-01

A stereo structural characterization of 2,5,6-thrimethylbenzimidazole (MBIZ) and 2-amino-benzimidaziole (2-NH 2-BI) and their N 1 protonation salts was carried out using a polarized solid state linear dichroic infrared spectral (IR-LD) analysis in nematic liquid crystal suspension. All experimental predicted structures were compared with the theoretical ones, obtained by ab initio calculations. The Cs to C2v* symmetry transformation as a result of protonation processes, with a view of its reflection on the infrared spectral characteristics was described.

Ionic Graphitization of Ultrathin Films of Ionic Compounds.

PubMed

Kvashnin, A G; Pashkin, E Y; Yakobson, B I; Sorokin, P B

2016-07-21

On the basis of ab initio density functional calculations, we performed a comprehensive investigation of the general graphitization tendency in rocksalt-type structures. In this paper, we determine the critical slab thickness for a range of ionic cubic crystal systems, below which a spontaneous conversion from a cubic to a layered graphitic-like structure occurs. This conversion is driven by surface energy reduction. Using only fundamental parameters of the compounds such as the Allen electronegativity and ionic radius of the metal atom, we also develop an analytical relation to estimate the critical number of layers.

13C CP MAS NMR and GIAO-CHF calculations of coumarins.

PubMed

Zolek, Teresa; Paradowska, Katarzyna; Wawer, Iwona

2003-01-01

13C cross-polarization magic-angle spinning NMR spectra were recorded for a series of solid coumarins. Ab initio calculations of shielding constants were performed with the use of GIAO-CHF method. The combined CPMAS NMR and theoretical approach was successful in characterizing solid-state conformations of coumarins; a relationship sigma (ppm) = -1.032 xdelta + 205.28 (R(2) = 0.9845) can be used to obtain structural information for coumarins, for which solid-state NMR or crystal structure data are not available. Copyright 2002 Elsevier Science (USA)

Protonation of benzimidazoles and 1,2,3-benzotriazoles Solid-state linear dichroic infrared (IR-LD) spectral analysis and ab initio calculations

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka B.; Pindeva, Liliya I.

2006-09-01

IR-LD spectroscopic data obtained by the orientated solid samples as a suspension in a nematic liquid crystal of 1-hydroxy-1,2,3-benzotriazole, 2-methyl-, 2-acetonitrilebenzimidazoles and their protonated salts have been presented. The stereo-structures have been predicted and compared with theoretical ones. The IR-characteristic bands assignments of all molecule systems have been achieved.

Structural, electronic and elastic properties of heavy fermion YbRh2 Laves phase compound

NASA Astrophysics Data System (ADS)

Pawar, Harsha; Shugani, Mani; Aynyas, Mahendra; Sanyal, Sankar P.

2018-05-01

The structural, electronic and elastic properties of YbRh2 Laves phase intermetallic compound which crystallize in cubic (MgCu2-type) structure have been investigated using ab-initio full potential linearized augmented plane wave (FP- LAPW) method with LDA and LDA+U approximation. The calculated ground state properties such as lattice parameter (a0), bulk modulus (B) and its pressure derivative (B') are in good agreement with available experimental and theoretical data. The electronic properties are analyzed from band structures and density of states. Elastic constants are predicted first time for this compound which obeys the stability criteria for cubic system.

Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

2016-09-01

Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.

Hyperfine field and electronic structure of magnetite below the Verwey transition

NASA Astrophysics Data System (ADS)

Řezníček, R.; Chlan, V.; Štěpánková, H.; Novák, P.

2015-03-01

Magnetite represents a prototype compound with a mixed valence of iron cations. Its structure and electron ordering below the Verwey transition have been studied for decades. A recently published precise crystallographic structure [Senn et al., Nature (London) 481, 173 (2012), 10.1038/nature10704] accompanied by a suggestion of a "trimeron" model has given a new impulse to magnetite research. Here we investigate hyperfine field anisotropy in the C c phase of magnetite by quantitative reanalysis of published measurements of the dependences of the 57Fe nuclear magnetic resonance frequencies on the external magnetic field direction. Further, ab initio density-functional-theory-based calculations of hyperfine field depending on the magnetization direction using the recently reported crystal structure are carried out, and analogous hyperfine anisotropy data linked to particular crystallographic sites are determined. These two sets of data are compared, and mutually matching groups of the iron B sites in the 8:5:3 ratio are found. Moreover, information on electronic structure is obtained from the ab initio calculations. Our results are compared with the trimeron model and with an alternative analysis [Patterson, Phys. Rev. B 90, 075134 (2014), 10.1103/PhysRevB.90.075134] as well.

Density functional theory determination of structural and electronic properties of struvite.

PubMed

Romanowski, Zbigniew; Kempisty, Paweł; Prywer, Jolanta; Krukowski, Stanisław; Torzewska, Agnieszka

2010-07-29

Crystallographic structure, total energy, electronic structure, and the most important elastic properties of struvite, NH(4)MgPO(4).6H(2)O, the main component of infectious urinary stones, are presented. The calculations were performed using ab initio full-electron calculations within the density functional theory-generalized gradient approximation (DFT-GGA) framework. The obtained crystallographic symmetry and the calculated lattice parameters and also the elastic constants are in good agreement with the experimental data. The elastic properties are essential for establishing an optimal response of urinary stones during shock-wave lithotripsy. The calculated electronic charge distribution confirms the layered structure of the struvite crystals. The polar character of the crystal, well-known from crystal growth experiments, was also confirmed by the magnitude of spontaneous polarization which was obtained from direct determination of the electrical dipole density. The calculated value of spontaneous polarization is equal to -8.8 microC cm(-2). This feature may play a key role in struvite crystallization, electrically binding the charged active impurities and other active species, and consequently determining urinary stone formation. We also present the results of our own experiment of the mineralization of struvite induced to growth by Proteus bacteria which are mainly isolated from infectious urinary stones.

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

PubMed

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

2006-04-27

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

Anharmonic and Quantum Fluctuations in Molecular Crystals from Ab Initio Simulations

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

Molecular crystals often exist in multiple competing polymorphs which are challenging to be predicted computationally, but show significantly different physicochemical properties. This challenge is not due only to the combinatorial search space, but also to the complex interplay of subtle effects determine the relative stability of different structures. Here we estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects, by using a series of different flavors of thermodynamic integration. As an example, for the two most stable forms of paracetamol we find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our studies indicate that anharmonic free energies could play an important role for molecular crystals composed by large molecules and opens the way for a systematic inclusion of these effects in order to obtain a predictive screening of structures.

Aromatic dipeptides and their salts—Solid-state linear-dichroic infrared (IR-LD) spectral analysis and ab initio calculations

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka B.

2008-07-01

Stereo-structural analysis and IR-bands assignment of the aromatic dipeptides L-tryrosyl- L-phenylalanine ( Tyr-Phe), L-phenylalanyl- L-tyrosine ( Phe-Tyr) and their hydrochloride salts have been carried out by means of IR-LD spectroscopy of oriented as nematic liquid crystal suspension solid samples. The experimental data are compared with known crystallographic ones and theoretical predicted geometries at RHF/ and UHF/6-31G**.

Structural characterization of the RNA chaperone Hfq from the nitrogen-fixing bacterium Herbaspirillum seropedicae SmR1.

PubMed

Kadowaki, Marco Antonio Seiki; Iulek, Jorge; Barbosa, João Alexandre Ribeiro Gonçalves; Pedrosa, Fábio de Oliveira; de Souza, Emanuel Maltempi; Chubatsu, Leda Satie; Monteiro, Rose Adele; de Oliveira, Marco Aurélio Schüler; Steffens, Maria Berenice Reynaud

2012-02-01

The RNA chaperone Hfq is a homohexamer protein identified as an E. coli host factor involved in phage Qβ replication and it is an important posttranscriptional regulator of several types of RNA, affecting a plethora of bacterial functions. Although twenty Hfq crystal structures have already been reported in the Protein Data Bank (PDB), new insights into these protein structures can still be discussed. In this work, the structure of Hfq from the β-proteobacterium Herbaspirillum seropedicae, a diazotroph associated with economically important agricultural crops, was determined by X-ray crystallography and small-angle X-ray scattering (SAXS). Biochemical assays such as exclusion chromatography and RNA-binding by the electrophoretic shift assay (EMSA) confirmed that the purified protein is homogeneous and active. The crystal structure revealed a conserved Sm topology, composed of one N-terminal α-helix followed by five twisted β-strands, and a novel π-π stacking intra-subunit interaction of two histidine residues, absent in other Hfq proteins. Moreover, the calculated ab initio envelope based on small-angle X-ray scattering (SAXS) data agreed with the Hfq crystal structure, suggesting that the protein has the same folding structure in solution. Copyright © 2011 Elsevier B.V. All rights reserved.

Relevance of 4f-3d exchange to finite-temperature magnetism of rare-earth permanent magnets: An ab-initio-based spin model approach for NdFe{sub 12}N

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

Matsumoto, Munehisa; Akai, Hisazumi; Doi, Shotaro

2016-06-07

A classical spin model derived ab initio for rare-earth-based permanent magnet compounds is presented. Our target compound, NdFe{sub 12}N, is a material that goes beyond today's champion magnet compound Nd{sub 2}Fe{sub 14}B in its intrinsic magnetic properties with a simpler crystal structure. Calculated temperature dependence of the magnetization and the anisotropy field agrees with the latest experimental results in the leading order. Having put the realistic observables under our numerical control, we propose that engineering 5d-electron-mediated indirect exchange coupling between 4f-electrons in Nd and 3d-electrons from Fe would most critically help enhance the material's utility over the operation-temperature range.

6-Aminopenicillanic acid revisited: A combined solid state NMR and in silico refinement

NASA Astrophysics Data System (ADS)

Aguiar, Daniel Lima Marques de; San Gil, Rosane Aguiar da Silva; Alencastro, Ricardo Bicca de; Souza, Eugenio Furtado de; Borré, Leandro Bandeira; Vaiss, Viviane da Silva; Leitão, Alexandre Amaral

2016-09-01

13C/15N (experimental and ab initio) solid-state NMR was used to achieve an affordable way to improve hydrogen refinement of 6-aminopenicillanic acid (6-APA) structure. The lattice effect on the isotropic chemical shifts was probed by using two different magnetic shielding calculations: isolated molecules and periodic crystal structure. The electron density difference maps of optimized and non-optimized structures were calculated in order to investigate the interactions inside the 6-APA unit cell. The 13C and 15N chemical shifts assignments were unambiguously stablished. In addition, some of the literature 13C resonances ambiguities could be properly solved.

First principle study of UHTC ternary diboride, Cr2AlB2

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Structural, elastic and electronic properties of typical NdMgT4 (T = Co, Ni, Cu) alloys from ab initio calculation

NASA Astrophysics Data System (ADS)

Wang, Na; Zhang, Wei-bing; Tang, Bi-yu; Gao, Hai-Tao; He, En-jie; Wang, Lei

2018-07-01

The crystal structure, elastic and magnetic properties of important ternary Mg-based alloys NdMgT4 (T = Co, Ni, Cu) have been studied using reliable ab initio calculations. Both cohesive energy and charge density difference suggest that three alloys have good structural stability with the order: NdMgCo4 > NdMgNi4 > NdMgCu4. It shows that NdMgCo4 alloy has magnetic moments with the Co atoms being the main contribution, which is also in agreement with the calculated electronic structures. We find that NdMgT4 (T = Co, Ni, Cu) alloys are all ductile materials with bulk-to-shear modulus (B/G) values higher than 1.75. The trends of calculated values for the shear moduli Cs and C44 are consistent with that of shear modulus G and young's modulus E, proving that NdMgT4 (T = Co, Ni, Cu) alloys exhibit good plasticity with the trend: NdMgNi4 > NdMgCu4 > NdMgCo4. These calculated results give the basis guidance for the design of rare earth-magnesium-transition metal (R-Mg-T) alloys with improved mechanical properties.

Ab initio study of properties of BaBiO3 at high pressure

NASA Astrophysics Data System (ADS)

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

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

X-ray diffraction, crystal structure, and spectral features of the optical susceptibilities of single crystals of the ternary borate oxide lead bismuth tetraoxide, PbBiBO4.

PubMed

Reshak, Ali Hussain; Kityk, I V; Auluck, S; Chen, Xuean

2009-05-14

The all-electron full-potential linearized augmented plane-wave method has been used for an ab initio theoretical study of the band structure, the spectral features of the optical susceptibilities, the density of states, and the electron charge density for PbBiBO4. Our calculations show that the valence-band maximum (VBM) and conduction-band minimum (CBM) are located at the center of the Brillouin zone, resulting in a direct energy gap of about 3.2 eV. We have synthesized the PbBiBO4 crystal by employing a conventional solid-state reaction method. The theoretical calculations in this work are based on the structure built from our measured atomic parameters. We should emphasize that the observed experimental X-ray diffraction (XRD) pattern is in good agreement with the theoretical one, confirming that our structural model is valid. Our calculated bond lengths show excellent agreement with the experimental data. This agreement is attributed to our use of full-potential calculations. The spectral features of the optical susceptibilities show a small positive uniaxial anisotropy.

High-pressure synthesis, amorphization, and decomposition of silane.

PubMed

Hanfland, Michael; Proctor, John E; Guillaume, Christophe L; Degtyareva, Olga; Gregoryanz, Eugene

2011-03-04

By compressing elemental silicon and hydrogen in a diamond anvil cell, we have synthesized polymeric silicon tetrahydride (SiH(4)) at 124 GPa and 300 K. In situ synchrotron x-ray diffraction reveals that the compound forms the insulating I4(1)/a structure previously proposed from ab initio calculations for the high-pressure phase of silane. From a series of high-pressure experiments at room and low temperature on silane itself, we find that its tetrahedral molecules break up, while silane undergoes pressure-induced amorphization at pressures above 60 GPa, recrystallizing at 90 GPa into the polymeric crystal structures.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Structural, Electronic and Elastic Properties of Heavy Fermion YbTM2 (TM= Ir and Pt) Laves Phase Compounds

NASA Astrophysics Data System (ADS)

Pawar, H.; Shugani, M.; Aynyas, M.; Sanyal, S. P.

2018-02-01

The structural, electronic and elastic properties of YbTM2 (TM = Ir and Pt) Laves phase intermetallic compounds which crystallize in cubic (MgCu2-type) structure, have been investigated using ab-initio full potential linearized augmented plane wave (FP-LAPW) method with LDA and LDA+U approximation. The calculated ground state properties such as lattice parameter (a0), bulk modulus (B) and its pressure derivative (B‧) are in good agreement with available experimental and theoretical data. The electronic properties are analyzed from band structures and density of states. Elastic constants are predicted first time for these compounds which obey the stability criteria for cubic system.

Photomagnetic switching of heterometallic complexes [M(dmf)4(H2O)3(mu-CN)Fe(CN)5].H2O (M=Nd, La, Gd, Y) analyzed by single-crystal X-ray diffraction and ab initio theory.

PubMed

Svendsen, Helle; Overgaard, Jacob; Chevallier, Marie A; Collet, Eric; Chen, Yu-Sheng; Jensen, Frank; Iversen, Bo B

2010-06-25

Single-crystal X-ray diffraction measurements have been carried out on [Nd(dmf)(4)(H(2)O)(3)(mu-CN)Fe(CN)(5)].H(2)O (1; dmf=dimethylformamide), [Nd(dmf)(4)(H(2)O)(3)(mu-CN)Co(CN)(5)].H(2)O (2), [La(dmf)(4)(H(2)O)(3)(mu-CN)Fe(CN)(5)].H(2)O (3), [Gd(dmf)(4)(H(2)O)(3)(mu-CN)Fe(CN)(5)].H(2)O (4), and [Y(dmf)(4)(H(2)O)(3)(mu-CN)Fe(CN)(5)].H(2)O (5), at 15(2) K with and without UV illumination of the crystals. Significant changes in unit-cell parameters were observed for all the iron-containing complexes, whereas 2 showed no response to UV illumination. Photoexcited crystal structures have been determined for 1, 3, and 4 based on refinements of two-conformer models, and excited-state occupancies of 78.6(1), 84(6), and 86.6(7)% were reached, respectively. Significant bond-length changes were observed for the Fe-ligand bonds (up to 0.19 A), the cyano bonds (up to 0.09 A), and the lanthanide-ligand bonds (up to 0.10 A). Ab initio theoretical calculations were carried out for the experimental ground-state geometry of 1 to understand the electronic structure changes upon UV illumination. The calculations suggest that UV illumination gives a charge transfer from the cyano groups on the iron atom to the lanthanide ion moiety, {Nd(dmf)(4)(H(2)O)(3)}, with a distance of approximately 6 A from the iron atom. The charge transfer is accompanied by a reorganization of the spin state on the {Fe(CN)(6)} complex, and a change in geometry that produces a metastable charge-transfer state with an increased number of unpaired electrons, thus accounting for the observed photomagnetic effect.

Atomistic Structure, Strength, and Kinetic Properties of Intergranular Films in Ceramics

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

Garofalini, Stephen H

2015-01-08

Intergranular films (IGFs) present in polycrystalline oxide and nitride ceramics provide an excellent example of nanoconfined glasses that occupy only a small volume percentage of the bulk ceramic, but can significantly influence various mechanical, thermal, chemical, and optical properties. By employing molecular dynamics computer simulations, we have been able to predict structures and the locations of atoms at the crystal/IGF interface that were subsequently verified with the newest electron microscopies. Modification of the chemistry of the crystal surface in the simulations provided the necessary mechanism for adsorption of specific rare earth ions from the IGF in the liquid state tomore » the crystal surface. Such results had eluded other computational approaches such as ab-initio calculations because of the need to include not only the modified chemistry of the crystal surfaces but also an accurate description of the adjoining glassy IGF. This segregation of certain ions from the IGF to the crystal caused changes in the local chemistry of the IGF that affected fracture behavior in the simulations. Additional work with the rare earth ions La and Lu in the silicon oxynitride IGFs showed the mechanisms for their different affects on crystal growth, even though both types of ions are seen adhering to a bounding crystal surface that would normally imply equivalent affects on grain growth.« less

Structural investigation of the C-O complex in GaAs

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

Alt, H. Ch.; Kersch, A.; Wagner, H. E.

A carbon-oxygen complex occurring in gallium arsenide crystals after annealing at around 700 °C is studied. Fourier transform infrared absorption measurements on the associated vibrational band at 2060 cm-1 under uniaxial stress reveal that the center has tetragonal symmetry. From the intensity of the {sup 18}O-related satellite band it is concluded that four oxygen atoms are involved. Ab initio local density calculations show that a tetragonal CO{sub 4} molecule forms a stable entity in the gallium arsenide lattice.

Layered crystal structure, conformational and vibrational properties of 2,2,2-trichloroethoxysulfonamide: An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Gil, Diego M.; Piro, Oscar E.; Echeverría, Gustavo A.; Tuttolomondo, María E.; Altabef, Aída Ben

2013-12-01

The molecular structure of 2,2,2-trichloroethoxysulfonamide, CCl3CH2OSO2NH2, has been determined in the solid state by X-ray diffraction data and in the gas phase by ab initio (MP2) and DFT calculations. The substance crystallizes in the monoclinic P21/c space group with a = 9.969(3) Å, b = 22.914(6) Å, c = 7.349(2) Å, β = 91.06(3)°, and Z = 8 molecules per unit cell. There are two independent, but closely related molecular conformers in the crystal asymmetric unit. They only differ in the angular orientation of the sulfonamide (sbnd SO2NH2) group. The conformers are arranged in the lattice as center-symmetric Nsbnd H⋯O(sulf)-bonded dimers. Neighboring dimers are linked through further Nsbnd H⋯O(sulf) bonds giving rise to a crystal layered structure. The solid state infrared and Raman spectra have been recorded and the observed bands assigned to the molecular vibration modes. Also, the thermal behavior of the substance was investigated by TG-DT analysis. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using natural bond (NBO) analysis.

ab initio MD simulations of geomaterials with ~1000 atoms

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

Structure of 1:1 complex of 1-naphthylmethyl ester of monensin A with sodium perchlorate studied by X-ray, FT-IR and ab initio methods

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.

Charge transport in organic molecular semiconductors from first principles: The bandlike hole mobility in a naphthalene crystal

NASA Astrophysics Data System (ADS)

Lee, Nien-En; Zhou, Jin-Jian; Agapito, Luis A.; Bernardi, Marco

2018-03-01

Predicting charge transport in organic molecular crystals is notoriously challenging. Carrier mobility calculations in organic semiconductors are dominated by quantum chemistry methods based on charge hopping, which are laborious and only moderately accurate. We compute from first principles the electron-phonon scattering and the phonon-limited hole mobility of naphthalene crystal in the framework of ab initio band theory. Our calculations combine GW electronic bandstructures, ab initio electron-phonon scattering, and the Boltzmann transport equation. The calculated hole mobility is in very good agreement with experiment between 100 -300 K , and we can predict its temperature dependence with high accuracy. We show that scattering between intermolecular phonons and holes regulates the mobility, though intramolecular phonons possess the strongest coupling with holes. We revisit the common belief that only rigid molecular motions affect carrier dynamics in organic molecular crystals. Our paper provides a quantitative and rigorous framework to compute charge transport in organic crystals and is a first step toward reconciling band theory and carrier hopping computational methods.

Overall conformation of covalently stabilized domain-swapped dimer of human cystatin C in solution

NASA Astrophysics Data System (ADS)

Murawska, Magdalena; Szymańska, Aneta; Grubb, Anders; Kozak, Maciej

2017-11-01

Human cystatin C (HCC), a small protein, plays a crucial role in inhibition of cysteine proteases. The most common structural form of human cystatin C in crystals is a dimer, which has been evidenced both for the native protein and its mutants. In these structures, HCC dimers were formed through the mechanism of domain swapping. The structure of the monomeric form of human cystatin C was determined for V57N mutant and the mutant with the engineered disulfide bond (L47C)-(G69C) (known as stab1-HCC). On the basis of stab1-HCC, a number of covalently stabilized oligomers, including also dimers have been obtained. The aim of this study was to analyze the structure of the covalently stabilized dimer HCC in solution by the small angle X-ray scattering (SAXS) technique and synchrotron radiation. Experimental data confirmed that in solution this protein forms a dimer, which is characterized by the radius of gyration RG = 3.1 nm and maximum intramolecular distance Dmax = 10.3 nm. Using the ab initio method and program DAMMIN, we propose a low resolution structure of stabilized covalently cystatin C in solution. Stab-HCC dimer adopts in solution an elongated conformation, which is well reconstructed by the ab initio model.

Superconductivity in metastable phases of phosphorus-hydride compounds under high pressure

NASA Astrophysics Data System (ADS)

Flores Livas, Jose; Amsler, Maximilian; Sanna, Antonio; Heil, Christoph; Boeri, Lilia; Profeta, Gianni; Wolverton, Crhis; Goedecker, Stefan; Gross, E. K. U.

Recently, compressed phosphine was reported to metallize at pressures above 45 GPa, reaching a superconducting transition temperature (Tc) of 100 K at 200 GPa. However, neither the exact composition nor the crystal structure of the superconducting phase have been conclusively determined. In this work the phase diagram of PHn (n = 1 , 2 , 3 , 4 , 5 , 6) was extensively explored by means of ab initio crystal structure prediction methods. The results do not support the existence of thermodynamically stable PHn compounds, which exhibit a tendency for elemental decomposition at high pressure even when vibrational contributions to the free energies are taken into account. Although the lowest energy phases of PH1 , 2 , 3 display Tc's comparable to experiments, it remains questionable if the measured values of Tc can be fully attributed to a phase-pure compound of PHn. This work was done within the NCCR MARVEL project.

Localized diabatization applied to excitons in molecular crystals

NASA Astrophysics Data System (ADS)

Jin, Zuxin; Subotnik, Joseph E.

2017-06-01

Traditional ab initio electronic structure calculations of periodic systems yield delocalized eigenstates that should be understood as adiabatic states. For example, excitons are bands of extended states which superimpose localized excitations on every lattice site. However, in general, in order to study the effects of nuclear motion on exciton transport, it is standard to work with a localized description of excitons, especially in a hopping regime; even in a band regime, a localized description can be helpful. To extract localized excitons from a band requires essentially a diabatization procedure. In this paper, three distinct methods are proposed for such localized diabatization: (i) a simple projection method, (ii) a more general Pipek-Mezey localization scheme, and (iii) a variant of Boys diabatization. Approaches (i) and (ii) require localized, single-particle Wannier orbitals, while approach (iii) has no such dependence. These methods should be very useful for studying energy transfer through solids with ab initio calculations.

Room-temperature spin-orbit torque in NiMnSb

NASA Astrophysics Data System (ADS)

Ciccarelli, C.; Anderson, L.; Tshitoyan, V.; Ferguson, A. J.; Gerhard, F.; Gould, C.; Molenkamp, L. W.; Gayles, J.; Železný, J.; Šmejkal, L.; Yuan, Z.; Sinova, J.; Freimuth, F.; Jungwirth, T.

2016-09-01

Materials that crystallize in diamond-related lattices, with Si and GaAs as their prime examples, are at the foundation of modern electronics. Simultaneously, inversion asymmetries in their crystal structure and relativistic spin-orbit coupling led to discoveries of non-equilibrium spin-polarization phenomena that are now extensively explored as an electrical means for manipulating magnetic moments in a variety of spintronic structures. Current research of these relativistic spin-orbit torques focuses primarily on magnetic transition-metal multilayers. The low-temperature diluted magnetic semiconductor (Ga, Mn)As, in which spin-orbit torques were initially discovered, has so far remained the only example showing the phenomenon among bulk non-centrosymmetric ferromagnets. Here we present a general framework, based on the complete set of crystallographic point groups, for identifying the potential presence and symmetry of spin-orbit torques in non-centrosymmetric crystals. Among the candidate room-temperature ferromagnets we chose to use NiMnSb, which is a member of the broad family of magnetic Heusler compounds. By performing all-electrical ferromagnetic resonance measurements in single-crystal epilayers of NiMnSb we detect room-temperature spin-orbit torques generated by effective fields of the expected symmetry and of a magnitude consistent with our ab initio calculations.

Modeling the SHG activities of diverse protein crystals

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

Haupert, Levi M.; DeWalt, Emma L.; Simpson, Garth J., E-mail: gsimpson@purdue.edu

2012-11-01

The origins of the diversity in the SHG signal from protein crystals are investigated and potential protein-crystal coverage by SHG microscopy is assessed. A symmetry-additive ab initio model for second-harmonic generation (SHG) activity of protein crystals was applied to assess the likely protein-crystal coverage of SHG microscopy. Calculations were performed for 250 proteins in nine point-group symmetries: a total of 2250 crystals. The model suggests that the crystal symmetry and the limit of detection of the instrument are expected to be the strongest predictors of coverage of the factors considered, which also included secondary-structural content and protein size. Much ofmore » the diversity in SHG activity is expected to arise primarily from the variability in the intrinsic protein response as well as the orientation within the crystal lattice. Two or more orders-of-magnitude variation in intensity are expected even within protein crystals of the same symmetry. SHG measurements of tetragonal lysozyme crystals confirmed detection, from which a protein coverage of ∼84% was estimated based on the proportion of proteins calculated to produce SHG responses greater than that of tetragonal lysozyme. Good agreement was observed between the measured and calculated ratios of the SHG intensity from lysozyme in tetragonal and monoclinic lattices.« less

Absorption spectra analysis of hydrated uranium(III) complex chlorides

NASA Astrophysics Data System (ADS)

Karbowiak, M.; Gajek, Z.; Drożdżyński, J.

2000-11-01

Absorption spectra of powdered samples of hydrated uranium(III) complex chlorides of the formulas NH 4UCl 4 · 4H 2O and CsUCl 4 · 3H 2O have been recorded at 4.2 K in the 4000-26 000 cm -1 range. The analysis of the spectra enabled the determination of crystal-field parameters and assignment of 83 and 77 crystal-field levels for the tetrahydrate and trihydrate, respectively. The energies of the levels were computed by applying a simplified angular overlap model as well as a semiempirical Hamiltonian representing the combined atomic and crystal-field interactions. Ab initio calculations have enabled the application of a simplified parameterization and the determination of the starting values of the AOM parameters. The received results have proved that the AOM approach can quite well predict both the structure of the ground multiplet and the positions of the crystal-field levels in the 17 000-25 000 cm -1 range, usually obscured by strong f-d bands.

Colour centres and nanostructures on the surface of laser crystals

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

Kulagin, N A

2012-11-30

This paper presents a study of structural and radiationinduced colour centres in the bulk and ordered nanostructures on the surface of doped laser crystals: sapphire, yttrium aluminium garnet and strontium titanate. The influence of thermal annealing, ionising radiation and plasma exposure on the spectroscopic properties of high-purity materials and crystals containing Ti, V and Cr impurities is examined. Colour centres resulting from changes in the electronic state of impurities and plasma-induced surface modification of the crystals are studied by optical, EPR and X-ray spectroscopies, scanning electron microscopy and atomic force microscopy. X-ray line valence shift measurements are used to assessmore » changes in the electronic state of some impurity and host ions in the bulk and on the surface of oxide crystals. Conditions are examined for the formation of one- and two-level arrays of ordered crystallites 10{sup -10} to 10{sup -7} m in size on the surface of crystals doped with irongroup and lanthanoid ions. The spectroscopic properties of the crystals are analysed using ab initio self-consistent field calculations for Me{sup n+} : [O{sup 2-}]{sub k} clusters. (interaction of laser radiation with matter. laser plasma)« less

Lattice dynamics of A Sb2O6 (A =Cu , Co) with trirutile structure

NASA Astrophysics Data System (ADS)

Maimone, D. T.; Christian, A. B.; Neumeier, J. J.; Granado, E.

2018-03-01

Raman spectroscopy experiments on single crystals of CuSb2O6 and CoSb2O6 quasi-one-dimensional antiferromagnets with trirutile crystal structure were performed, with a focus on the first material. The observed Raman-active phonon modes and previously reported infrared-active modes were identified with the aid of ab initio lattice dynamics calculations. The structural transition between monoclinic β -CuSb2O6 and tetragonal α -CuSb2O6 phases at Ts=400 K is manifested in our spectra by a "repulsion" of two accidentally quasidegenerate symmetric modes below Ts, caused by a phonon mixing effect that is only operative in the monoclinic β -CuSb2O6 phase due to symmetry restrictions. Also, two specific phonons, associated with CuO6 octahedra rotation and with a Jahn-Teller elongation mode, soften and broaden appreciably as T →Ts . A crossover from a displacive to an order-disorder transition at Ts is inferred.

Semiconducting cubic titanium nitride in the Th 3 P 4 structure

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

Bhadram, Venkata S.; Liu, Hanyu; Xu, Enshi

We report the discovery of a long-sought-after phase of titanium nitride with stoichiometry Ti 3 N 4 using diamond anvil cell experiments combined with in situ high-resolution x-ray diffraction and Raman spectroscopy techniques, supported by ab initio calculations. Ti 3 N 4 crystallizes in the cubic Th 3 P 4 structure [space group I ¯ 4 3 d (220)] from a mixture of TiN and N 2 above ≈ 75 GPa and ≈ 2400 K. The density ( ≈ 5.22 g/cc) and bulk modulus ( K 0 = 290 GPa) of cubic- Ti 3 N 4 ( c - Timore » 3 N 4 ) at 1 atm, estimated from the pressure-volume equation of state, are comparable to rocksalt TiN. Ab initio calculations based on the GW approximation and using hybrid functionals indicate that c - Ti 3 N 4 is a semiconductor with a direct band gap between 0.8 and 0.9 eV, which is larger than the previously predicted values. The c - Ti 3 N 4 phase is not recoverable to ambient pressure due to dynamic instabilities, but recovery of Ti 3 N 4 in the defect rocksalt (or related) structure may be feasible.« less

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

Elasticity and wave velocity in fcc iron (austenite) at elevated temperatures - Experimental verification of ab-initio calculations.

PubMed

Hutchinson, Bevis; Malmström, Mikael; Lönnqvist, Johan; Bate, Pete; Ehteshami, Hossein; Korzhavyi, Pavel A

2018-07-01

High temperature crystal elasticity constants for face centred cubic austenite are important for interpreting the ultrasonic properties of iron and steels but cannot be determined by normal single crystal methods. Values of these constants have recently been calculated using an ab-initio approach and the present work was carried out to test their applicability using laser-ultrasonic measurements. Steel samples having a known texture were examined at temperatures between 800 °C and 1100 °C to measure the velocity of longitudinal P-waves which were found to be in good agreement with modelled values. Copyright © 2018 Elsevier B.V. All rights reserved.

A General Approach to Access Morphologies of Polyoxometalates in Solution by Using SAXS: An Ab Initio Modeling Protocol.

PubMed

Li, Mu; Wang, Weiyu; Yin, Panchao

2018-05-02

Herein, we reported a general protocol for an ab initio modeling approach to deduce structure information of polyoxometalates (POMs) in solutions from scattering data collected by the small-angle X-ray scattering (SAXS) technique. To validate the protocol, the morphologies of a serious of known POMs in either aqueous or organic solvents were analyzed. The obtained particle morphologies were compared and confirmed with previous reported crystal structures. To extend the feasibility of the protocol to an unknown system of aqueous solutions of Na 2 MoO 4 with the pH ranging from -1 to 8.35, the formation of {Mo 36 } clusters was probed, identified, and confirmed by SAXS. The approach was further optimized with a multi-processing capability to achieve fast analysis of experimental data, thereby, facilitating in situ studies of formations of POMs in solutions. The advantage of this approach is to generate intuitive 3D models of POMs in solutions without confining information such as symmetries and possible sizes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electronic structure of α-SrB4O7: experiment and theory

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Kesler, V. G.; Zaitsev, A. I.; Molokeev, M. S.; Aleksandrovsky, A. S.; Kuzubov, A. A.; Ignatova, N. Y.

2013-02-01

The investigation of valence band structure and electronic parameters of constituent element core levels of α-SrB4O7 has been carried out with x-ray photoemission spectroscopy. Optical-quality crystal α-SrB4O7 has been grown by the Czochralski method. Detailed photoemission spectra of the element core levels have been recorded from the powder sample under excitation by nonmonochromatic Al Kα radiation (1486.6 eV). The band structure of α-SrB4O7 has been calculated by ab initio methods and compared to XPS measurements. It has been found that the band structure of α-SrB4O7 is weakly dependent on the Sr-related states.

The galactoside 2-α-L-fucosyltransferase FUT1 from Arabidopsis thaliana: crystallization and experimental MAD phasing.

PubMed

Rocha, Joana; Cicéron, Félix; Lerouxel, Olivier; Breton, Christelle; de Sanctis, Daniele

2016-07-01

The plant cell wall is a complex network of polysaccharides made up of cellulose, hemicelluloses and pectins. Xyloglucan (XyG), which is the main hemicellulosic component of dicotyledonous plants, has attracted much attention for its role in plant development and for its many industrial applications. The XyG-specific fucosyltransferase (FUT1) adds a fucose residue from GDP-fucose to the 2-O position of the terminal galactosyl residues on XyG side chains. Recombinant FUT1 from Arabidopsis thaliana was crystallized in two different crystal forms, with the best diffracting crystals (up to 1.95 Å resolution) belonging to the monoclinic space group P21, with unit-cell parameters a = 87.6, b = 84.5, c = 150.3 Å, β = 96.3°. Ab initio phases were determined using a two-wavelength anomalous dispersion experiment on a tantalum bromide-derivatized crystal with data collected at the rising and descending inflection points of the Ta white line. An interpretable electron-density map was obtained after elaborate density modification. Model completion and structural analysis are currently under way.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Quantitative analysis of weak interactions by Lattice energy calculation, Hirshfeld surface and DFT studies of sulfamonomethoxine

NASA Astrophysics Data System (ADS)

Patel, Kinjal D.; Patel, Urmila H.

2017-01-01

Sulfamonomethoxine, 4-Amino-N-(6-methoxy-4-pyrimidinyl) benzenesulfonamide (C11H12N4O3S), is investigated by single crystal X-ray diffraction technique. Pair of N-H⋯N and C-H⋯O intermolecular interactions along with π···π interaction are responsible for the stability of the molecular packing of the structure. In order to understand the nature of the interactions and their quantitative contributions towards the crystal packing, the 3D Hirshfeld surface and 2D fingerprint plot analysis are carried out. PIXEL calculations are performed to determine the lattice energies correspond to intermolecular interactions in the crystal structure. Ab initio quantum chemical calculations of sulfamonomethoxine (SMM) have been performed by B3LYP method, using 6-31G** basis set with the help of Schrodinger software. The computed geometrical parameters are in good agreement with the experimental data. The Mulliken charge distribution, calculated using B3LYP method to confirm the presence of electron acceptor and electron donor atoms, responsible for intermolecular hydrogen bond interactions hence the molecular stability.

The CH/π hydrogen bond: Implication in chemistry

NASA Astrophysics Data System (ADS)

Nishio, M.

2012-06-01

The CH/π hydrogen bond is the weakest extreme of hydrogen bonds that occurs between a soft acid CH and a soft base π-system. Implication in chemistry of the CH/π hydrogen bond includes issues of conformation, crystal packing, and specificity in host/guest complexes. The result obtained by analyzing the Cambridge Structural Database is reviewed. The peculiar axial preference of isopropyl group in α-phellandrene and folded conformation of levopimaric acid have been explained in terms of the CH/π hydrogen bond, by high-level ab initio MO calculations. Implication of the CH/π hydrogen bond in structural biology is also discussed, briefly.

Energetics of defects formation and oxygen migration in pyrochlore compounds from first principles calculations

NASA Astrophysics Data System (ADS)

Li, Yan; Kowalski, Piotr M.

2018-07-01

In order to get better understanding of the selective order-disorder transition in pyrochlore compounds, using ab initio methods we calculated the formation energies of coupled cation anti-site and anion Frenkel pair defects and the energy barriers for the oxygen migration for number of families of A2B2 O7 pyrochlore-type compounds. While these parameters have been previously computed with force field-based methods, the ab initio results provide more reliable values that can be confidently used in subsequent analysis. We found a fairly good correlation between the formation energies of the coupled defects and the stability field of pyrochlores. In line with previous studies, the compounds that crystallize in defect fluorite structure are found to have smaller values of coupled defect formation energies than those crystallizing in the pyrochlore phase, although the correlation is not that sharp as in the case of isolated anion Frenkel pair defect. The investigation of the energy barriers for the oxygen migration shows that it is not a good, sole indicator of the tendency of the order-disorder phase transition in pyrochlores. However, we found that the oxygen migration barrier is reduced in the presence of the cation antisite defect. This points at disordering-induced enhancement of oxygen diffusion in pyrochlore compounds.

Insights into the Distinct Lithiation/Sodiation of Porous Cobalt Oxide by in Operando Synchrotron X-ray Techniques and Ab Initio Molecular Dynamics Simulations.

PubMed

Xu, Gui-Liang; Sheng, Tian; Chong, Lina; Ma, Tianyuan; Sun, Cheng-Jun; Zuo, Xiaobing; Liu, Di-Jia; Ren, Yang; Zhang, Xiaoyi; Liu, Yuzi; Heald, Steve M; Sun, Shi-Gang; Chen, Zonghai; Amine, Khalil

2017-02-08

Sodium-ion batteries (SIBs) have been considered as one of the promising power source candidates for the stationary storage industries owing to the much lower cost of sodium than lithium. It is well-known that the electrode materials largely determine the energy density of the battery systems. However, recent discoveries on the electrode materials showed that most of them present distinct lithium and sodium storage performance, which is not yet well understood. In this work, we performed a comparative understanding on the structural changes of porous cobalt oxide during its electrochemical lithiation and sodiation process by in operando synchrotron small angel X-ray scattering, X-ray diffraction, and X-ray absorption spectroscopy. It was found that compared to the lithiation process, the porous cobalt oxide undergoes less pore structure changes, oxidation state, and local structure changes as well as crystal structure evolution during its sodiation process, which is attributed to the intrinsic low sodiation activity of cobalt oxide as evidenced by ab initio molecular dynamics simulations. Moreover, it was indicated that the sodiation activity of metal sulfides is higher than that of metal oxides, indicating a better candidate for SIBs. Such understanding is crucial for future design and improvement of high-performance electrode materials for SIBs.

Development of an Evolutionary Algorithm for the ab Initio Discovery of Two-Dimensional Materials

NASA Astrophysics Data System (ADS)

Revard, Benjamin Charles

Crystal structure prediction is an important first step on the path toward computational materials design. Increasingly robust methods have become available in recent years for computing many materials properties, but because properties are largely a function of crystal structure, the structure must be known before these methods can be brought to bear. In addition, structure prediction is particularly useful for identifying low-energy structures of subperiodic materials, such as two-dimensional (2D) materials, which may adopt unexpected structures that differ from those of the corresponding bulk phases. Evolutionary algorithms, which are heuristics for global optimization inspired by biological evolution, have proven to be a fruitful approach for tackling the problem of crystal structure prediction. This thesis describes the development of an improved evolutionary algorithm for structure prediction and several applications of the algorithm to predict the structures of novel low-energy 2D materials. The first part of this thesis contains an overview of evolutionary algorithms for crystal structure prediction and presents our implementation, including details of extending the algorithm to search for clusters, wires, and 2D materials, improvements to efficiency when running in parallel, improved composition space sampling, and the ability to search for partial phase diagrams. We then present several applications of the evolutionary algorithm to 2D systems, including InP, the C-Si and Sn-S phase diagrams, and several group-IV dioxides. This thesis makes use of the Cornell graduate school's "papers" option. Chapters 1 and 3 correspond to the first-author publications of Refs. [131] and [132], respectively, and chapter 2 will soon be submitted as a first-author publication. The material in chapter 4 is taken from Ref. [144], in which I share joint first-authorship. In this case I have included only my own contributions.

Ab initio molecular orbital studies of the positive muon and muonium in 4-arylmethyleneamino-TEMPO derivatives

NASA Astrophysics Data System (ADS)

Briere, T. M.; Jeong, J.; Das, T. P.; Ohira, S.; Nagamine, K.

2000-08-01

The muon and muonium bonding sites of the 4-arylmethyleneamino-2,2,6,6-tetramethylpiperidin-1-yloxyl radical crystals with aryl groups consisting of biphenyl and 4-pyridyl were studied via ab initio Hartree-Fock theory. The hyperfine fields, including both intramolecular and intermolecular interactions, were calculated at the sites of interest and compared to zero field μSR results.

Atomistic and Ab Initio Calculations or Ternary II-IV-V2 Semiconductors

DTIC Science & Technology

1999-12-07

consisting of two- and three-body terms is developed reproducing crystal lattice constants, elastic and dielectric constants very well. The calculated...the lattice . This difference may well be due to defect-induced lattice distortion which plays a key role in stabilizing the hole states in the... lattice . 15. SUBJECT TERMS Chalcopyrites, Defects, Atomistic and AB Initio Calculations 16. SECURITY CLASSIFICATION OF: a. REPORT u b. ABSTRACT U

High-pressure phase transitions of nitinol NiTi to a semiconductor with an unusual topological structure

NASA Astrophysics Data System (ADS)

Liu, Guangtao; Liu, Hanyu; Feng, Xiaolei; Redfern, Simon A. T.

2018-04-01

Systematic ab initio structure simulations have been used to explore the high-pressure behavior of nitinol (NiTi) at zero temperature. Our crystal structure prediction and first-principles calculations reveal that the known B 19 phase is dynamically unstable, and an orthorhombic structure (Pbcm) and a face-centered-cubic B 32 structure (F d 3 ¯m ) become stable above ˜4 and 29 GPa, respectively. The predicted, highest-pressure, B 32 phase is composed of two interpenetrating diamond structures, with a structural topology that is quite distinct from that of the other phases of NiTi. Interestingly, the B 32 phase shows an unusual semiconducting characteristic as a result of its unique band structure and the nature of 3 d orbitals localization, whose expected synthesis pressure is accessible to current experimental techniques.

Structural stability, electronic structure and mechanical properties of alkali gallium hydrides AGaH{sub 4} (A = Li, Na)

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

Santhosh, M.; Rajeswarapalanichamy, R., E-mail: rrpalanichamy@gmail.com; Manikandan, M.

2016-05-06

Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of alkali gallium hydrides AGaH{sub 4} (A = Li, Na) for three different crystal structures, namely tetragonal (P42{sub 1}c), tetragonal (P4{sub 2}/nmc) and monoclinic (P2{sub 1}/c). Among the considered structures, tetragonal (P42{sub 1}c) phase is found to be the most stable phase for these hydrides at normal pressure. A pressure induced structural phase transition from tetragonal (P42{sub 1}c) to tetragonal (P4{sub 2}/nmc) is observed. The electronic structure reveals that these hydrides are insulators. The calculated elastic constants indicate that these ternary imides are mechanically stablemore » at normal pressure.« less

Structure and Properties of Sn2Se3, a mixed valent tin selenium compound

NASA Astrophysics Data System (ADS)

Xing, Guangzong; Li, Yuwei; Fan, Xiaofeng; Zhang, Lijun; Singh, David

Sn2Se3 is a possibly expected phase based on analogy with Sn2S3 but it has never been reported. It is of interest due to reported phase change memories using this composition using transitions between an amorphous phase and an unknown crystalline phase. We identify the crystal structure Sn2Se3 and report its properties at ambient pressure based on the ab initio evolutionary methodology for crystal structure prediction implemented in the Calypso code. We find a structure based on Sn-Se ribbons with clear Sn(II)and Sn(IV)sites similar to the structure of Sn2S3. Compared with the known phase SnSe (Pnma) +SnSe2 (P-3m1), the energy is only 2.3meV/atom higher. The electronic structure of this phase shows mixed valent tins Sn2+ and Sn4+ in this compound. A small band gap of 0.023 eV is obtained from the band structure consistent with the small resistance reported by Kyung-Min Chung et al. Work at the University of Missouri is supported by DOE through the S3TEC EFRC.

The complex metal-rich boride Ti1+xRh2-x+yIr3-yB3 (x=0.68, y=1.06) with a new structure type containing B4 zigzag fragments: Synthesis, crystal chemistry and theoretical calculations

NASA Astrophysics Data System (ADS)

Goerens, Christian; Fokwa, Boniface P. T.

2012-08-01

Polycrystalline samples and single crystals of the new complex boride Ti1+xRh2-x+yIr3-yB3 (x=0.68; y=1.06) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere and characterized by X-Ray diffraction as well as EDX measurements. The crystal structure was refined on the basis of single crystal data. The new phase, which represents a new structure type containing trans zigzag B4 fragments as well as isolated boron atoms crystallizes in the orthorhombic space group Pbam (Nr. 55) with the lattice parameters a=8.620(1) Å, b=14.995(2) Å and c=3.234(1) Å. First-principles density functional theory calculations using the Vienna ab-initio simulation package (VASP) were performed on an appropriate structural model (using a supercell approach) and the experimental crystallographic data could be reproduced accurately. Based on this model, the density of states and crystal orbital Hamilton population (for bonding analysis) were calculated, using the linear muffin-tin orbital atomic sphere approximation (LMTO-ASA) method. According to these calculations, this metal-rich compound should be metallic, as expected. Furthermore, very strong boron-boron interactions are observed in the trans zigzag B4 fragment, which induce a clear differentiation of two types of metal-boron contacts with different strength. The observed three-dimensional metal-metal interaction is in good agreement with the predicted metallic behavior.

Ab initio structure determination and quantitative disorder analysis on nanoparticles by electron diffraction tomography.

PubMed

Krysiak, Yaşar; Barton, Bastian; Marler, Bernd; Neder, Reinhard B; Kolb, Ute

2018-03-01

Nanoscaled porous materials such as zeolites have attracted substantial attention in industry due to their catalytic activity, and their performance in sorption and separation processes. In order to understand the properties of such materials, current research focuses increasingly on the determination of structural features beyond the averaged crystal structure. Small particle sizes, various types of disorder and intergrown structures render the description of structures at atomic level by standard crystallographic methods difficult. This paper reports the characterization of a strongly disordered zeolite structure, using a combination of electron exit-wave reconstruction, automated diffraction tomography (ADT), crystal disorder modelling and electron diffraction simulations. Zeolite beta was chosen for a proof-of-principle study of the techniques, because it consists of two different intergrown polymorphs that are built from identical layer types but with different stacking sequences. Imaging of the projected inner Coulomb potential of zeolite beta crystals shows the intergrowth of the polymorphs BEA and BEB. The structures of BEA as well as BEB could be extracted from one single ADT data set using direct methods. A ratio for BEA/BEB = 48:52 was determined by comparison of the reconstructed reciprocal space based on ADT data with simulated electron diffraction data for virtual nanocrystals, built with different ratios of BEA/BEB. In this way, it is demonstrated that this smart interplay of the above-mentioned techniques allows the elaboration of the real structures of functional materials in detail - even if they possess a severely disordered structure.

How fragility makes phase-change data storage robust: insights from ab initio simulations

PubMed Central

Zhang, Wei; Ronneberger, Ider; Zalden, Peter; Xu, Ming; Salinga, Martin; Wuttig, Matthias; Mazzarello, Riccardo

2014-01-01

Phase-change materials are technologically important due to their manifold applications in data storage. Here we report on ab initio molecular dynamics simulations of crystallization of the phase change material Ag4In3Sb67Te26 (AIST). We show that, at high temperature, the observed crystal growth mechanisms and crystallization speed are in good agreement with experimental data. We provide an in-depth understanding of the crystallization mechanisms at the atomic level. At temperatures below 550 K, the computed growth velocities are much higher than those obtained from time-resolved reflectivity measurements, due to large deviations in the diffusion coefficients. As a consequence of the high fragility of AIST, experimental diffusivities display a dramatic increase in activation energies and prefactors at temperatures below 550 K. This property is essential to ensure fast crystallization at high temperature and a stable amorphous state at low temperature. On the other hand, no such change in the temperature dependence of the diffusivity is observed in our simulations, down to 450 K. We also attribute this different behavior to the fragility of the system, in combination with the very fast quenching times employed in the simulations. PMID:25284316

Electron-phonon scattering rates in complex polar crystals

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

Prange, M. P.; Campbell, L. W.; Kerisit, S.

2017-09-01

The thermalization of fast electrons by phonons is studied in CsI, NaI, SrI2, and YAP. This numerical study uses an improvement to a recently developed ab initio method based on a density functional perturbation theoretical description of the phonon modes that provides a way to go beyond widely used phonon models based on binary crystals. Improvements to this method are described, and scattering rates are presented and discussed. The results here treat polar and nonpolar scattering on equal footing and allow an assessment of the relative importance of the two types of scattering. The relative activity of the numerous phononmore » modes in materials with complicated structures is discussed, and a simple criterion for finding the modes that scatter strongly is presented.« less

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

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

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. Themore » results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.« less

Structure and dynamics of ND3BF3 in the solid and gas phases: a combined NMR, neutron diffraction, and Ab initio study.

PubMed

Penner, Glenn H; Ruscitti, Bruno; Reynolds, Julie; Swainson, Ian

2002-12-30

The decrease in D-->A bond lengths, previously reported for some Lewis acid/base complexes, in going from the gas to the solid phases is investigated by obtaining an accurate crystal structure of solid ND(3)BF(3) by powder neutron diffraction. The B-N internuclear distance is 1.554(3) A, 0.118 A shorter than the most recent gas-phase microwave value and 0.121 A shorter than the single molecule geometry optimized (1.672 A, CISD/6-311++G(d,p)) bond length. The crystal structure also shows N-D.F-B hydrogen bonds. The effects of this change in structure and of intermolecular hydrogen-bonding on nuclear magnetic shielding (i.e., chemical shifts) and the nuclear quadrupolar coupling constants (QCC) are investigated by ab initio molecular orbital and density functional theory calculations. These calculations show that the nitrogen ((15)N and (14)N) and boron ((11)B and (10)B) chemical shifts should be rather insensitive to changes in r(BN) and that the concomitant changes in molecular structure. Calculations on hydrogen-bonded clusters, based on the crystal structure, indicate that H-bonding should also have very little effect on the chemical shifts. On the other hand, the (11)B and (14)N QCCs show large changes because of both effects. An analysis of the (10)B[(19)F] line shape in solid ND(3)(10)BF(3) yields a (11)B QCC of +/-0.130 MHz. This is reasonably close an earlier value of +/-0.080 MHz and the value of +/-0.050 MHz calculated for a [NH(3)BF(3)](4) cluster. The gas-phase value is 1.20 MHz. Temperature-dependent deuterium T(1) measurements yield an activation energy for rotation of the ND(3) group in solid ND(3)BF(3) of 9.5 +/- 0.1 kJ/mol. Simulations of the temperature-dependent T(1) anisotropy gave an E(a) of 9.5 +/- 0.2 kJ/mol and a preexponential factor, A, of 3.0 +/- 0.1 x 10(12) s(-)(1). Our calculated value for a [NH(3)BF(3)](4) cluster is 16.4 kJ/mol. Both are much higher than the previous value of 3.9 kJ/mol, from solid-state proton T(1) measurements.

The influence of the long-range order on the vibrational spectra of structures based on sodalite cage.

PubMed

Mikuła, A; Król, M; Koleżyński, A

2015-06-05

Zeolites are a group of tecto-aluminosilicates with numerous practical applications, e.g. gas separators, molecular sieves and sorbents. The unique properties result from porous structure of channels and cages which are built from smaller units - the so-called Secondary Building Units (SBU), and sometimes also larger groups (Breck, 1974; Ciciszwili et al., 1974; Mozgawa, 2008; Čejka and van Bekkum, 2005). The aim of this study was the examination of the influence of long-range order on vibrational spectra of sodalite and zeolite A. Ab initio calculations (geometry optimizations and vibrational spectra calculations) of sodalite cage and selected SBU were carried out by means of Gaussian09 (Frisch et al., 2009) (in the case of isolated clusters) and Crystal09 (Dovesi et al., 2005, 2009) (for periodic structures). The obtained results were compared with the experimental spectra of sodalite and zeolite A crystal structures, synthesized under hydrothermal conditions. These results allowed analyzing of the long-range ordering influence on the vibrational spectra, as well as the identification of the characteristic vibrations in β cage based frameworks. It has been found, that based on small structural fragment (SBU) models a characteristic vibrations can be identify. However, full spectra analysis and especially the interpretation of far-infrared region of the spectra require using periodic models under the influence of translational crystal lattice. Copyright © 2015 Elsevier B.V. All rights reserved.

Multiscale Modeling of Grain Boundaries in ZrB2: Structure, Energetics, and Thermal Resistance

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Squire, Thomas H.; Bauschlicher, Charles W., Jr.

2012-01-01

A combination of ab initio, atomistic and finite element methods (FEM) were used to investigate the structures, energetics and lattice thermal conductance of grain boundaries for the ultra high temperature ceramic ZrB2. Atomic models of idealized boundaries were relaxed using density functional theory. Information about bonding across the interfaces was determined from the electron localization function. The Kapitza conductance of larger scale versions of the boundary models were computed using non-equilibrium molecular dynamics. The interfacial thermal parameters together with single crystal thermal conductivities were used as parameters in microstructural computations. FEM meshes were constructed on top of microstructural images. From these computations, the effective thermal conductivity of the polycrystalline structure was determined.

The ground state of two-dimensional silicon

NASA Astrophysics Data System (ADS)

Borlido, Pedro; Rödl, Claudia; Marques, Miguel A. L.; Botti, Silvana

2018-07-01

We perform ab initio structure-prediction calculations of the low-energy crystal structures of two-dimensional silicon. Besides the well-known silicene and a few other allotropes proposed earlier in the literature, we discover a wealth of new phases with interesting properties. In particular, we find that the ground state of two-dimensional silicon is an unreported structure formed by a honeycomb lattice with dumbbell atoms arranged in a zigzag pattern. This material, that we call zigzag dumbbell silicene, is 218 meV/atom more stable than silicene and displays a quasi-direct band gap of around 1.11 eV, with a very dispersive electron band. These properties should make it easier to synthesize than silicene and interesting for a wealth of opto-electronic applications.

Small-angle x-ray scattering study of polymer structure: Carbosilane dendrimers in hexane solution

NASA Astrophysics Data System (ADS)

Shtykova, E. V.; Feigin, L. A.; Volkov, V. V.; Malakhova, Yu. N.; Streltsov, D. R.; Buzin, A. I.; Chvalun, S. N.; Katarzhanova, E. Yu.; Ignatieva, G. M.; Muzafarov, A. M.

2016-09-01

The three-dimensional organization of monodisperse hyper-branched macromolecules of regular structure—carbosilane dendrimers of zero, third, and sixth generations—has been studied by small-angle X-ray scattering (SAXS) in solution. The use of modern methods of SAXS data interpretation, including ab initio modeling, has made it possible to determine the internal architecture of the dendrimers in dependence of the generation number and the number of cyclosiloxane end groups (forming the shell of dendritic macromolecules) and show dendrimers to be spherical. The structural results give grounds to consider carbosilane dendrimers promising objects for forming crystals with subsequent structural analysis and determining their structure with high resolution, as well as for designing new materials to be used in various dendrimer-based technological applications.

Crystal Structure of an Insect Antifreeze Protein and Its Implications for Ice Binding*

PubMed Central

Hakim, Aaron; Nguyen, Jennifer B.; Basu, Koli; Zhu, Darren F.; Thakral, Durga; Davies, Peter L.; Isaacs, Farren J.; Modis, Yorgo; Meng, Wuyi

2013-01-01

Antifreeze proteins (AFPs) help some organisms resist freezing by binding to ice crystals and inhibiting their growth. The molecular basis for how these proteins recognize and bind ice is not well understood. The longhorn beetle Rhagium inquisitor can supercool to below −25 °C, in part by synthesizing the most potent antifreeze protein studied thus far (RiAFP). We report the crystal structure of the 13-kDa RiAFP, determined at 1.21 Å resolution using direct methods. The structure, which contains 1,914 nonhydrogen protein atoms in the asymmetric unit, is the largest determined ab initio without heavy atoms. It reveals a compressed β-solenoid fold in which the top and bottom sheets are held together by a silk-like interdigitation of short side chains. RiAFP is perhaps the most regular structure yet observed. It is a second independently evolved AFP type in beetles. The two beetle AFPs have in common an extremely flat ice-binding surface comprising regular outward-projecting parallel arrays of threonine residues. The more active, wider RiAFP has four (rather than two) of these arrays between which the crystal structure shows the presence of ice-like waters. Molecular dynamics simulations independently reproduce the locations of these ordered crystallographic waters and predict additional waters that together provide an extensive view of the AFP interaction with ice. By matching several planes of hexagonal ice, these waters may help freeze the AFP to the ice surface, thus providing the molecular basis of ice binding. PMID:23486477

Nucleation of metastable aragonite CaCO3 in seawater.

PubMed

Sun, Wenhao; Jayaraman, Saivenkataraman; Chen, Wei; Persson, Kristin A; Ceder, Gerbrand

2015-03-17

Predicting the conditions in which a compound adopts a metastable structure when it crystallizes out of solution is an unsolved and fundamental problem in materials synthesis, and one which, if understood and harnessed, could enable the rational design of synthesis pathways toward or away from metastable structures. Crystallization of metastable phases is particularly accessible via low-temperature solution-based routes, such as chimie douce and hydrothermal synthesis, but although the chemistry of the solution plays a crucial role in governing which polymorph forms, how it does so is poorly understood. Here, we demonstrate an ab initio technique to quantify thermodynamic parameters of surfaces and bulks in equilibrium with an aqueous environment, enabling the calculation of nucleation barriers of competing polymorphs as a function of solution chemistry, thereby predicting the solution conditions governing polymorph selection. We apply this approach to resolve the long-standing "calcite-aragonite problem"--the observation that calcium carbonate precipitates as the metastable aragonite polymorph in marine environments, rather than the stable phase calcite--which is of tremendous relevance to biomineralization, carbon sequestration, paleogeochemistry, and the vulnerability of marine life to ocean acidification. We identify a direct relationship between the calcite surface energy and solution Mg:Ca [corrected] ion concentrations, showing that the calcite nucleation barrier surpasses that of metastable aragonite in solutions with Mg:Ca ratios consistent with modern seawater, allowing aragonite to dominate the kinetics of nucleation. Our ability to quantify how solution parameters distinguish between polymorphs marks an important step toward the ab initio prediction of materials synthesis pathways in solution.

Nucleation of metastable aragonite CaCO 3 in seawater

DOE PAGES

Sun, Wenhao; Jayaraman, Saivenkataraman; Chen, Wei; ...

2015-03-04

Predicting the conditions in which a compound adopts a metastable structure when it crystallizes out of solution is an unsolved and fundamental problem in materials synthesis, and one which, if understood and harnessed, could enable the rational design of synthesis pathways toward or away from metastable structures. Crystallization of metastable phases is particularly accessible via low-temperature solution-based routes, such as chimie douce and hydrothermal synthesis, but although the chemistry of the solution plays a crucial role in governing which polymorph forms, how it does so is poorly understood. Here, we demonstrate an ab initio technique to quantify thermodynamic parameters ofmore » surfaces and bulks in equilibrium with an aqueous environment, enabling the calculation of nucleation barriers of competing polymorphs as a function of solution chemistry, thereby predicting the solution conditions governing polymorph selection. We apply this approach to resolve the long-standing “calcite–aragonite problem”––the observation that calcium carbonate precipitates as the metastable aragonite polymorph in marine environments, rather than the stable phase calcite––which is of tremendous relevance to biomineralization, carbon sequestration, paleogeochemistry, and the vulnerability of marine life to ocean acidification. We identify a direct relationship between the calcite surface energy and solution Mg–Ca ion concentrations, showing that the calcite nucleation barrier surpasses that of metastable aragonite in solutions with Mg:Ca ratios consistent with modern seawater, allowing aragonite to dominate the kinetics of nucleation. The ability to quantify how solution parameters distinguish between polymorphs marks an important step toward the ab initio prediction of materials synthesis pathways in solution.« less

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

Sun, Wenhao; Jayaraman, Saivenkataraman; Chen, Wei

Predicting the conditions in which a compound adopts a metastable structure when it crystallizes out of solution is an unsolved and fundamental problem in materials synthesis, and one which, if understood and harnessed, could enable the rational design of synthesis pathways toward or away from metastable structures. Crystallization of metastable phases is particularly accessible via low-temperature solution-based routes, such as chimie douce and hydrothermal synthesis, but although the chemistry of the solution plays a crucial role in governing which polymorph forms, how it does so is poorly understood. Here, we demonstrate an ab initio technique to quantify thermodynamic parameters ofmore » surfaces and bulks in equilibrium with an aqueous environment, enabling the calculation of nucleation barriers of competing polymorphs as a function of solution chemistry, thereby predicting the solution conditions governing polymorph selection. We apply this approach to resolve the long-standing “calcite–aragonite problem”––the observation that calcium carbonate precipitates as the metastable aragonite polymorph in marine environments, rather than the stable phase calcite––which is of tremendous relevance to biomineralization, carbon sequestration, paleogeochemistry, and the vulnerability of marine life to ocean acidification. We identify a direct relationship between the calcite surface energy and solution Mg–Ca ion concentrations, showing that the calcite nucleation barrier surpasses that of metastable aragonite in solutions with Mg:Ca ratios consistent with modern seawater, allowing aragonite to dominate the kinetics of nucleation. The ability to quantify how solution parameters distinguish between polymorphs marks an important step toward the ab initio prediction of materials synthesis pathways in solution.« less

Phasing via pure crystallographic least squares: an unexpected feature.

PubMed

Burla, Maria Cristina; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Polidori, Giampiero

2018-03-01

Crystallographic least-squares techniques, the main tool for crystal structure refinement of small and medium-size molecules, are for the first time used for ab initio phasing. It is shown that the chief obstacle to such use, the least-squares severe convergence limits, may be overcome by a multi-solution procedure able to progressively recognize and discard model atoms in false positions and to include in the current model new atoms sufficiently close to correct positions. The applications show that the least-squares procedure is able to solve many small structures without the use of important ancillary tools: e.g. no electron-density map is calculated as a support for the least-squares procedure.

Electronic structure and orientation relationship of Li nanoclusters embedded in MgO studied by depth-selective positron annihilation two-dimensional angular correlation

NASA Astrophysics Data System (ADS)

Falub, C. V.; Mijnarends, P. E.; Eijt, S. W.; van Huis, M. A.; van Veen, A.; Schut, H.

2002-08-01

Quantum-confined positrons are sensitive probes for determining the electronic structure of nanoclusters embedded in materials. In this work, a depth-selective positron annihilation 2D-ACAR (two-dimensional angular correlation of annihilation radiation) method is used to determine the electronic structure of Li nanoclusters formed by implantation of 1016-cm-2 30-keV 6Li ions in MgO (100) and (110) crystals and by subsequent annealing at 950 K. Owing to the difference between the positron affinities of lithium and MgO, the Li nanoclusters act as quantum dots for positrons. 2D-ACAR distributions for different projections reveal a semicoherent fitting of the embedded metallic Li nanoclusters to the host MgO lattice. Ab initio Korringa-Kohn-Rostoker calculations of the momentum density show that the anisotropies of the experimental distributions are consistent with an fcc crystal structure of the Li nanoclusters. The observed reduction of the width of the experimental 2D-ACAR distribution is attributed to positron trapping in vacancies associated with Li clusters. This work proposes a method for studying the electronic structure of metallic quantum dots embedded in an insulating material.

Pressure-induced structural change in liquid GaIn eutectic alloy.

PubMed

Yu, Q; Ahmad, A S; Ståhl, K; Wang, X D; Su, Y; Glazyrin, K; Liermann, H P; Franz, H; Cao, Q P; Zhang, D X; Jiang, J Z

2017-04-25

Synchrotron x-ray diffraction reveals a pressure induced crystallization at about 3.4 GPa and a polymorphic transition near 10.3 GPa when compressed a liquid GaIn eutectic alloy up to ~13 GPa at room temperature in a diamond anvil cell. Upon decompression, the high pressure crystalline phase remains almost unchanged until it transforms to the liquid state at around 2.3 GPa. The ab initio molecular dynamics calculations can reproduce the low pressure crystallization and give some hints on the understanding of the transition between the liquid and the crystalline phase on the atomic level. The calculated pair correlation function g(r) shows a non-uniform contraction reflected by the different compressibility between the short (1st shell) and the intermediate (2nd to 4th shells). It is concluded that the pressure-induced liquid-crystalline phase transformation likely arises from the changes in local atomic packing of the nearest neighbors as well as electronic structures at the transition pressure.

Role of interatomic bonding in the mechanical anisotropy and interlayer cohesion of CSH crystals

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

Dharmawardhana, C.C.; Misra, A.; Aryal, S.

2013-10-15

Atomic scale properties of calcium silicate hydrate (CSH), the main binding phase of hardened Portland cement, are not well understood. Over a century of intense research has identified almost 50 different crystalline CSH minerals which are mainly categorized by their Ca/Si ratio. The electronic structure and interatomic bonding in four major CSH crystalline phases with structures close to those found in hardened cement are investigated via ab initio methods. Our result reveals the critical role of hydrogen bonding and importance of specifying precise locations for water molecules. Quantitative analysis of contributions from different bond types to the overall cohesion showsmore » that while the Si-O covalent bonds dominate, the hydrogen bonding and Ca-O bonding are also very significant. Calculated results reveal the correlation between bond topology and interlayer cohesion. The overall bond order density (BOD) is found to be a more critical measure than the Ca/Si ratio in classifying different CSH crystals.« less

Spontaneous ripple formation in phosphorene: electronic properties and possible applications.

PubMed

Zhou, Yungang; Yang, Li; Zu, Xiaotao; Gao, Fei

2016-06-09

According to the Mermin-Wagner theorem and theory of elasticity, long-range order in two-dimensional (2D) crystals will be inevitably destroyed due to a thermal fluctuation. Thus, a 2D lattice prefers a corrugation meaning that a 2D crystal is easy to present a ripple. In this work, we, via employing ab initio molecular dynamics (AIMD) simulations, for the first time evidenced that the inherent dynamics of phosphorene would lead to a spontaneous formation of ripples at room temperature. The height of a ripple closely associates with the temperature and the width. Via density functional theory (DFT) calculations, we further demonstrated that the emergence of ripples would remarkably reduce the bandgap of phosphorene. Via the construction of the unique phosphorene structure, we finally found that such a rippled structure is expected to be used in the light-emitting field. These results give us further knowledge of phosphorene, which goes beyond the current scope of phosphorene limited to the flat lattice.

AFLOW-SYM: platform for the complete, automatic and self-consistent symmetry analysis of crystals.

PubMed

Hicks, David; Oses, Corey; Gossett, Eric; Gomez, Geena; Taylor, Richard H; Toher, Cormac; Mehl, Michael J; Levy, Ohad; Curtarolo, Stefano

2018-05-01

Determination of the symmetry profile of structures is a persistent challenge in materials science. Results often vary amongst standard packages, hindering autonomous materials development by requiring continuous user attention and educated guesses. This article presents a robust procedure for evaluating the complete suite of symmetry properties, featuring various representations for the point, factor and space groups, site symmetries and Wyckoff positions. The protocol determines a system-specific mapping tolerance that yields symmetry operations entirely commensurate with fundamental crystallographic principles. The self-consistent tolerance characterizes the effective spatial resolution of the reported atomic positions. The approach is compared with the most used programs and is successfully validated against the space-group information provided for over 54 000 entries in the Inorganic Crystal Structure Database (ICSD). Subsequently, a complete symmetry analysis is applied to all 1.7+ million entries of the AFLOW data repository. The AFLOW-SYM package has been implemented in, and made available for, public use through the automated ab initio framework AFLOW.

Importance of nonlocal electron correlation in the BaNiS2 semimetal from quantum oscillations studies

NASA Astrophysics Data System (ADS)

Klein, Yannick; Casula, Michele; Santos-Cottin, David; Audouard, Alain; Vignolles, David; Fève, Gwendal; Freulon, Vincent; Plaçais, Bernard; Verseils, Marine; Yang, Hancheng; Paulatto, Lorenzo; Gauzzi, Andrea

2018-02-01

By means of Shubnikov-de Haas and de Haas-van Alphen oscillations, and ab initio calculations, we have studied the Fermi surface of high-quality BaNiS2 single crystals, with mean free path l ˜400 Å . The angle and temperature dependence of quantum oscillations indicates a quasi-two-dimensional Fermi surface, made of an electronlike tube centered at Γ , and of four holelike cones, generated by Dirac bands, weakly dispersive in the out-of-plane direction. Ab initio electronic structure calculations, in the density functional theory framework, show that the inclusion of screened exchange is necessary to account for the experimental Fermi pockets. Therefore, the choice of the functional becomes crucial. A modified HSE hybrid functional with 7% of exact exchange outperforms both GGA and GGA +U density functionals, signaling the importance of nonlocal screened-exchange interactions in BaNiS2, and, more generally, in 3 d compensated semimetals.

Localized diabatization applied to excitons in molecular crystals

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

Jin, Zuxin; Subotnik, Joseph E.

Traditional ab initio electronic structure calculations of periodic systems yield delocalized eigenstates that should be understood as adiabatic states. For example, excitons are bands of extended states which superimpose localized excitations on every lattice site. However, in general, in order to study the effects of nuclear motion on exciton transport, it is standard to work with a localized description of excitons, especially in a hopping regime; even in a band regime, a localized description can be helpful. To extract localized excitons from a band requires essentially a diabatization procedure. In this paper, three distinct methods are proposed for such localizedmore » diabatization: (i) a simple projection method, (ii) a more general Pipek-Mezey localization scheme, and (iii) a variant of Boys diabatization. Approaches (i) and (ii) require localized, single-particle Wannier orbitals, while approach (iii) has no such dependence. Lastly, these methods should be very useful for studying energy transfer through solids with ab initio calculations.« less

Localized diabatization applied to excitons in molecular crystals

DOE PAGES

Jin, Zuxin; Subotnik, Joseph E.

2017-06-28

Traditional ab initio electronic structure calculations of periodic systems yield delocalized eigenstates that should be understood as adiabatic states. For example, excitons are bands of extended states which superimpose localized excitations on every lattice site. However, in general, in order to study the effects of nuclear motion on exciton transport, it is standard to work with a localized description of excitons, especially in a hopping regime; even in a band regime, a localized description can be helpful. To extract localized excitons from a band requires essentially a diabatization procedure. In this paper, three distinct methods are proposed for such localizedmore » diabatization: (i) a simple projection method, (ii) a more general Pipek-Mezey localization scheme, and (iii) a variant of Boys diabatization. Approaches (i) and (ii) require localized, single-particle Wannier orbitals, while approach (iii) has no such dependence. Lastly, these methods should be very useful for studying energy transfer through solids with ab initio calculations.« less

Multiscale Modeling of UHTC: Thermal Conductivity

NASA Technical Reports Server (NTRS)

Lawson, John W.; Murry, Daw; Squire, Thomas; Bauschlicher, Charles W.

2012-01-01

We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.

Role of Molecular Structure on X-ray Diffraction in Thermotropic Uniaxial and Biaxial Nematic Liquid Crystal Phases

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

Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

2009-08-27

X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

Role of Molecular Structure on X-ray Diffraction in Uniaxial and Biaxial Phases of Thermotropic Liquid Crystals

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

Acharya, Bharat R.; Kang, Shin-Woong; Prasad, Veena

2009-04-29

X-ray diffraction is one of the most definitive methods to determine the structure of condensed matter phases, and it has been applied to unequivocally infer the structures of conventional calamitic and lyotropic liquid crystals. With the advent of bent-core and tetrapodic mesogens and the discovery of the biaxial nematic phase in them, the experimental results require more careful interpretation and analysis. Here, we present ab-initio calculations of X-ray diffraction patterns in the isotropic, uniaxial nematic, and biaxial nematic phases of bent-core mesogens. A simple Meier-Saupe-like molecular distribution function is employed to describe both aligned and unaligned mesophases. The distribution functionmore » is decomposed into two, polar and azimuthal, distribution functions to calculate the effect of the evolution of uniaxial and biaxial nematic orientational order. The calculations provide satisfactory semiquantitative interpretations of experimental results. The calculations presented here should provide a pathway to more refined and quantitative analysis of X-ray diffraction data from the biaxial nematic phase.« less

Theoretical calculations of high-pressure phases of NiF2: An ab initio constant-pressure study

NASA Astrophysics Data System (ADS)

Kürkçü, Cihan; Merdan, Ziya; Öztürk, Hülya

2016-12-01

We have studied the structural properties of the antiferromagnetic NiF2 tetragonal structure with P42/ mnm symmetry using density functional theory (DFT) under rapid hydrostatic pressure up to 400 GPa. For the exchange correlation energy we used the local density approximation (LDA) of Ceperley and Alder (CA). Two phase transformations are successfully observed through the simulations. The structures of XF2-type compounds crystallize in rutile-type structure. NiF2 undergoes phase transformations from the tetragonal rutile-type structure with space group P42/ mnm to orthorhombic CaCl2-type structure with space group Pnnm and from this orthorhombic phase to monoclinic structure with space group C2/ m at 152 GPa and 360 GPa, respectively. These phase changes are also studied by total energy and enthalpy calculations. According to these calculations, we perdict these phase transformations at about 1.85 and 30 GPa.

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

PubMed

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

2014-01-24

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

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

NASA Astrophysics Data System (ADS)

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

2014-01-01

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

Theoretical study on elastic properties of Si2N2O by ab initio calculation

NASA Astrophysics Data System (ADS)

Tsuboi, Seiya; Adachi, Kanta; Nagakubo, Akira; Ogi, Hirotsugu

2018-07-01

The elastic constants of crystalline Si2N2O remain unknown since it was discovered in the 1960s. We determine the nine independent elastic constants of orthorhombic Si2N2O by ab initio calculations. We applied various deformation modes with strains up to ±0.01 to a unit cell, calculated the energy-strain relationships, and deduced all the elastic constants by fitting the harmonic-oscillation function. Our results are as follows: C 11 = 311.1, C 22 = 238.5, C 33 = 317.9, C 44 = 136.1, C 55 = 57.6, C 66 = 73.9, C 12 = 79.6, C 13 = 52.2, and C 23 = 33.6 GPa. Despite the different crystal structures and symmetries, the direction-over-averaged Young’s modulus of Si2N2O is well explained by the nitrogen content and Young’s moduli of α-SiO2 and β-Si3N4. The anisotropy of sound-wave velocity was investigated, and its origin was examined on the basis of the crystallographic structure. The quasi-isotropic plane for the longitudinal-wave propagation was identified.

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions.

PubMed

Hartman, Joshua D; Day, Graeme M; Beran, Gregory J O

2016-11-02

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13 C and 15 N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study.

Enhanced NMR Discrimination of Pharmaceutically Relevant Molecular Crystal Forms through Fragment-Based Ab Initio Chemical Shift Predictions

PubMed Central

2016-01-01

Chemical shift prediction plays an important role in the determination or validation of crystal structures with solid-state nuclear magnetic resonance (NMR) spectroscopy. One of the fundamental theoretical challenges lies in discriminating variations in chemical shifts resulting from different crystallographic environments. Fragment-based electronic structure methods provide an alternative to the widely used plane wave gauge-including projector augmented wave (GIPAW) density functional technique for chemical shift prediction. Fragment methods allow hybrid density functionals to be employed routinely in chemical shift prediction, and we have recently demonstrated appreciable improvements in the accuracy of the predicted shifts when using the hybrid PBE0 functional instead of generalized gradient approximation (GGA) functionals like PBE. Here, we investigate the solid-state 13C and 15N NMR spectra for multiple crystal forms of acetaminophen, phenobarbital, and testosterone. We demonstrate that the use of the hybrid density functional instead of a GGA provides both higher accuracy in the chemical shifts and increased discrimination among the different crystallographic environments. Finally, these results also provide compelling evidence for the transferability of the linear regression parameters mapping predicted chemical shieldings to chemical shifts that were derived in an earlier study. PMID:27829821

Ab-initio studies of the electronic and optical properties of Al2O3:Ti3+ laser crystals

NASA Astrophysics Data System (ADS)

Brik, M. G.

2018-03-01

The structural and electronic properties of pure and Ti3+-doped α-Al2O3 were calculated in the present paper by using the first-principles methods. Special attention has been paid to the location of the Ti3+ states (3d1 electron configuration) in the band gap; the lowest 3d states are at about 4.78 eV above the top of the valence band. The crystal field strength 10Dq at the Ti3+ site was estimated from the density of states diagrams to be about 17,700 cm-1. The structural optimization of the unit cell was also performed at elevated hydrostatic pressure in the range from 0 to 25 GPa. By application of the Murnaghan equation to the obtained results, the bulk modulus of α-Al2O3 was estimated to be 225.69 GPa. In addition, from the analysis of the Ti3+3d density of states the distance dependence of the crystal field strength was found to be described by the following function: 10Dq=61.744/R4.671, where R is expressed in Å and 10Dq in eV.

Influence of Si and N additions on structure and phase stability of Ge(2)Sb(2)Te(5) thin films.

PubMed

Kölpin, Helmut; Music, Denis; Laptyeva, Galyna; Ghadimi, Reza; Merget, Florian; Richter, Silvia; Mykhaylonka, Ruslàn; Mayer, Joachim; Schneider, Jochen M

2009-10-28

The influence of Si and N in Ge(2)Sb(2)Te(5) (space group [Formula: see text]) on structure and phase stability thereof was studied experimentally by thin film growth and characterization as well as theoretically by ab initio calculations. It was found that Si and N most probably accumulate in the amorphous matrix embedding Ge(2)Sb(2)Te(5) grains. The incorporation of Si and N in these samples causes an increase of the crystallization temperature and the formation of finer grains. N is more efficient in increasing the crystallization temperature and in reducing the grain size than Si which can be understood based on the bonding analysis. The incorporation of both Si and N in Ge(2)Sb(2)Te(5) is energetically unfavourable, leading to finer grains and larger crystallization temperatures. While in the case of Si additions no significant changes in bonding are observed, N additions appear to enable the formation of strong Te-N bonds in the amorphous matrix, which are shown to be almost twice as strong as the strongest bonds in unalloyed Ge(2)Sb(2)Te(5).

Electronic structure of Ag7GeS5I superionic compound

NASA Astrophysics Data System (ADS)

Bletskan, Dmytro; Studenyak, Ihor; Bletskan, Mykhailo; Vakulchak, Vasyl

2018-05-01

This paper presents the originally results of ab initio calculations of electronic structure, total and partial densities of electronic states as well as electronic charge density distribution of Ag7GeS5I crystal performed within the density functional theory (DFT) in the local density approximation (LDA) for exchange-correlation potential. According to performed calculations, Ag7GeS5I is the direct-gap semiconductor with the valence band top and the conductivity band bottom in the Γ point of Brillouin zone. The band gap width calculated in the LDA-approximation is Egd = 0.73 eV. The analysis of total and partial densities of electronic states allow us to identify the atomic orbital contributions into the crystal orbitals as well as the formation data of chemical bond in the studied crystal. In the top part of Ag7GeS5I valence band it was revealed the considerable mixing (hybridization) of the occupied d-states of Ag noble metal and the delocalized p-states of sulfur and iodine, which is undoubtedly associated with the covalent character of chemical bond between S, I atoms and noble metal atom.

Insights into the distinct lithiation/sodiation of porous cobalt oxide by in operando synchrotron x-ray techniques and ab initio molecular dynamics simulations

DOE PAGES

Xu, Gui -Liang; Sheng, Tian; Chong, Lina; ...

2017-01-10

Sodium-ion batteries (SIBs) have been considered as one of the promising power source candidates for the stationary storage industries owing to the much lower cost of sodium than lithium. It is well-known that the electrode materials largely determine the energy density of the battery systems. However, recent discoveries on the electrode materials showed that most of them present distinct lithium and sodium storage performance, which is not yet well understood. In this work, we performed a comparative understanding on the structural changes of porous cobalt oxide during its electrochemical lithiation and sodiation process by in operando synchrotron small angel X-raymore » scattering, X-ray diffraction, and X-ray absorption spectroscopy. It was found that compared to the lithiation process, the porous cobalt oxide undergoes less pore structure changes, oxidation state, and local structure changes as well as crystal structure evolution during its sodiation process, which is attributed to the intrinsic low sodiation activity of cobalt oxide as evidenced by ab initio molecular dynamics simulations. Moreover, it was indicated that the sodiation activity of metal sulfides is higher than that of metal oxides, indicating a better candidate for SIBs. Furthermore, such understanding is crucial for future design and improvement of high-performance electrode materials for SIBs.« less

SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang

2017-10-01

As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

Computer Simulation of Energy Parameters and Magnetic Effects in Fe-Si-C Ternary Alloys

NASA Astrophysics Data System (ADS)

Ridnyi, Ya. M.; Mirzoev, A. A.; Mirzaev, D. A.

2018-06-01

The paper presents ab initio simulation with the WIEN2k software package of the equilibrium structure and properties of silicon and carbon atoms dissolved in iron with the body-centered cubic crystal system of the lattice. Silicon and carbon atoms manifest a repulsive interaction in the first two nearest neighbors, in the second neighbor the repulsion being stronger than in the first. In the third and next-nearest neighbors a very weak repulsive interaction occurs and tends to zero with increasing distance between atoms. Silicon and carbon dissolution reduces the magnetic moment of iron atoms.

Structural characterization of a new high-pressure phase of GaAsO4.

PubMed

Santamaría-Pérez, David; Haines, Julien; Amador, Ulises; Morán, Emilio; Vegas, Angel

2006-12-01

As in SiO2 which, at high pressures, undergoes the alpha-quartz-->stishovite transition, GaAsO4 transforms into a dirutile structure at 9 GPa and 1173 K. In 2002, a new GaAsO4 polymorph was found by quenching the compound from 6 GPa and 1273 K to ambient conditions. The powder diagram was indexed on the basis of a hexagonal cell (a=8.2033, c=4.3941 A, V=256.08 A3), but the structure did not correspond to any known structure of other AXO4 compounds. We report here the ab initio crystal structure determination of this hexagonal polymorph from powder data. The new phase is isostructural to beta-MnSb2O6 and it can be described as a lacunary derivative of NiAs with half the octahedral sites being vacant, but it also contains fragments of the rutile-like structure.

First principles investigations of the electronic structure and chemical bonding of U3Si2C2 - A uranium silicide-carbide with the rare [SiC] unit

NASA Astrophysics Data System (ADS)

Matar, S. F.; Pöttgen, R.

2012-10-01

The electronic structure of U3Si2C2, with the rare [SiC] unit is examined from ab initio with an assessment of the properties of chemical bonding. We show that plain GGA fails describing the experimental lattice parameters and the electronic structure. A better agreement with experiment (crystal determination and magnetic properties) is obtained with the GGA + U method and U = 4 eV. The energy-volume equation of state and the set of elastic constants are obtained showing incompressibility along the c-axis with U-C-Si alignment and a brittle material. Bonding of U1 and U2 selectively with Si and C and Si-C bonds are remarkable

Structural and Biophysical Characterization of Cajanus cajan Protease Inhibitor.

PubMed

Shamsi, Tooba Naz; Parveen, Romana; Ahamad, Shahzaib; Fatima, Sadaf

2017-01-01

A large number of studies have proven that Protease inhibitors (PIs), specifically serine protease inhibitors, show immense divergence in regulation of proteolysis by targeting their specific proteases and hence, they play a key role in healthcare. We aimed to access in-vitro anticancer potential of PI from Cajanus cajan (CCPI). Also, crystallization of CCPI was targetted alongwith structure determination and its structure-function relationship. CCPI was purified from Cajanus cajan seeds by chromatographic techniques. The purity and molecular mass was determined by SDS-PAGE. Anticancer potential of CCPI was determined by MTT assay in normal HEK and cancerous A549 cells. The crystallization screening of CCPI was performed by commercially available screens. CCPI sequence was subject to BLASTp with homologous PIs. Progressive multiple alignment was performed using clustalw2 and was modelled using ab initio protocol of I-TASSER. The results showed ~14kDa CCPI was purified in homogeneity. Also, CCPI showed low cytotoxic effects of in HEK i.e., 27% as compared with 51% cytotoxicity in A549 cells. CCPI crystallized at 16°C using 15% PEG 6000 in 0.1M potassium phosphate buffer (pH 6.0) in 2-3weeks as rod or needles visualized as clusters under the microscope. The molecular modelling revealed that it contains 3 beta sheets, 3 beta hairpins, 2 β-bulges, 6 strands, 3 helices, 1helix-helix interaction, 41 β-turns and 27 γ-turns. The results indicate that CCPI may help to treat cancer in vivo aswell. Also, this is the first report on preliminary crystallization and structural studies of CCPI.

Crystal structure and magnetic properties of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' containing residual {alpha}-Fe prepared by low-temperature ammonia nitridation

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

Yamashita, S.; Masubuchi, Y.; Nakazawa, Y.

2012-10-15

Slight enhancement of saturation magnetization to 219 A m{sup 2} kg{sup -1} was observed from 199 A m{sup 2} kg{sup -1} for the original {alpha}-Fe on the intermediate nitrided mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' with residual {alpha}-Fe among the low temperature ammonia nitridation products under 5 T magnetic field at room temperature. The value changed not linearly against the yield as had been expected. Crystal structure refinement indicated that the phase similar to {alpha} Prime Prime -Fe{sub 16}N{sub 2} had deviations on its lattice constants and positional parameters, compared to previously reported values for {alpha} Prime Primemore » -Fe{sub 16}N{sub 2}. Spin-polarized total energy calculations were performed using the projector-augmented wave method as implemented in the Vienna ab-initio simulation package (VASP) to calculate magnetic moment on the refined crystal structure of the intermediate '{alpha} Prime Prime -Fe{sub 16}N{sub 2}'. The calculations supported the observed magnetization enhancement in the intermediate nitridation product. - Graphical abstract: Crystal structural parameters slightly change in the intermediate nitrided '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' from those in {alpha} Prime Prime -Fe{sub 16}N{sub 2} to show the magnetization maxima in the mixture of '{alpha} Prime Prime -Fe{sub 16}N{sub 2}' and the residual {alpha}-F. Highlights: Black-Right-Pointing-Pointer Larger magnetization was observed than the value of Fe{sub 16}N{sub 2} on its intermediate nitrided mixture with residual {alpha}-Fe. Black-Right-Pointing-Pointer The enhancement was related to the crystal structural deviation from Fe{sub 16}N{sub 2} on the intermediate nitride. Black-Right-Pointing-Pointer It was supported by spin-polarized total energy calculation using the deviated structure.« less

The LPO Iron Pattern beneath the Earth's Inner Core Boundary

NASA Astrophysics Data System (ADS)

Mattesini, Maurizio; Belonoshko, Anatoly; Tkalčić, Hrvoje

2017-04-01

An Earth's inner core surface pattern for the iron Lattice Preferred Orientation (LPO) has been addressed for various iron crystal polymorphs. The geographical distribution of the amount of crystal alienation was achieved by bridging high-quality inner core probing seismic data [PKP(bc-df)] together with ab initio computed elastic constants. We show that the proposed topographic crystal alignment may be used as a boundary condition for dynamo simulations, providing an additional way to discriminate in between different and, often controversial, geodynamical scenarios.

The LPO Iron Pattern beneath the Earth's Inner Core Boundary

NASA Astrophysics Data System (ADS)

Mattesini, M.; Tkalcic, H.; Belonoshko, A. B.; Buforn, E.; Udias, A.

2015-12-01

An Earth's inner core surface pattern for the iron Lattice Preferred Orientation (LPO) has been addressed for various iron crystal polymorphs. The geographical distribution of the amount of crystal alienation was achieved by bridging high-quality inner core probing seismic data [PKP(bc-df)] together with ab initio computed elastic constants. We show that the proposed topographic crystal alignment may be used as a boundary condition for dynamo simulations, providing an additional way to discriminate in between different and, often controversial, geodynamical scenarios.

Postaragonite phases of CaCO3 at lower mantle pressures

NASA Astrophysics Data System (ADS)

Smith, Dean; Lawler, Keith V.; Martinez-Canales, Miguel; Daykin, Austin W.; Fussell, Zachary; Smith, G. Alexander; Childs, Christian; Smith, Jesse S.; Pickard, Chris J.; Salamat, Ashkan

2018-01-01

The stability, structure, and properties of carbonate minerals at lower mantle conditions have significant impact on our understanding of the global carbon cycle and the composition of the interior of the Earth. In recent years there has been significant interest in the behavior of carbonates at lower mantle conditions, specifically in their carbon hybridization, which has relevance for the storage of carbon within the deep mantle. Using high-pressure synchrotron x-ray diffraction in a diamond anvil cell coupled with direct laser heating of CaCO3 using a CO2 laser, we identify a crystalline phase of the material above 40 GPa—corresponding to a lower mantle depth of around 1000 km—which has first been predicted by ab initio structure predictions. The observed s p2 carbon hybridized species at 40 GPa is monoclinic with P 21/c symmetry and is stable up to 50 GPa, above which it transforms into a structure which cannot be indexed by existing known phases. A combination of ab initio random structure search (AIRSS) and quasiharmonic approximation (QHA) calculations are used to re-explore the relative phase stabilities of the rich phase diagram of CaCO3. Nudged elastic band (NEB) calculations are used to investigate the reaction mechanisms between relevant crystal phases of CaCO3 and we postulate that the mineral is capable of undergoing s p2-s p3 hybridization change purely in the P 21/c structure—forgoing the accepted postaragonite P m m n structure.

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

PubMed

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

2013-07-30

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

Improvement of the ab initio embedded cluster method for luminescence properties of doped materials by taking into account impurity induced distortions: the example of Y2O3:Bi(3+).

PubMed

Réal, Florent; Ordejón, Belén; Vallet, Valérie; Flament, Jean-Pierre; Schamps, Joël

2009-11-21

New ab initio embedded-cluster calculations devoted to simulating the electronic spectroscopy of Bi(3+) impurities in Y(2)O(3) sesquioxide for substitutions in either S(6) or C(2) cationic sites have been carried out taking special care of the quality of the environment. A considerable quantitative improvement with respect to previous studies [F. Real et al. J. Chem. Phys. 125, 174709 (2006); F. Real et al. J. Chem. Phys. 127, 104705 (2007)] is brought by using environments of the impurities obtained via supercell techniques that allow the whole (pseudo) crystal to relax (WCR geometries) instead of environments obtained from local relaxation of the first coordination shell only (FSR geometries) within the embedded cluster approach, as was done previously. In particular the uniform 0.4 eV discrepancy of absorption energies found previously with FSR environments disappears completely when the new WCR environments of the impurities are employed. Moreover emission energies and hence Stokes shifts are in much better agreement with experiment. These decisive improvements are mainly due to a lowering of the local point-group symmetry (S(6)-->C(3) and C(2)-->C(1)) when relaxing the geometry of the emitting (lowest) triplet state. This symmetry lowering was not observed in FSR embedded cluster relaxations because the crystal field of the embedding frozen at the genuine pure crystal positions seems to be a more important driving force than the interactions within the cluster, thus constraining the overall symmetry of the system. Variations of the doping rate are found to have negligible influence on the spectra. In conclusion, the use of WCR environments may be crucial to render the structural distortions occurring in a doped crystal and it may help to significantly improve the embedded-cluster methodology to reach the quantitative accuracy necessary to interpret and predict luminescence properties of doped materials of this type.

Theoretical investigation of the structural, elastic, electronic and optical properties of the ternary indium sulfide layered structures AInS2 (A = K, Rb and Cs)

NASA Astrophysics Data System (ADS)

Bouchenafa, M.; Sidoumou, M.; Halit, M.; Benmakhlouf, A.; Bouhemadou, A.; Maabed, S.; Bentabet, A.; Bin-Omran, S.

2018-02-01

Ab initio calculations were performed to investigate the structural, elastic, electronic and optical properties of the ternary layered systems AInS2 (A = K, Rb and Cs). The calculated structural parameters are in good agreement with the existing experimental data. Analysis of the electronic band structure shows that the three studied materials are direct band-gap semiconductors. Density of states, charge transfers and charge density distribution maps were computed and analyzed. Numerical estimations of the elastic moduli and their related properties for single-crystal and polycrystalline aggregates were predicted. The optical properties were calculated for incident radiation polarized along the [100], [010] and [001] crystallographic directions. The studied materials exhibit a noticeable anisotropic behaviour in the elastic and optical properties, which is expected due to the symmetry and the layered nature of these compounds.

Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes▿

PubMed Central

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

Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

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

Kemege, Kyle E.; Hickey, John M.; Lovell, 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)more » 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.« less

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

PubMed

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

2014-07-03

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

First Principles Predictions of the Structure and Function of G-Protein-Coupled Receptors: Validation for Bovine Rhodopsin

PubMed Central

Trabanino, Rene J.; Hall, Spencer E.; Vaidehi, Nagarajan; Floriano, Wely B.; Kam, Victor W. T.; Goddard, William A.

2004-01-01

G-protein-coupled receptors (GPCRs) are involved in cell communication processes and with mediating such senses as vision, smell, taste, and pain. They constitute a prominent superfamily of drug targets, but an atomic-level structure is available for only one GPCR, bovine rhodopsin, making it difficult to use structure-based methods to design receptor-specific drugs. We have developed the MembStruk first principles computational method for predicting the three-dimensional structure of GPCRs. In this article we validate the MembStruk procedure by comparing its predictions with the high-resolution crystal structure of bovine rhodopsin. The crystal structure of bovine rhodopsin has the second extracellular (EC-II) loop closed over the transmembrane regions by making a disulfide linkage between Cys-110 and Cys-187, but we speculate that opening this loop may play a role in the activation process of the receptor through the cysteine linkage with helix 3. Consequently we predicted two structures for bovine rhodopsin from the primary sequence (with no input from the crystal structure)—one with the EC-II loop closed as in the crystal structure, and the other with the EC-II loop open. The MembStruk-predicted structure of bovine rhodopsin with the closed EC-II loop deviates from the crystal by 2.84 Å coordinate root mean-square (CRMS) in the transmembrane region main-chain atoms. The predicted three-dimensional structures for other GPCRs can be validated only by predicting binding sites and energies for various ligands. For such predictions we developed the HierDock first principles computational method. We validate HierDock by predicting the binding site of 11-cis-retinal in the crystal structure of bovine rhodopsin. Scanning the whole protein without using any prior knowledge of the binding site, we find that the best scoring conformation in rhodopsin is 1.1 Å CRMS from the crystal structure for the ligand atoms. This predicted conformation has the carbonyl O only 2.82 Å from the N of Lys-296. Making this Schiff base bond and minimizing leads to a final conformation only 0.62 Å CRMS from the crystal structure. We also used HierDock to predict the binding site of 11-cis-retinal in the MembStruk-predicted structure of bovine rhodopsin (closed loop). Scanning the whole protein structure leads to a structure in which the carbonyl O is only 2.85 Å from the N of Lys-296. Making this Schiff base bond and minimizing leads to a final conformation only 2.92 Å CRMS from the crystal structure. The good agreement of the ab initio-predicted protein structures and ligand binding site with experiment validates the use of the MembStruk and HierDock first principles' methods. Since these methods are generic and applicable to any GPCR, they should be useful in predicting the structures of other GPCRs and the binding site of ligands to these proteins. PMID:15041637

Supramolecular architecture based on [Fe(CN)6]3- metallotectons and melaminium synthons

NASA Astrophysics Data System (ADS)

Krichen, Firas; Walha, Siwar; Lhoste, Jérôme; Bulou, Alain; Kabadou, Ahlem; Goutenoire, François

2017-10-01

Assembly involving [Fe(CN)6]3- metallotectons as building units and melaminium organic cation has been envisioned in order to elaborate a hybrid supramolecular based on ionic H-bonds with formula {(H-mel)4[Fe(CN)6]Cl} (H-mel+: melaminium cation). The compound has been prepared by diffusion method and characterized by single-crystal X-ray diffraction, EDX analysis, and Raman-IR spectroscopies with assignment from ab initio calculations. The melaminium exhibit self cationic coupling with cyclic hydrogen bonds to give a one dimensional {[H-mel]+}∝ synthon. Therefore, these cationic ribbons are inter-linked via hydrogen bonds by the anionic tectons [Fe(CN)6]3- and chlorine anion resulting on a 3D network. Molecular hirshfeld surfaces revealed that the crystal structure has been supported mainly by Nsbnd H⋯N and Nsbnd H⋯Cl intermolecular Hydrogen bonds and by favoured C⋯C and C⋯N weak interactions.

Crystal-defect-induced facet-dependent electrocatalytic activity of 3D gold nanoflowers for the selective nanomolar detection of ascorbic acid.

PubMed

De, Sandip Kumar; Mondal, Subrata; Sen, Pintu; Pal, Uttam; Pathak, Biswarup; Rawat, Kuber Singh; Bardhan, Munmun; Bhattacharya, Maireyee; Satpati, Biswarup; De, Amitabha; Senapati, Dulal

2018-06-14

Understanding and exploring the decisive factors responsible for superlative catalytic efficiency is necessary to formulate active electrode materials for improved electrocatalysis and high-throughput sensing. This research demonstrates the ability of bud-shaped gold nanoflowers (AuNFs), intermediates in the bud-to-blossom gold nanoflower synthesis, to offer remarkable electrocatalytic efficiency in the oxidation of ascorbic acid (AA) at nanomolar concentrations. Multicomponent sensing in a single potential sweep is measured using differential pulse voltammetry while the kinetic parameters are estimated using electrochemical impedance spectroscopy. The outstanding catalytic activity of bud-structured AuNF [iAuNFp(Bud)/iGCp ≅ 100] compared with other bud-to-blossom intermediate nanostructures is explained by studying their structural transitions, charge distributions, crystalline patterns, and intrinsic irregularities/defects. Detailed microscopic analysis shows that density of crystal defects, such as edges, terraces, steps, ledges, kinks, and dislocation, plays a major role in producing the high catalytic efficiency. An associated ab initio simulation provides necessary support for the projected role of different crystal facets as selective catalytic sites. Density functional theory corroborates the appearance of inter- and intra-molecular hydrogen bonding within AA molecules to control the resultant fingerprint peak potentials at variable concentrations. Bud-structured AuNF facilitates AA detection at nanomolar levels in a multicomponent pathological sample.

Probing the Unique Role of Gallium in Amorphous Oxide Semiconductors through Structure-Property Relationships

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

Moffitt, Stephanie L.; Zhu, Qimin; Ma, Qing

This study explores the unique role of Ga in amorphous (a-) In[BOND]Ga[BOND]O oxide semiconductors through combined theory and experiment. It reveals substitutional effects that have not previously been attributed to Ga, and that are investigated by examining how Ga influences structure–property relationships in a series of pulsed laser deposited a-In[BOND]Ga[BOND]O thin films. Element-specific structural studies (X-ray absorption and anomalous scattering) show good agreement with the results of ab initio molecular dynamics simulations. This structural knowledge is used to understand the results of air-annealing and Hall effect electrical measurements. The crystallization temperature of a-IO is shown to increase by as muchmore » as 325 °C on substituting Ga for In. This increased thermal stability is understood on the basis of the large changes in local structure that Ga undergoes, as compared to In, during crystallization. Hall measurements reveal an initial sharp drop in both carrier concentration and mobility with increasing Ga incorporation, which moderates at >20 at% Ga content. This decline in both the carrier concentration and mobility with increasing Ga is attributed to dilution of the charge-carrying In[BOND]O matrix and to increased structural disorder. The latter effect saturates at high at% Ga.« less

First- and second-order Raman scattering from MoTe2 single crystal

NASA Astrophysics Data System (ADS)

Caramazza, Simone; Collina, Arianna; Stellino, Elena; Ripanti, Francesca; Dore, Paolo; Postorino, Paolo

2018-02-01

We report on Raman experiments performed on a MoTe2 single crystal. The system belongs to the wide family of transition metal dichalcogenides which includes several of the most interesting two-dimensional materials for both basic and applied physics. Measurements were performed in the standard basal plane configuration, by placing the ab plane of the crystal perpendicular to the wave vector k i of the incident beam to explore the in-plane vibrational modes, and in the edge plane configuration with k i perpendicular to the crystal c axis, thus mainly exciting out-of-plane modes. For both configurations we performed a polarization-dependent study of the first-order Raman components and detailed computation of the corresponding selection rules. We were thus able to provide a complete assignment of the observed first-order Raman peaks, in agreement with previous literature results. A thorough analysis of the second-order Raman bands, as observed in both basal and edge plane configurations, provides new information and allows a precise assignment of these spectral structures. In particular, we have observed and assigned Raman active modes of the M point of the Brillouin zone previously predicted by ab initio calculations but never previously measured.

Prediction of weak topological insulators in layered semiconductors.

PubMed

Yan, Binghai; Müchler, Lukas; Felser, Claudia

2012-09-14

We report the discovery of weak topological insulators by ab initio calculations in a honeycomb lattice. We propose a structure with an odd number of layers in the primitive unit cell as a prerequisite for forming weak topological insulators. Here, the single-layered KHgSb is the most suitable candidate for its large bulk energy gap of 0.24 eV. Its side surface hosts metallic surface states, forming two anisotropic Dirac cones. Although the stacking of even-layered structures leads to trivial insulators, the structures can host a quantum spin Hall layer with a large bulk gap, if an additional single layer exists as a stacking fault in the crystal. The reported honeycomb compounds can serve as prototypes to aid in the finding of new weak topological insulators in layered small-gap semiconductors.

Enhancing AFLOW Visualization using Jmol

NASA Astrophysics Data System (ADS)

Lanasa, Jacob; New, Elizabeth; Stefek, Patrik; Honaker, Brigette; Hanson, Robert; Aflow Collaboration

The AFLOW library is a database of theoretical solid-state structures and calculated properties created using high-throughput ab initio calculations. Jmol is a Java-based program capable of visualizing and analyzing complex molecular structures and energy landscapes. In collaboration with the AFLOW consortium, our goal is the enhancement of the AFLOWLIB database through the extension of Jmol's capabilities in the area of materials science. Modifications made to Jmol include the ability to read and visualize AFLOW binary alloy data files, the ability to extract from these files information using Jmol scripting macros that can be utilized in the creation of interactive web-based convex hull graphs, the capability to identify and classify local atomic environments by symmetry, and the ability to search one or more related crystal structures for atomic environments using a novel extension of inorganic polyhedron-based SMILES strings

Discovery of a Superconducting Cu-Bi Intermetallic Compound by High-Pressure Synthesis

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

Clarke, Samantha M.; Walsh, James P. S.; Amsler, Maximilian

A new intermetallic compound, the first to be structurally identified in the Cu-Bi binary system, is reported. This compound is accessed by high-pressure reaction of the elements. Its detailed characterization, physical property measurements, and ab initio calculations are described. The commensurate crystal structure of Cu 11Bi 7 is a unique variation of the NiAs structure type. Temperature-dependent electrical resistivity and heat capacity measurements reveal a bulk superconducting transition at T c=1.36 K. Density functional theory calculations further demonstrate that Cu 11Bi 7 can be stabilized (relative to decomposition into the elements) at high pressure and temperature. These results highlight themore » ability of high-pressure syntheses to allow for inroads into heretofore-undiscovered intermetallic systems for which no thermodynamically stable binaries are known.« less

Structural analysis of LaVO3 thin films under epitaxial strain

NASA Astrophysics Data System (ADS)

Meley, H.; Karandeep, Oberson, L.; de Bruijckere, J.; Alexander, D. T. L.; Triscone, J.-M.; Ghosez, Ph.; Gariglio, S.

2018-04-01

Rare earth vanadate perovskites exhibit a phase diagram in which two different types of structural distortions coexist: the strongest, the rotation of the oxygen octahedra, comes from the small tolerance factor of the perovskite cell (t = 0.88 for LaVO3) and the smaller one comes from inter-site d-orbital interactions manifesting as a cooperative Jahn-Teller effect. Epitaxial strain acts on octahedral rotations and crystal field symmetry to alter this complex lattice-orbit coupling. In this study, LaVO3 thin film structures have been investigated by X-ray diffraction and scanning transmission electron microscopy. The analysis shows two different orientations of octahedral tilt patterns, as well as two distinct temperature behaviors, for compressive and tensile film strain states. Ab initio calculations capture the strain effect on the tilt pattern orientation in agreement with experimental data.

An ab initio-based Er–He interatomic potential in hcp Er

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

Yang, Li; ye, Yeting; Fan, K. M.

2014-09-01

We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations.more » The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.« less

Thermodynamic stability and structure of cuprous chloride surfaces: a DFT investigation.

PubMed

Suleiman, Ibrahim A; Radny, Marian W; Gladys, Michael J; Smith, Phillip V; Mackie, John C; Kennedy, Eric M; Dlugogorski, Bogdan Z

2015-03-14

Density functional theory together with ab initio atomistic thermodynamics has been utilized to study the structures and stabilities of the low index CuCl surfaces. It is shown that the Cl-terminated structures are more stable than the Cu-terminated configurations, and that the defective CuCl(110)-Cu structure is more stable than the stoichiometric CuCl(110) surface. The equilibrium shape of a cuprous chloride nanostructure terminated by low-index CuCl surfaces has also been predicted using a Wulff construction. It was found that the (110) facets dominate at low chlorine concentration. As the chlorine concentration is increased, however, the contributions of the (100) and (111) facets to the Wulff construction also increase giving the crystal a semi-prism shape. At high chlorine concentration, and close to the rich limit, the (111) facets were found to be the only contributors to the Wulff construction, resulting in prismatic nanocrystals.

Structural investigation of the (010) surface of the Al13 Fe4 catalyst.

PubMed

Ledieu, J; Gaudry, É; Loli, L N Serkovic; Villaseca, S Alarcón; de Weerd, M-C; Hahne, M; Gille, P; Grin, Y; Dubois, J-M; Fournée, V

2013-02-15

We have investigated the structure of the Al(13)Fe(4)(010) surface using both experimental and ab initio computational methods. The results indicate that the topmost surface layers correspond to incomplete puckered (P) planes present in the bulk crystal structure. The main building block of the corrugated termination consists of two adjacent pentagons of Al atoms, each centered by a protruding Fe atom. These motifs are interconnected via additional Al atoms referred to as "glue" atoms which partially desorb above 873 K. The surface structure of lower atomic density compared to the bulk P plane is explained by a strong Fe-Al-Fe covalent polar interaction that preserves intact clusters at the surface. The proposed surface model with identified Fe-containing atomic ensembles could explain the Al(13)Fe(4) catalytic properties recently reported in line with the site-isolation concept [M. Armbrüster et al., Nat. Mater. 11, 690 (2012)].

Ab-initio study of electronic, magnetic and thermoelectric behaviors of LiV2O4 and LiCr2O4 using modified Becke-Johson (mBJ) potential

NASA Astrophysics Data System (ADS)

Ali, Saima; Rashid, Muhammad; Hassan, M.; Noor, N. A.; Mahmood, Q.; Laref, A.; Haq, Bakhtiar Ul

2018-05-01

Owing to the large energy storage capacity and higher working voltage, the spinel oxides LiV2O4 and LiCr2O4, have remained under intense research attention for utilization as electrode materials in lithium-ion batteries. In this study, we explore the half-metallic nature and thermoelectric response in both LiV2O4 and LiCr2O4 spinel oxides using ab-initio density functional theory (DFT) based computations. The ground-state energies of these compounds have been studied at the optimized structural parameters in the ferromagnetic phase. In order to obtain a correct picture of the electronic structure and magnetic properties, the modified Becke-Johnson (mBJ) potential is applied to compute the electronic structures. The half-metallic behavior is confirmed by the spin-polarized electronic band structures and density of state plots. The magnetic nature is elucidated by computing the John-Teller energy, direct and indirect exchange and crystal field splitting energies. Our computations indicate strong hybridization decreasing the V/Cr site magnetic moments and increasing magnetic momenta at the nonmagnetic atomic sites. We also present the computed parameters significant for expressing the thermoelectric response, which are electrical conductivity, thermal conductivity, See-beck coefficient and power factor. The computed properties are of immense interest owing to the potential spintronics and Li-ion battery applications of the studied spinel materials.

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

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

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

2015-08-14

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

(CaO)nIrO2 (n = 1, 2, 4) family: Chemical scissors effects of CaO on structural characteristics correlated to physical properties. Ab initio study

NASA Astrophysics Data System (ADS)

Matar, Samir F.; Etourneau, Jean

2017-11-01

Based on crystal chemistry analysis within Ca-Ir-O ternary, the generic (CaO)nIrO2 formula leading to CaIrO3 for n = 1, Ca2IrO4 for n = 2 and Ca4IrO6 for n = 4 actual chemical compounds show significant structural changes regarding the spatial arrangement of IrO6 octahedra whereby increasing amounts of CaO act as 'chemical scissor' decreasing the dimensionality of stacking octahedra from 3D (IrO2) to 0D (Ca4IrO6). This is accompanied by changes in the electronic structure investigated within density functional theory. Such changes are particularly exhibited by linear increase of Ir density of states at the Fermi level revealing increasing localization of d states with crystal field effects. Eventually only for Ca4IrO6 a magnetic instability occurs in non magnetic configuration. Spin polarized calculations lead to development of small magnitude but finite magnetization on Ir with M 0.50 μB totally polarized along minority spin channel ↓.

Positron annihilation 2D-ACAR study of semi-coherent Li nanoclusters in MgO( 1 0 0 ) and MgO( 1 1 0 )

NASA Astrophysics Data System (ADS)

Falub, C. V.; Mijnarends, P. E.; Eijt, S. W. H.; van Huis, M. A.; van Veen, A.; Schut, H.

2002-05-01

Depth selective positron annihilation two-dimensional angular correlation of annihilation radiation (2D-ACAR) is used to determine the electronic structure of Li nanoclusters formed by implantation of 10 16 cm -26Li ions (with an energy of 30 keV) in MgO(1 0 0) and (1 1 0) crystals, and subsequently annealed at 950 K. The 2D-ACAR spectra of Li-implanted MgO obtained with 4 keV positrons reveal the semi-coherent ordering state of the embedded metallic Li nanoclusters. The results agree with ab initio Korringa-Kohn-Rostoker calculations.

Molecular Fingerprints in the Electronic Properties of Crystalline Organic Semiconductors: From Experiment to Theory

NASA Astrophysics Data System (ADS)

Ciuchi, S.; Hatch, R. C.; Höchst, H.; Faber, C.; Blase, X.; Fratini, S.

2012-06-01

By comparing photoemission spectroscopy with a nonperturbative dynamical mean field theory extension to many-body ab initio calculations, we show in the prominent case of pentacene crystals that an excellent agreement with experiment for the bandwidth, dispersion, and lifetime of the hole carrier bands can be achieved in organic semiconductors, provided that one properly accounts for the coupling to molecular vibrational modes and the presence of disorder. Our findings rationalize the growing experimental evidence that even the best band structure theories based on a many-body treatment of electronic interactions cannot reproduce the experimental photoemission data in this important class of materials.

Structural and Biophysical Characterization of Cajanus cajan Protease Inhibitor

PubMed Central

Shamsi, Tooba Naz; Parveen, Romana; Ahamad, Shahzaib; Fatima, Sadaf

2017-01-01

Context: A large number of studies have proven that Protease inhibitors (PIs), specifically serine protease inhibitors, show immense divergence in regulation of proteolysis by targeting their specific proteases and hence, they play a key role in healthcare. Objective: We aimed to access in-vitro anticancer potential of PI from Cajanus cajan (CCPI). Also, crystallization of CCPI was targetted alongwith structure determination and its structure-function relationship. Materials and Methods: CCPI was purified from Cajanus cajan seeds by chromatographic techniques. The purity and molecular mass was determined by SDS-PAGE. Anticancer potential of CCPI was determined by MTT assay in normal HEK and cancerous A549 cells. The crystallization screening of CCPI was performed by commercially available screens. CCPI sequence was subject to BLASTp with homologous PIs. Progressive multiple alignment was performed using clustalw2 and was modelled using ab initio protocol of I-TASSER. Results: The results showed ~14kDa CCPI was purified in homogeneity. Also, CCPI showed low cytotoxic effects of in HEK i.e., 27% as compared with 51% cytotoxicity in A549 cells. CCPI crystallized at 16°C using 15% PEG 6000 in 0.1M potassium phosphate buffer (pH 6.0) in 2-3weeks as rod or needles visualized as clusters under the microscope. The molecular modelling revealed that it contains 3 beta sheets, 3 beta hairpins, 2 β-bulges, 6 strands, 3 helices, 1helix-helix interaction, 41 β-turns and 27 γ-turns. Discussion and Conclusion: The results indicate that CCPI may help to treat cancer in vivo aswell. Also, this is the first report on preliminary crystallization and structural studies of CCPI. PMID:28781485

Comparative study of elastic constantd of α-, β- and Cubic- silicon nitride

NASA Astrophysics Data System (ADS)

Yao, Hongzhi; Ouyang, Lizhi; Ching, Wai-Yim

2003-03-01

Silicon nitride is an important structural ceramic and dielectric insulator. Recently, the new high pressure cubic phase of silicon nitride in spinel structure has attracted a lot of attention.^[1] We have carried out a detailed ab-initio calculation of all independent elastic constants for all three phases of Si_3N4 by using the Vienna Ab-initio Simulation Package (VASP) in both LDA and GGA approxmations. The results for β-Si_3N4 are in reasonable agreement with a experimental measurement on single crystal samples.^[2] For cubic-Si_3N4 , The three independent elastic constants are predicted to be C_11 = 504.16 GPa, C_12 = 176.66 GPa, C_44 = 326.65 GPa and a bulk modulus B = 286 GPa. This value is very close to the experimental value of 300 GPa.^[1] All these results will be compared with those obtained by using the OLCAO method based on localized orbital approach.^[3] [1]. Wai-Yim Ching, Yong-Nian Xu, Jukian D. Gale, and Manfred Ruhle, J. Am. Ceram. Soc. 81, 3189 (1998) [2]. R. Vogelgesang, M. Grimsditch, and J. S. Wallace, Appl. Phys. Lett. 76, 8 (2000) [3]. W.Y.Ching, Lizhi Ouyang, and Julian D. Gale, Phys. Rev. B61, 13, (2000)

Multiscale Modeling of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2: Application to Lattice Thermal Conductivity

NASA Technical Reports Server (NTRS)

Lawson, John W.; Daw, Murray S.; Squire, Thomas H.; Bauschlicher, Charles W.

2012-01-01

We are developing a multiscale framework in computational modeling for the ultra high temperature ceramics (UHTC) ZrB2 and HfB2. These materials are characterized by high melting point, good strength, and reasonable oxidation resistance. They are candidate materials for a number of applications in extreme environments including sharp leading edges of hypersonic aircraft. In particular, we used a combination of ab initio methods, atomistic simulations and continuum computations to obtain insights into fundamental properties of these materials. Ab initio methods were used to compute basic structural, mechanical and thermal properties. From these results, a database was constructed to fit a Tersoff style interatomic potential suitable for atomistic simulations. These potentials were used to evaluate the lattice thermal conductivity of single crystals and the thermal resistance of simple grain boundaries. Finite element method (FEM) computations using atomistic results as inputs were performed with meshes constructed on SEM images thereby modeling the realistic microstructure. These continuum computations showed the reduction in thermal conductivity due to the grain boundary network.

Ab Initio Molecular Dynamics and Lattice Dynamics-Based Force Field for Modeling Hexagonal Boron Nitride in Mechanical and Interfacial Applications.

PubMed

Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel

2018-04-05

Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.

An ab initio study on the structural, electronic and mechanical properties of quaternary full-Heusler alloys FeMnCrSn and FeMnCrSb

NASA Astrophysics Data System (ADS)

Erkişi, Aytaç

2018-06-01

The quaternary full Heusler alloys FeMnCrSn and FeMnCrSb, which have face-centred cubic (FCC) crystal structure and conform to ? space group with 216 space number, have been investigated using Generalised Gradient Approximation (GGA) in the Density Functional Theory (DFT) as implemented in VASP (Vienna Ab initio Simulation Package) software. These alloys are considered in ferromagnetic (FM) order. After the investigation of structural stability of these alloys, their mechanical and thermal properties and also electronic band structures have been examined. The calculated spin-polarised electronic band structures and total electronic density of states (DOS) within GGA approximation show that these alloys can exhibit both metallic and half-metallic characters in different structural phases. The calculated formation enthalpies and the plotted energy-volume graphs show that Type-III phase is most stable structural phase for these materials. Also, FeMnCrSb alloy in Type-I/Type-III phases and FeMnCrSn alloy in Type-III phase show half-metallic behaviour with integer total magnetic moments almost 2 and 1 μB per formula unit, respectively, since there are band gaps observed in spin-down states, whereas they have metallic behaviour in majority bands. Other structural phases of both systems are also metallic. Moreover, the calculated elastic constants and the estimated anisotropy shear factors indicate that these materials are stable mechanically in all of three phases except FeMnCrSn in Type-I phase that does not satisfy Born stability criteria in this phase and have high anisotropic behaviour.

Polymorphism in Strontium Tungstate SrWO4 under Quasi-Hydrostatic Compression.

PubMed

Santamaria-Perez, David; Errandonea, Daniel; Rodriguez-Hernandez, Placida; Muñoz, Alfonso; Lacomba-Perales, Raul; Polian, Alain; Meng, Yue

2016-10-03

The structural and vibrational properties of SrWO 4 have been studied experimentally up to 27 and 46 GPa, respectively, by angle-dispersive synchrotron X-ray diffraction and Raman spectroscopy measurements as well as using ab initio calculations. The existence of four polymorphs upon quasi-hydrostatic compression is reported. The three phase transitions were found at 11.5, 19.0, and 39.5 GPa. The ambient-pressure SrWO 4 tetragonal scheelite-type structure (S.G. I4 1 /a) undergoes a transition to a monoclinic fergusonite-type structure (S.G. I2/a) at 11.5 GPa with a 1.5% volume decrease. Subsequently, at 19.0 GPa, another structural transformation takes place. Our calculations indicate two possible post-fergusonite phases, one monoclinic and the other orthorhombic. In the diffraction experiments, we observed the theoretically predicted monoclinic LaTaO 4 -type phase coexisting with the fergusonite-type phase up to 27 GPa. The coexistence of the two phases and the large volume collapse at the transition confirm a kinetic hindrance typical of first-order phase transitions. Significant changes in Raman spectra suggest a third pressure-induced transition at 39.5 GPa. The conclusions extracted from the experiments are complemented and supported by ab initio calculations. Our data provides insight into the structural mechanism of the first transition, with the formation of two additional W-O contacts. The fergusonite-type phase can be therefore considered as a structural bridge between the scheelite structure, composed of [WO 4 ] tetrahedra, and the new higher pressure phases, which contain [WO 6 ] octahedra. All the observed phases are compatible with the high-pressure structural systematics predicted for ABO 4 compounds using crystal-chemistry arguments such as the diagram proposed by Bastide.

Low-Dimensional Material: Structure-Property Relationship and Applications in Energy and Environmental Engineering

NASA Astrophysics Data System (ADS)

Xiao, Hang

In the past several decades, low-dimensional materials (0D materials, 1D materials and 2D materials) have attracted much interest from both the experimental and theoretical points of view. Because of the quantum confinement effect, low-dimensional materials have exhibited a kaleidoscope of fascinating phenomena and unusual physical and chemical properties, shedding light on many novel applications. Despite the enormous success has been achieved in the research of low-dimensional materials, there are three fundamental challenges of research in low-dimensional materials: 1) Develop new computational tools to accurately describe the properties of low-dimensional materials with low computational cost. 2) Predict and synthesize new low-dimensional materials with novel properties. 3) Reveal new phenomenon induced by the interaction between low-dimensional materials and the surrounding environment. In this thesis, atomistic modelling tools have been applied to address these challenges. We first developed ReaxFF parameters for phosphorus and hydrogen to give an accurate description of the chemical and mechanical properties of pristine and defected black phosphorene. ReaxFF for P/H is transferable to a wide range of phosphorus and hydrogen containing systems including bulk black phosphorus, blue phosphorene, edge-hydrogenated phosphorene, phosphorus clusters and phosphorus hydride molecules. The potential parameters were obtained by conducting global optimization with respect to a set of reference data generated by extensive ab initio calculations. We extended ReaxFF by adding a 60° correction term which significantly improved the description of phosphorus clusters. Emphasis was placed on the mechanical response of black phosphorene with different types of defects. Compared to the nonreactive SW potential of phosphorene, ReaxFF for P/H systems provides a significant improvement in describing the mechanical properties of the pristine and defected black phosphorene, as well as the thermal stability of phosphorene nanotubes. A counterintuitive phenomenon was observed that single vacancies weaken the black phosphorene more than double vacancies with higher formation energy. Our results also showed that the mechanical response of black phosphorene is more sensitive to defects in the zigzag direction than that in the armchair direction. Since ReaxFF allows straightforward extensions to the heterogeneous systems, such as oxides, nitrides, the proposed ReaxFF parameters for P/H systems also underpinned the reactive force field description of heterogeneous P systems, including P-containing 2D van der Waals heterostructures, oxides, etc. Based on the evolutionary algorithm driven structural search, we proposed a new stable trisulfur dinitride (S3N2) 2D crystal that is a covalent network composed solely of S-N sigma bonds. S3N 2 crystal is dynamically, thermally and chemically stable as confirmed by the computed phonon spectrum and ab initio molecular dynamics simulations. GW calculations showed that the 2D S3N2 crystal is a wide, direct band-gap (3.92 eV) semiconductor with a small hole effective mass. The anisotropic optical response of 2D S3N 2 crystal was revealed by GW-BSE calculations. Our result not only marked the prediction of the first 2D crystal composed of nitrogen and sulfur, but also underpinned potential innovations in 2D electronics, optoelectronics, etc. Inspired by the discovery of S3N2 2D crystal, we proposed a new 2D crystal, diphosphorus trisulfide (P2S3), based on the extensive evolutionary algorithm driven structural search. The 2D P2S3 crystal was confirmed to be dynamically, thermally and chemically stable by the computed phonon spectrum and ab initio molecular dynamics simulations. This 2D crystalline phase of P 2S3 corresponds to the global minimum in the Born-Oppenheimer surface of the phosphorus sulfide monolayers with 2:3 stoichiometry. It is a wide band gap (4.55 eV) semiconductor with P-S ? bonds. The electronic properties of P2S3 structure can be tuned by stacking into multilayer P2S3 structures, forming P2S3 nanoribbons or rolling into P2S3 nanotubes, expanding its potential applications for the emerging field of 2D electronics. Then we showed that the hydrolysis reaction is strongly affected by relative humidity. The hydrolysis of CO32- with n = 1-8 water molecules was investigated by ab initio method. For n = 1-5 water molecules, all the reactants follow a stepwise pathway to the transition state. For n = 6-8 water molecules, all the reactants undergo a direct proton transfer to the transition state with overall lower activation free energy. The activation free energy of the reaction is dramatically reduced from 10.4 to 2.4 kcal/mol as the number of water molecules increases from 1 to 6. Meanwhile, the degree of the hydrolysis of CO32- is significantly increased compared to the bulk water solution scenario. The incomplete hydration shells facilitate the hydrolysis of CO3 2- with few water molecules to be not only thermodynamically favorable but also kinetically favorable. We showed that the chemical kinetics is not likely to constrain the speed of CO2 air capture driven by the humidity-swing. (Abstract shortened by ProQuest.).

Universal fragment descriptors for predicting properties of inorganic crystals

NASA Astrophysics Data System (ADS)

Isayev, Olexandr; Oses, Corey; Toher, Cormac; Gossett, Eric; Curtarolo, Stefano; Tropsha, Alexander

2017-06-01

Although historically materials discovery has been driven by a laborious trial-and-error process, knowledge-driven materials design can now be enabled by the rational combination of Machine Learning methods and materials databases. Here, data from the AFLOW repository for ab initio calculations is combined with Quantitative Materials Structure-Property Relationship models to predict important properties: metal/insulator classification, band gap energy, bulk/shear moduli, Debye temperature and heat capacities. The prediction's accuracy compares well with the quality of the training data for virtually any stoichiometric inorganic crystalline material, reciprocating the available thermomechanical experimental data. The universality of the approach is attributed to the construction of the descriptors: Property-Labelled Materials Fragments. The representations require only minimal structural input allowing straightforward implementations of simple heuristic design rules.

Universal fragment descriptors for predicting properties of inorganic crystals.

PubMed

Isayev, Olexandr; Oses, Corey; Toher, Cormac; Gossett, Eric; Curtarolo, Stefano; Tropsha, Alexander

2017-06-05

Although historically materials discovery has been driven by a laborious trial-and-error process, knowledge-driven materials design can now be enabled by the rational combination of Machine Learning methods and materials databases. Here, data from the AFLOW repository for ab initio calculations is combined with Quantitative Materials Structure-Property Relationship models to predict important properties: metal/insulator classification, band gap energy, bulk/shear moduli, Debye temperature and heat capacities. The prediction's accuracy compares well with the quality of the training data for virtually any stoichiometric inorganic crystalline material, reciprocating the available thermomechanical experimental data. The universality of the approach is attributed to the construction of the descriptors: Property-Labelled Materials Fragments. The representations require only minimal structural input allowing straightforward implementations of simple heuristic design rules.

Crystal structures of carbonates up to Mbar pressures determined by single crystal synchrotron radiation diffraction

NASA Astrophysics Data System (ADS)

Merlini, M.

2013-12-01

The recent improvements at synchrotron beamlines, currently allow single crystal diffraction experiments at extreme pressures and temperatures [1,2] on very small single crystal domains. We successfully applied such technique to determine the crystal structure adopted by carbonates at mantle pressures. The knowledge of carbon-bearing phases is in fact fundamental for any quantitative modelling of global carbon cycle. The major technical difficulty arises after first order transitions or decomposition reactions, since original crystal (apx. 10x10x5 μm3) is transformed in much smaller crystalline domains often with random orientation. The use of 3D reciprocal space visualization software and the improved resolution of new generation flat panel detectors, however, allow both identification and integration of each single crystal domain, with suitable accuracy for ab-initio structure solution, performed with direct and charge-flipping methods and successive structure refinements. The results obtained on carbonates, indicate two major crystal-chemistry trends established at high pressures. The CO32- units, planar and parallel in ambient pressure calcite and dolomite structures, becomes non parallel in calcite- and dolomite-II and III phases, allowing more flexibility in the structures with possibility to accommodate strain arising from different cation sizes (Ca and Mg in particular). Dolomite-III is therefore also observed to be thermodynamically stable at lower mantle pressures and temperatures, differently from dolomite, which undergoes decomposition into pure end-members in upper mantle. At higher pressure, towards Mbar (lowermost mantle and D'' region) in agreement with theoretical calculations [3,4] and other experimental results [5], carbon coordination transform into 4-fold CO4 units, with different polymerisation in the structure depending on carbonate composition. The second important crystal chemistry feature detected is related to Fe2+ in Fe-bearing magnesite, which spontaneously oxidises at HP/HT, forming Fe3+ carbonates, Fe3+ oxides and reduced carbon (diamonds). Single crystal diffraction approach allowed full structure determination of these phases, yielding to the discovery of few unpredicted structures, such as Mg2Fe2C4O13 and Fe13O19, which can be well reproduced in different experiments. Mg2Fe2C4O13 carbonate present truncated chain C4O13 groups, and Fe13O19 oxide, whose stoichiometry is intermediate between magnetite and hematite, is a one-layer structure, with features encountered in superconducting materials. The results fully support the ideas of unexpected complexities in the mineralogy of the lowermost mantle, and single crystal technique, once properly optimized in ad-hoc synchrotron beamlines, is fundamental for extracting accurate structural information, otherwise rarely accessible with other experimental techniques. References: [1] Merlini M., Hanfland M. (2013). Single crystal diffraction at Mbar conditions by synchrotron radiation. High Pressure Research, in press. [2] Dubrovinsky et al., (2010). High Pressure Research, 30, 620-633. [3] Arapan et al. (1997). Phys. Rev. Lett., 98, 268501. [4] Oganov et al. (2008) EPSL, 273, 38-47. [5] Boulard et al. (2011) PNAS, 108, 5184-5187.

Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

NASA Astrophysics Data System (ADS)

Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

2015-03-01

Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

Experimental evidence and structural modeling of nonstoichiometric (010) surfaces coexisting in hydroxyapatite nano-crystals.

PubMed

Ospina, C A; Terra, J; Ramirez, A J; Farina, M; Ellis, D E; Rossi, A M

2012-01-01

High-resolution transmission electron microscopy (HRTEM) and ab initio quantum-mechanical calculations of electronic structure were combined to investigate the structure of the hydroxyapatite (HA) (010) surface, which plays an important role in HA interactions with biological media. HA was synthesized by in vitro precipitation at 37°C. HRTEM images revealed thin elongated rod nanoparticles with preferential growth along the [001] direction and terminations parallel to the (010) plane. The focal series reconstruction (FSR) technique was applied to develop an atomic-scale structural model of the high-resolution images. The HRTEM simulations identified the coexistence of two structurally distinct terminations for (010) surfaces: a rather flat Ca(II)-terminated surface and a zig-zag structure with open OH channels. Density functional theory (DFT) was applied in a periodic slab plane-wave pseudopotential approach to refine details of atomic coordination and bond lengths of Ca(I) and Ca(II) sites in hydrated HA (010) surfaces, starting from the HRTEM model. Copyright © 2011 Elsevier B.V. All rights reserved.

Chemical Bonding in Sulfide Minerals

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

Vaughan, David J.; Rosso, Kevin M.

An understanding of chemical bonding and electronic structure in sulfide minerals is central to any attempt at understanding their crystal structures, stabilities and physical properties. It is also an essential precursor to understanding reactivity through modeling surface structure at the molecular scale. In recent decades, there have been remarkable advances in first principles (ab initio) methods for the quantitative calculation of electronic structure. These advances have been made possible by the very rapid development of high performance computers. Several review volumes that chart the applications of these developments in mineralogy and geochemistry are available (Tossell and Vaughan, 1992; Cygan andmore » Kubicki, 2001). An important feature of the sulfide minerals is the diversity of their electronic structures, as evidenced by their electrical and magnetic properties (see Pearce et al. 2006, this volume). Thus, sulfide minerals range from insulators through semiconductors to metals, and exhibit every type of magnetic behavior. This has presented problems for those attempting to develop bonding models for sulfides, and also led to certain misconceptions regarding the kinds of models that may be appropriate. In this chapter, chemical bonding and electronic structure models for sulfides are reviewed with emphasis on more recent developments. Although the fully ab initio quantitative methods are now capable of a remarkable degree of sophistication in terms of agreement with experiment and potential to interpret and predict behavior with varying conditions, both qualitative and more simplistic quantitative approaches will also be briefly discussed. This is because we believe that the insights which they provide are still helpful to those studying sulfide minerals. In addition to the application of electronic structure models and calculations to solid sulfides, work on sulfide mineral surfaces (Rosso and Vaughan 2006a,b) and solution complexes and clusters (Rickard and Luther, 2006) are discussed in detail later in this volume.« less

Ab initio structure determination of n-diamond.

PubMed

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.

An Automated Ab Initio Framework for Identifying New Ferroelectrics

NASA Astrophysics Data System (ADS)

Smidt, Tess; Reyes-Lillo, Sebastian E.; Jain, Anubhav; Neaton, Jeffrey B.

Ferroelectric materials have a wide-range of technological applications including non-volatile RAM and optoelectronics. In this work, we present an automated first-principles search for ferroelectrics. We integrate density functional theory, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known and proposed ferroelectrics. We screen thousands of candidates using symmetry relations between nonpolar and polar structure pairs. We use two search strategies 1) polar-nonpolar pairs with the same composition and 2) polar-nonpolar structure type pairs. Results are automatically parsed, stored in a database, and accessible via a web interface showing distortion animations and plots of polarization and total energy as a function of distortion. We benchmark our results against experimental data, present new ferroelectric candidates found through our search, and discuss future work on expanding this search methodology to other material classes such as anti-ferroelectrics and multiferroics.

Ab-initio study of double perovskite Ba2YSbO6

NASA Astrophysics Data System (ADS)

Mondal, Golak; Jha, D.; Himanshu, A. K.; Lahiri, J.; Singh, B. K.; Kumar, Uday; Ray, Rajyavardhan

2018-04-01

The density functional theory with generalized gradient approximation has been used to investigate the electronic structure of double perovskite oxide Ba2YSbO6 (BYS) synthesized in polycrystalline form by solid state reaction. Structural characterization of the compound was done through X-ray diffraction (XRD) followed by Riedvelt analysis of the XRD pattern. The crystal structure is cubic, space group being Fm-3m (No. 225) with the lattice parameter, a = 8.424 Å. Optical band-gap of this system has been calculated using UV-Vis Spectroscopy and Kubelka-Munk (KM) function, having the value 4.56eV. A detailed study of the electronic properties has also been carried out using the Full-Potential Linear Augmented Plane Wave (FPLAPW) as implemented in WIEN2k. BYS is found to be a large band-gap insulator with potential technological applications, such as dielectric resonators and filters in microwave applications.

Theoretical study of some nitrososulfamide compounds with antitumor activity.

PubMed

Djameleddine, Khatmi; Soumeya, Seridi; Fatiha, Madi

2004-09-30

The lowest-energy conformations of four 2-chloroethylnitrososulfamides were determined using the MM+ molecular mechanics method as implemented in Hyperchem 6.0. Some of the calculated structural parameters, angles and bonds lengths were compared with the crystal structure data of N-nitroso-N-(2-chloroethyl)-N'-sulfamoyl- proline. Using MM+, AM1 and PM3 the anti conformation was predicted to be more stable than the syn conformation in each of these compounds. With these methods we found that the relative energy of the transition state (TS) was considerably higher, but with the ab initio method using RHF with minimal basic function STO-3G we found that the syn conformation is predicted to be slightly more stable. The determination of some atomic charges of a selection of atoms on the syn, anti and TS structures of the various compounds provided some details about the nature of the transition state.

Synthesis, spectral characterization and X-ray crystal structure studies of 3-(benzo[d][1,3]dioxol-5-yl)-5-(3-methylthiophen-2-yl)-4,5-dihydro-1H-pyrazole-1-carboxamide: Hirshfeld surface, DFT and thermal analysis

NASA Astrophysics Data System (ADS)

Kumara, Karthik; Dileep Kumar, A.; Naveen, S.; Ajay Kumar, K.; Lokanath, N. K.

2018-06-01

A novel pyrazole derivative, 3-(benzo[d][1,3]dioxol-5-yl)-5-(3-methylthiophen-2-yl)-4,5-dihydro-1H-pyrazole-1-carboxamide was synthesized and characterized by elemental analysis, FT-IR, NMR (1H and 13C), MS, UV-visible spectra and finally the structure was confirmed by the single crystal X-ray diffraction studies. The title compound (C16H15N3O3S) crystallized in the triclinic crystal system, with the space group Pī. A dihedral angle of 65.84(1)° between the pyrazole and the thiophene rings confirms the twisted conformation between them. The X-ray structure revealed that the pyrazole ring adopts an E-form and an envelope conformation on C7 atom. The crystal and molecular structure of the title compound is stabilized by inter molecular hydrogen bonds. The compound possesses three dimensional supramolecular self-assembly, in which Csbnd H⋯O and Nsbnd H⋯O chains build up two dimensional arrays, which are extended to 3D network through Csbnd H···Cg and Csbnd O···Cg interactions. The structure also exhibits intramolecular hydrogen bonds of the type Nsbnd H⋯N and π···π stacking interactions, which contributes to the crystal packing. Further, Hirshfeld surface analysis was carried out for the graphical visualization of several short intermolecular interactions on the molecular surface while the 2D finger-print plot provides percentage contribution of each individual atom-to-atom interactions. The thermal decomposition of the compound has been studied by thermogravimetric analysis. The molecular geometries and electronic structures of the compounds were fully optimized, calculated with ab-initio methods by HF, DFT/B3LYP functional in combination of different basis set with different solvent environment and the structural parameters were compared with the experimental data. The Mulliken atomic charges and molecular electrostatic potential on molecular van der Waals (vdW) surface were calculated to know the electrophilic and nucleophilic regions of the molecular surface. Nonlinear optical properties of the title compound were also discussed based on the polarizability and hyperpolarizability values.

Quantum-mechanical ab initio simulation of the Raman and IR spectra of Mn3Al2Si3O12 spessartine

NASA Astrophysics Data System (ADS)

Valenzano, Loredana; Meyer, Alessio; Demichelis, Raffaella; Civalleri, Bartolomeo; Dovesi, Roberto

2009-07-01

The IR and Raman spectra of spessartine garnet Mn3Al2Si3O12, are simulated with the periodic ab initio CRYSTAL code by adopting an all-electron Gaussian-type basis set and the B3LYP Hamiltonian. The frequencies of the 25 Raman active modes (3 of A 1 g , 8 of E g and 14 of F 2 g symmetry) and of the two sets of 17 F 1 u transverse-optical and longitudinal-optical frequencies are generated, as well as the IR oscillator strength. The agreement between calculated and experimental data is excellent: for the IR and Raman sets, the mean absolute difference overline{|Updelta|} is 4.0 and 6.8 cm-1, respectively. Isotopic substitution permits to highlight the Mn, Al and Si participation to the various zones of the spectrum. Graphical animation, available on the authors’ web-site ( http://www.crystal.unito.it/vibs/garnets/spessartine/ ), provides a very readable description of the movement of atoms and groups in each vibrational mode.

Ab initio study of single-crystalline and polycrystalline elastic properties of Mg-substituted calcite crystals.

PubMed

Zhu, L-F; Friák, M; Lymperakis, L; Titrian, H; Aydin, U; Janus, A M; Fabritius, H-O; Ziegler, A; Nikolov, S; Hemzalová, P; Raabe, D; Neugebauer, J

2013-04-01

We employ ab initio calculations and investigate the single-crystalline elastic properties of (Ca,Mg)CO3 crystals covering the whole range of concentrations from pure calcite CaCO3 to pure magnesite MgCO3. Studying different distributions of Ca and Mg atoms within 30-atom supercells, our theoretical results show that the energetically most favorable configurations are characterized by elastic constants that nearly monotonously increase with the Mg content. Based on the first principles-derived single-crystalline elastic anisotropy, the integral elastic response of (Ca,Mg)CO3 polycrystals is determined employing a mean-field self-consistent homogenization method. As in case of single-crystalline elastic properties, the computed polycrystalline elastic parameters sensitively depend on the chemical composition and show a significant stiffening impact of Mg atoms on calcite crystals in agreement with the experimental findings. Our analysis also shows that it is not advantageous to use a higher-scale two-phase mix of stoichiometric calcite and magnesite instead of substituting Ca atoms by Mg ones on the atomic scale. Such two-phase composites are not significantly thermodynamically favorable and do not provide any strong additional stiffening effect. Copyright © 2013 Elsevier Ltd. All rights reserved.

Structural characterization of analgesic isothiazolopyridines of Mannich base type; X-ray analysis of 2-[(4-phenylpiperazin-1-yl)ethyl]- and 2-[(4-methylpiperazin-1-yl)methyl]-4,6-dimethylisothiazolo[5,4- b]pyridin-3(2 H)-ones

NASA Astrophysics Data System (ADS)

Karczmarzyk, Zbigniew; Malinka, Wiesław

2008-10-01

The crystal and molecular structures of the title 2-[(4-phenylpiperazin-1-yl)ethyl], 6, and 2-[(4-methylpiperazin-1-yl)methyl], 7, derivatives of isothiazolo[5,4- b]pyridine were determined. The molecular packing in 6 is influenced by C-H…X (X = N, O) hydrogen bonds and π… π interactions of the pairs of isothiazolopyridine rings belonging to inversion related molecules. The crystal structure of 7 contains the net of O-H…N and C-H…O intermolecular hydrogen bonds. Moreover, isothiazole and pyridine rings show significant stacking with the shortest π… π distances of 3.453 Å. The conformations of the molecules 6 and 7 were compared with those observed in the crystals of related analgesic 4-arylpiperazine ( 2, 3) and 4-arylpiperidine ( 4, 5) derivatives of isothiazolopyridine of Mannich base type. Additionally, the computational investigations using semi-empirical AM1 and RHF/6-31G∗∗ ab initio methods are performed within series 2- 7 in order to find correlation between geometrical and electronic parameters of the molecules and their analgesic action. Results of the theoretical calculations show that the charge distribution on the piperazine N atoms is correlated with conformation of the (4-arylpiperazin-1-yl)methyl side chain and analgesic action of isothiazolopyridines analyzed.

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

Genome-wide protein structure prediction and structure-based function annotation have been a long-term goal in molecular biology but not yet become possible due to difficulties in modeling distant-homology targets. We developed a hybrid pipeline combining ab initio folding and template-based modeling for genome-wide structure prediction applied to the Escherichia coli genome. The pipeline was tested on 43 known sequences, where QUARK-based ab initio folding simulation generated models with TM-score 17% higher than that by traditional comparative modeling methods. For 495 unknown hard sequences, 72 are predicted to have a correct fold (TM-score > 0.5) and 321 have a substantial portion of structure correctly modeled (TM-score > 0.35). 317 sequences can be reliably assigned to a SCOP fold family based on structural analogy to existing proteins in PDB. The presented results, as a case study of E. coli, represent promising progress towards genome-wide structure modeling and fold family assignment using state-of-the-art ab initio folding algorithms. PMID:23719418

Determination of the three-dimensional structure of oligosaccharides in the solid state from experimental 13C NMR data and ab initio chemical shift surfaces.

PubMed

Sergeyev, Ivan; Moyna, Guillermo

2005-05-02

A novel method for the determination of the three-dimensional (3D) structure of oligosaccharides in the solid state using experimental 13C NMR data is presented. The approach employs this information, combined with 13C chemical shift surfaces (CSSs) for the glycosidic bond carbons in the generation of NMR pseudopotential energy functions suitable for use as constraints in molecular modeling simulations. Application of the method to trehalose, cellobiose, and cellotetraose produces 3D models that agree remarkably well with the reported X-ray structures, with phi and psi dihedral angles that are within 10 degrees from the ones observed in the crystals. The usefulness of the approach is further demonstrated in the determination of the 3D structure of the cellohexaose, an hexasaccharide for which no X-ray data has been reported, as well as in the generation of accurate structural models for cellulose II and amylose V6.

Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

PubMed Central

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; Wang, Shibing; Lin, Yu; Zeng, Qiaoshi; Xu, Gang; Liu, Zhenxian; Solanki, G. K.; Patel, K. D.; Cui, Yi; Hwang, Harold Y.; Mao, Wendy L.

2015-01-01

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe2 up to ∼60 GPa using multiple experimental techniques and ab-initio calculations. MoSe2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSe2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides. PMID:26088416

New Convex and Spherical Structures of Bare Boron Clusters

NASA Astrophysics Data System (ADS)

Boustani, Ihsan

1997-10-01

New stable structures of bare boron clusters can easily be obtained and constructed with the help of an "Aufbau Principle" suggested by a systematicab initioHF-SCF and direct CI study. It is concluded that boron cluster formation can be established by elemental units of pentagonal and hexagonal pyramids. New convex and small spherical clusters different from the classical known forms of boron crystal structures are obtained by a combination of both basic units. Convex structures simulate boron surfaces which can be considered as segments of open or closed spheres. Both convex clusters B16and B46have energies close to those of their conjugate quasi-planar clusters, which are relatively stable and can be considered to act as a calibration mark. The closed spherical clusters B12, B22, B32, and B42are less stable than the corresponding conjugated quasi-planar structures. As a consequence, highly stable spherical boron clusters can systematically be predicted when their conjugate quasi-planar clusters are determined and energies are compared.

Pressure induced metallization with absence of structural transition in layered molybdenum diselenide

DOE PAGES

Zhao, Zhao; Zhang, Haijun; Yuan, Hongtao; ...

2015-06-19

Layered transition-metal dichalcogenides have emerged as exciting material systems with atomically thin geometries and unique electronic properties. Pressure is a powerful tool for continuously tuning their crystal and electronic structures away from the pristine states. Here, we systematically investigated the pressurized behavior of MoSe 2 up to ~60 GPa using multiple experimental techniques and ab-initio calculations. MoSe 2 evolves from an anisotropic two-dimensional layered network to a three-dimensional structure without a structural transition, which is a complete contrast to MoS 2. The role of the chalcogenide anions in stabilizing different layered patterns is underscored by our layer sliding calculations. MoSemore » 2 possesses highly tunable transport properties under pressure, determined by the gradual narrowing of its band-gap followed by metallization. The continuous tuning of its electronic structure and band-gap in the range of visible light to infrared suggest possible energy-variable optoelectronics applications in pressurized transition-metal dichalcogenides.« less

Quaternary structure of human, Drosophila melanogaster and Caenorhabditis elegans MFE-2 in solution from synchrotron small-angle X-ray scattering.

PubMed

Mehtälä, Maija L; Haataja, Tatu J K; Blanchet, Clément E; Hiltunen, J Kalervo; Svergun, Dmitri I; Glumoff, Tuomo

2013-02-14

Multifunctional enzyme type 2 (MFE-2) forms part of the fatty acid β-oxidation pathway in peroxisomes. MFE-2s from various species reveal proteins with structurally homologous functional domains assembled in different compilations. Crystal structures of all domain types are known. SAXS data from human, fruit fly and Caenorhabditiselegans MFE-2s and their constituent domains were collected, and both ab initio and rigid body models constructed. Location of the putative substrate binding helper domain SCP-2L (sterol carrier protein 2-like), which is not part of MFE-2 protein in every species and not seen as part of any previous MFE-2 structures, was determined. The obtained models of human and C. elegans MFE-2 lend a direct structural support to the idea of the biological role of SCP-2L. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

X-ray structures of the anticoagulants coumatetralyl and chlorophacinone. Theoretical calculations and SAR investigations on thirteen anticoagulant rodenticides

NASA Astrophysics Data System (ADS)

Dolmella, A.; Gatto, S.; Girardi, E.; Bandoli, G.

1999-12-01

Coumatetralyl and chlorophacinone, two substances related to 4-hydroxycoumarin (HC) and to 1,3-indandione (ID), respectively, show activity as anticoagulant rodenticides. In the present study we have investigated the solid-state structures of coumatetralyl and chlorophacinone by means of X-ray single-crystal and powder diffraction, along with thermal analysis. The crystal structures of the two compounds have been used as input geometries for a series of computational chemistry efforts, involving other anticoagulant derivatives as well. Thus, ab initio, semiempirical molecular orbital, molecular mechanics and molecular dynamics/simulated annealing calculations have been performed on thirteen anticoagulant rodenticides. In particular, the annealing calculations have been made to assess the conformational freedom of the compounds under scrutiny. All the generated conformers have been classified into families. The classification has first been made empirically, and then validated by means of a cluster analysis. A number of structural and physico-chemical parameters derived from the calculations has been used in turn for structure-activity relationships (SARs) investigations. In the latter, we have assessed how the selected parameters affect toxicity. The results seem to be consistent with a three-dimensional biophore model, in which higher toxicity is predicted for the more voluminous rodenticides. We suggest that these compounds better fit the active site of the target enzyme vitamin K 2,3-epoxide reductase (KO-reductase).

Critical Intermediate Structure That Directs the Crystalline Texture and Surface Morphology of Organo-Lead Trihalide Perovskite.

PubMed

Chia, Hao-Chung; Sheu, Hwo-Shuenn; Hsiao, Yu-Yun; Li, Shao-Sian; Lan, Yi-Kang; Lin, Chung-Yao; Chang, Je-Wei; Kuo, Yen-Chien; Chen, Chia-Hao; Weng, Shih-Chang; Su, Chun-Jen; Su, An-Chung; Chen, Chun-Wei; Jeng, U-Ser

2017-10-25

We have identified an often observed yet unresolved intermediate structure in a popular processing with dimethylformamide solutions of lead chloride and methylammonium iodide for perovskite solar cells. With subsecond time-resolved grazing-incidence X-ray scattering and X-ray photoemission spectroscopy, supplemental with ab initio calculation, the resolved intermediate structure (CH 3 NH 3 ) 2 PbI 2 Cl 2 ·CH 3 NH 3 I features two-dimensional (2D) perovskite bilayers of zigzagged lead-halide octahedra and sandwiched CH 3 NH 3 I layers. Such intermediate structure reveals a hidden correlation between the intermediate phase and the composition of the processing solution. Most importantly, the 2D perovskite lattice of the intermediate phase is largely crystallographically aligned with the [110] planes of the three-dimensional perovskite cubic phase; consequently, with sublimation of Cl ions from the organo-lead octahedral terminal corners in prolonged annealing, the zigzagged octahedral layers of the intermediate phase can merge with the intercalated methylammonium iodide layers for templated growth of perovskite crystals. Regulated by annealing temperature and the activation energies of the intermediate and perovskite, deduced from analysis of temperature-dependent structural kinetics, the intermediate phase is found to selectively mature first and then melt along the layering direction for epitaxial conversion into perovskite crystals. The unveiled epitaxial conversion under growth kinetics controls might be general for solution-processed and intermediate-templated perovskite formation.

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

PubMed

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

2017-09-05

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

Effect of Defects on Mechanisms of Initiation and Energy Release in Energetic Molecular Crystals

DTIC Science & Technology

2011-02-10

dynamics of NEEMs ," Aberdeen, MD, Mar. 2010. 60. Dana Dlott (invited) American Chemical Society Annual Meeting, "Vibrational Energy in Molecules with High...hydrocarbons to ascertain their stability under extreme conditions. Also, HEs are often mixed with fuel oils as well so we sought to separately...dependence of the EOS. Ab initio calculations were performed to extract the complete equation of state for an organic molecular crystal over a

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

DTIC Science & Technology

2006-11-01

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

Desolvation-Driven 100-Fold Slow-down of Tunneling Relaxation Rate in Co(II)-Dy(III) Single-Molecule Magnets through a Single-Crystal-to-Single-Crystal Process

NASA Astrophysics Data System (ADS)

Liu, Jun-Liang; Wu, Jie-Yi; Huang, Guo-Zhang; Chen, Yan-Cong; Jia, Jian-Hua; Ungur, Liviu; Chibotaru, Liviu F.; Chen, Xiao-Ming; Tong, Ming-Liang

2015-11-01

Single-molecule magnets (SMMs) are regarded as a class of promising materials for spintronic and ultrahigh-density storage devices. Tuning the magnetic dynamics of single-molecule magnets is a crucial challenge for chemists. Lanthanide ions are not only highly magnetically anisotropic but also highly sensitive to the changes in the coordination environments. We developed a feasible approach to understand parts of the magneto-structure correlations and propose to regulate the relaxation behaviors via rational design. A series of Co(II)-Dy(III)-Co(II) complexes were obtained using in situ synthesis; in this system of complexes, the relaxation dynamics can be greatly improved, accompanied with desolvation, via single-crystal to single-crystal transformation. The effective energy barrier can be increased from 293 cm-1 (422 K) to 416 cm-1 (600 K), and the tunneling relaxation time can be grown from 8.5 × 10-4 s to 7.4 × 10-2 s. These remarkable improvements are due to the change in the coordination environments of Dy(III) and Co(II). Ab initio calculations were performed to better understand the magnetic dynamics.

Magneto-Structural Correlations in Pseudotetrahedral Forms of the [Co(SPh)4]2- Complex Probed by Magnetometry, MCD Spectroscopy, Advanced EPR Techniques, and ab Initio Electronic Structure Calculations.

PubMed

Suturina, Elizaveta A; Nehrkorn, Joscha; Zadrozny, Joseph M; Liu, Junjie; Atanasov, Mihail; Weyhermüller, Thomas; Maganas, Dimitrios; Hill, Stephen; Schnegg, Alexander; Bill, Eckhard; Long, Jeffrey R; Neese, Frank

2017-03-06

The magnetic properties of pseudotetrahedral Co(II) complexes spawned intense interest after (PPh 4 ) 2 [Co(SPh) 4 ] was shown to be the first mononuclear transition-metal complex displaying slow relaxation of the magnetization in the absence of a direct current magnetic field. However, there are differing reports on its fundamental magnetic spin Hamiltonian (SH) parameters, which arise from inherent experimental challenges in detecting large zero-field splittings. There are also remarkable changes in the SH parameters of [Co(SPh) 4 ] 2- upon structural variations, depending on the counterion and crystallization conditions. In this work, four complementary experimental techniques are utilized to unambiguously determine the SH parameters for two different salts of [Co(SPh) 4 ] 2- : (PPh 4 ) 2 [Co(SPh) 4 ] (1) and (NEt 4 ) 2 [Co(SPh) 4 ] (2). The characterization methods employed include multifield SQUID magnetometry, high-field/high-frequency electron paramagnetic resonance (HF-EPR), variable-field variable-temperature magnetic circular dichroism (VTVH-MCD), and frequency domain Fourier transform THz-EPR (FD-FT THz-EPR). Notably, the paramagnetic Co(II) complex [Co(SPh) 4 ] 2- shows strong axial magnetic anisotropy in 1, with D = -55(1) cm -1 and E/D = 0.00(3), but rhombic anisotropy is seen for 2, with D = +11(1) cm -1 and E/D = 0.18(3). Multireference ab initio CASSCF/NEVPT2 calculations enable interpretation of the remarkable variation of D and its dependence on the electronic structure and geometry.

Prediction of a two-dimensional S3N2 solid for optoelectronic applications

NASA Astrophysics Data System (ADS)

Xiao, Hang; Shi, Xiaoyang; Liao, Xiangbiao; Zhang, Yayun; Chen, Xi

2018-02-01

Two-dimensional materials have attracted tremendous attention for their fascinating electronic, optical, chemical, and mechanical properties. However, the band gaps of most reported two-dimensional (2D) materials are smaller than 2.0 eV, which has greatly restricted their optoelectronic applications in the blue and ultraviolet range of the spectrum. Here, we propose a stable trisulfur dinitride (S3N2 ) 2D crystal that is a covalent network composed solely of S-N σ bonds. The S3N2 crystal is dynamically, thermally, and chemically stable, as confirmed by the computed phonon spectrum and ab initio molecular dynamics simulations. GW calculations show that the S3N2 crystal is a wide, direct band-gap (3.92 eV) semiconductor with a small-hole effective mass. In addition, the band gap of S3N2 structures can be tuned by forming multilayer S3N2 crystals, S3N2 nanoribbons, and S3N2 nanotubes, expanding its potential applications. The anisotropic optical response of the 2D S3N2 crystal is revealed by GW-Bethe-Salpeter-equation calculations. The optical band gap of S3N2 is 2.73 eV and the exciton binding energy of S3N2 is 1.19 eV, showing a strong excitonic effect. Our result not only marks the prediction of a 2D crystal composed of nitrogen and sulfur, but also underpins potential innovations in 2D electronics and optoelectronics.

First-principles study of the structural properties of Ge

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

Chang, K.J.; Cohen, M.L.

1986-12-15

With the use of an ab initio pseudopotential method, the structural properties of Ge are investigated at normal and high pressures. The pressure-induced structural phase transitions from cubic diamond to ..beta..-Sn, to simple hexagonal (sh), and to double hexagonal close packed (dhcp) are examined. With the possible exception of the dhcp structure, the calculated transition pressures, transition volumes, and axial ratios are in good agreement with experimental results. We find that sh Ge has characteristics similar to those of sh Si; the bonds between hexagonal layers are stronger than intralayer bonds and the transverse phonon modes become soft near themore » transitions from the sh to ..beta..-Sn and the sh to hcp structures. At normal pressures, we compare the crystal energies for the cubic diamond, hexagonal 2H, and hexagonal 4H structures. Because of the similar sp/sup 3/ bonds in these structures, the structural energy differences are less than about 14 meV, and the 2H and 4H phases are metastable with respect to the cubic diamond structure. The equation of state is also presented and compared with experiment.« less

Resolution of ab initio shapes determined from small-angle scattering.

PubMed

Tuukkanen, Anne T; Kleywegt, Gerard J; Svergun, Dmitri I

2016-11-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.

Resolution of ab initio shapes determined from small-angle scattering

PubMed Central

Tuukkanen, Anne T.; Kleywegt, Gerard J.; Svergun, Dmitri I.

2016-01-01

Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models. PMID:27840683

Ab Initio study on structural, electronic, magnetic and dielectric properties of LSNO within Density Functional Perturbation Theory

NASA Astrophysics Data System (ADS)

Petersen, John; Bechstedt, Friedhelm; Furthmüller, Jürgen; Scolfaro, Luisa

LSNO (La2-xSrxNiO4) is of great interest due to its colossal dielectric constant (CDC) and rich underlying physics. While being an antiferromagnetic insulator, localized holes are present in the form of stripes in the Ni-O planes which are commensurate with the inverse of the Sr concentration. The stripes are a manifestation of charge density waves with period approximately 1/x and spin density waves with period approximately 2/x. Here, the spin ground state is calculated via LSDA + U with the PAW method implemented in VASP. Crystal structure and the effective Hubbard U parameter are optimized before calculating ɛ∞ within the independent particle approximation. ɛ∞ and the full static dielectric constant (including the lattice polarizability) ɛ0 are calculated within Density Functional Perturbation Theory.

Ab-initio calculations of structural, electronic, and optical properties of Zn3(VO4)2

NASA Astrophysics Data System (ADS)

Ahmed, Nisar; Mukhtar, S.; Gao, Wei; Zafar Ilyas, Syed

2018-03-01

The structural, electronic, and optical properties of Zn3(VO4)2 are investigated using full potential linearized augmented plane wave (FP-LAPW) method within the framework of density functional theory (DFT). Various approaches are adopted to treat the exchange and correlation potential energy such as generalized gradient approximation (GGA), GGA+U, and the Tran–Blaha modified Becke–Johnson (TB-mBJ) potential. The calculated band gap of 3.424 eV by TB-mBJ is found to be close to the experimental result (3.3 eV). The optical anisotropy is analyzed through optical constants, such as dielectric function and absorption coefficient along parallel and perpendicular crystal orientations. The absorption coefficient reveals high absorption (1.5× {10}6 {cm}}-1) of photons in the ultraviolet region.

Raman and infrared spectra and theoretical calculations of dipicolinic acid, dinicotinic acid, and their dianions

NASA Astrophysics Data System (ADS)

McCann, Kathleen; Laane, Jaan

2008-11-01

The Raman and infrared spectra of dipicolinic acid (DPA) and dinicotinic acid (DNic) and their salts (CaDPA, Na 2DPA, and CaDNic) have been recorded and the spectra have been assigned. Ab initio and DFT calculations were carried out to predict the structures and vibrational spectra and were compared to the experimental results. Because of extensive intermolecular hydrogen bonding in the crystals of these molecules, the calculated structures and spectra for the individual molecules agree only moderately well with the experimental values. Theoretical calculations were also carried out for DPA dimers and DPA·2H 2O to better understand the intermolecular interactions. The spectra do show that DPA and its calcium salt, which are present in anthrax spores, can be distinguished from the very similar DNic and CaDNic.

Investigation of hydrogen interaction with defects in zirconia

NASA Astrophysics Data System (ADS)

Melikhova, O.; Kuriplach, J.; Čížek, J.; Procházka, I.; Brauer, G.; Anwand, W.

2010-04-01

Defect studies of a ZrO2 + 9 mol. % Y2O3 single crystal were performed in this work using a high resolution positron lifetime spectroscopy combined with slow positron implantation spectroscopy. In order to elucidate the nature of positron trapping sites observed experimentally, the structural relaxations of several types of vacancy-like defects in zirconia were performed and positron characteristics for them were calculated. Relaxed atomic configurations of studied defects were obtained by means of ab initio pseudopotential method within the supercell approach. Theoretical calculations indicated that neither oxygen vacancies nor their neutral complexes with substitute yttrium atoms are capable of positron trapping. On the other hand, zirconium vacancies are deep positron traps and are most probably responsible for the saturated positron trapping observed in yttria stabilized zirconia single crystals. However, the calculated positron lifetime for zirconium vacancy is apparently longer than the experimental value corresponding to a single-component spectrum measured for the cubic ZrO2 + 9 mol. % Y2O3 single crystal. It was demonstrated that this effect can be explained by hydrogen trapped in zirconium vacancies. On the basis of structure relaxations, we found that zirconium vacancy - hydrogen complexes represent deep positron traps with the calculated lifetime close to the experimental one. In zirconium vacancy - hydrogen complexes the hydrogen atom forms an O-H bond with one of the nearest neighbour oxygen atoms. The calculated bond length is close to 1 Å.

Transition to collapsed tetragonal phase in CaFe2As2 single crystals as seen by 57Fe Mössbauer spectroscopy

NASA Astrophysics Data System (ADS)

Bud'ko, Sergey L.; Ma, Xiaoming; Tomić, Milan; Ran, Sheng; Valentí, Roser; Canfield, Paul C.

2016-01-01

Temperature dependent measurements of 57Fe Mössbauer spectra on CaFe2As2 single crystals in the tetragonal and collapsed tetragonal phases are reported. Clear features in the temperature dependencies of the isomer shift, relative spectra area, and quadrupole splitting are observed at the transition from the tetragonal to the collapsed tetragonal phase. From the temperature dependent isomer shift and spectral area data, an average stiffening of the phonon modes in the collapsed tetragonal phase is inferred. The quadrupole splitting increases by ˜25 % on cooling from room temperature to ˜100 K in the tetragonal phase and is only weakly temperature dependent at low temperatures in the collapsed tetragonal phase, in agreement with the anisotropic thermal expansion in this material. In order to gain microscopic insight about these measurements, we perform ab initio density functional theory calculations of the electric field gradient and the electron density of CaFe2As2 in both phases. By comparing the experimental data with the calculations we are able to fully characterize the crystal structure of the samples in the collapsed-tetragonal phase through determination of the As z coordinate. Based on the obtained temperature dependent structural data we are able to propose charge saturation of the Fe-As bond region as the mechanism behind the stabilization of the collapsed-tetragonal phase at ambient pressure.

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

PubMed

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

2017-11-22

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

Anisotropy of atomic bonds formed by p-type dopants in bulk GaN crystals

NASA Astrophysics Data System (ADS)

Lawniczak-Jablonska, K.; Suski, T.; Gorczyca, I.; Christensen, N. E.; Libera, J.; Kachniarz, J.; Lagarde, P.; Cortes, R.; Grzegory, I.

The anisotropy of atomic bonds formed by acceptor dopants with nitrogen in bulk wurtzite GaN crystals was studied by means of linearly polarized synchrotron radiation used in measurements of X-ray-absorption spectra for the K-edgeof Mg and Zn dopants. These spectra correspond to i) a single acceptor N bond along the c-axis and ii) three bonds realized with N atoms occupying the ab-plane perpendicular to the c-axis. The Zn dopant formed resonant spectra similar to that characteristic for Ga cations. In the case of the Mg dopant, similarity to Ga cations was observed for triple bonds in the ab-plane, only. Practically no resonant structure for spectra detected along the c-axis was observed. The absorption spectra were compared with ab initio calculations using the full-potential linear muffin-tin-orbital method. These calculations were also used for determination of the bond length for Mg-N and Zn-N in wurtzite GaN crystals and show that introducing dopants causes an increase of the lengths of the bonds formed by both dopants. Extended X-ray-absorption fine-structure measurements performed for bulk GaN:Zn confirmed the prediction of the theory in the case of the Zn-N bond. Finally, it is suggested that the anisotropy in the length of the Mg-N bonds, related to their larger strength in the case of bonds in the ab-plane, can explain preferential formation of a superlattice consisting of Mg-rich layers arranged in ab-planes of several bulk GaN:Mg crystals observed by transmission electron microscopy. Within the sensitivity of the method used, no parasitic metallic clusters or oxide compounds formed by the considered acceptors in GaN crystals were found.

Extremely Large Magnetoresistance in a Topological Semimetal Candidate Pyrite PtBi2

NASA Astrophysics Data System (ADS)

Gao, Wenshuai; Hao, Ningning; Zheng, Fa-Wei; Ning, Wei; Wu, Min; Zhu, Xiangde; Zheng, Guolin; Zhang, Jinglei; Lu, Jianwei; Zhang, Hongwei; Xi, Chuanying; Yang, Jiyong; Du, Haifeng; Zhang, Ping; Zhang, Yuheng; Tian, Mingliang

2017-06-01

While pyrite-type PtBi2 with a face-centered cubic structure has been predicted to be a three-dimensional (3D) Dirac semimetal, experimental study of its physical properties remains absent. Here we report the angular-dependent magnetoresistance measurements of a PtBi2 single crystal under high magnetic fields. We observed extremely large unsaturated magnetoresistance (XMR) up to (11.2 ×106)% at T =1.8 K in a magnetic field of 33 T, which is comparable to the previously reported Dirac materials, such as WTe2 , LaSb, and NbP. The crystals exhibit an ultrahigh mobility and significant Shubnikov-de Hass quantum oscillations with a nontrivial Berry phase. The analysis of Hall resistivity indicates that the XMR can be ascribed to the nearly compensated electron and hole. Our experimental results associated with the ab initio calculations suggest that pyrite PtBi2 is a topological semimetal candidate that might provide a platform for exploring topological materials with XMR in noble metal alloys.

Determination of the topological shape of integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria in the detergent solution by small-angle X-ray scattering.

PubMed

Hong, Xinguo; Weng, Yu-Xiang; Li, Ming

2004-02-01

The topological shape of the integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria Rhodobacter spheroides 2.4.1 in detergent solution has been determined from synchrotron small-angle X-ray scattering data using direct curve-fitting by the ellipsoid, ab initio shape determination methods of simulated annealing algorithm and multipole expansion, respectively. The results indicate that the LH2 protein in aqueous solution is encapsulated by a monolayered detergent shell. The detergent-stabilized structure has the shape of an oblate plate, with a thickness of 40 A, a long axis of 110 A, and a short axis of 85 A. After correction for the detergent shell, the shape of the LH2 core is also an oblate plate with a height of 40 A, a long axis of 80 A, and a short axis of 55 A. In contrast to the cylindrical crystal structure with a height of 40 A and a diameter of 68 A, the molecular shape of the LH2 complex in detergent solution clearly deviates from the ringlike crystal structure, with an eccentricity found to be 0.59-consistent with the result of single molecular spectroscopy study of the isolated single LH2 molecules.

Determination of the Topological Shape of Integral Membrane Protein Light-Harvesting Complex LH2 from Photosynthetic Bacteria in the Detergent Solution by Small-Angle X-Ray Scattering

PubMed Central

Hong, Xinguo; Weng, Yu-Xiang; Li, Ming

2004-01-01

The topological shape of the integral membrane protein light-harvesting complex LH2 from photosynthetic bacteria Rhodobacter spheroides 2.4.1 in detergent solution has been determined from synchrotron small-angle X-ray scattering data using direct curve-fitting by the ellipsoid, ab initio shape determination methods of simulated annealing algorithm and multipole expansion, respectively. The results indicate that the LH2 protein in aqueous solution is encapsulated by a monolayered detergent shell. The detergent-stabilized structure has the shape of an oblate plate, with a thickness of 40 Å, a long axis of 110 Å, and a short axis of 85 Å . After correction for the detergent shell, the shape of the LH2 core is also an oblate plate with a height of 40 Å, a long axis of 80 Å, and a short axis of 55 Å. In contrast to the cylindrical crystal structure with a height of 40 Å and a diameter of 68 Å, the molecular shape of the LH2 complex in detergent solution clearly deviates from the ringlike crystal structure, with an eccentricity found to be 0.59—consistent with the result of single molecular spectroscopy study of the isolated single LH2 molecules. PMID:14747343

Building a model of the blue cone pigment based on the wild type rhodopsin structure with QM/MM methods.

PubMed

Frähmcke, Jan S; Wanko, Marius; Elstner, Marcus

2012-03-15

Understanding the mechanism of color tuning of the retinal chromophore by its host protein became one of the key issues in the research on rhodopsins. While early mutation studies addressed its genetic origin, recent studies advanced to investigate its structural origin, based on X-ray crystallographic structures. For the human cone pigments, no crystal structures have been produced, and homology models were employed to elucidate the origin of its blue-shifted absorption. In this theoretical study, we take a different route to establish a structural model for human blue. Starting from the well-resolved structure of bovine rhodopsin, we derive multiple mutant models by stepwise mutation and equilibration using molecular dynamics simulations in a hybrid quantum mechanics/molecular mechanics framework. Our 30fold mutant reproduces the experimental UV-vis absorption shift of 0.45 eV and provides new insights about both structural and genetic factors that affect the excitation energy. Electrostatic effects of individual amino acids and collaborative structural effects are analyzed using semiempirical (OM2/MRCI) and ab initio (SORCI) multireference approaches. © 2012 American Chemical Society

Identification and properties of the non-cubic phases of Mg 2Pb

DOE PAGES

Li, Yuwei; Bian, Guang; Singh, David J.

2016-12-20

Mg 2Pb occurs in the cubic fluorite structure and is a semimetal with a band structure strongly affected by spin-orbit interaction on the Pb p states. Its properties are therefore of interest in the context of topological materials. In addition a different phase of Mg 2Pb was experimentally reported, but its crystal structure and properties remain unknown. Here we determine the structure of this phase using ab initio evolutionary methods and report its properties. The energy of one tetragonal phase, space group P4/ nmm, is 2 meV per atom higher than that of the ground state structure supporting the experimentalmore » observation. We find this tetragonal phase to be a compenstated anisotropic metal with strong spin orbit effects. As a result, many other metastable structures have also been identified, especially one orthorhombic structure, space group Pnma, of which energy is 17 meV per atom higher than that of ground state structure and which perhaps could be the phase that was reported based on similarity of lattice parameters.« less

Structural Investigation of the (010) Surface of the Al13Fe4 Catalyst

NASA Astrophysics Data System (ADS)

Ledieu, J.; Gaudry, É.; Loli, L. N. Serkovic; Villaseca, S. Alarcón; de Weerd, M.-C.; Hahne, M.; Gille, P.; Grin, Y.; Dubois, J.-M.; Fournée, V.

2013-02-01

We have investigated the structure of the Al13Fe4(010) surface using both experimental and ab initio computational methods. The results indicate that the topmost surface layers correspond to incomplete puckered (P) planes present in the bulk crystal structure. The main building block of the corrugated termination consists of two adjacent pentagons of Al atoms, each centered by a protruding Fe atom. These motifs are interconnected via additional Al atoms referred to as “glue” atoms which partially desorb above 873 K. The surface structure of lower atomic density compared to the bulk P plane is explained by a strong Fe-Al-Fe covalent polar interaction that preserves intact clusters at the surface. The proposed surface model with identified Fe-containing atomic ensembles could explain the Al13Fe4 catalytic properties recently reported in line with the site-isolation concept [M. Armbrüster , Nat. Mater. 11, 690 (2012)NMAACR1476-1122].

First-Principles Characterization of the Unknown Crystal Structure and Ionic Conductivity of Li7P2S8I as a Solid Electrolyte for High-Voltage Li Ion Batteries.

PubMed

Kang, Joonhee; Han, Byungchan

2016-07-21

Using first-principles density functional theory calculations and ab initio molecular dynamics (AIMD) simulations, we demonstrate the crystal structure of the Li7P2S8I (LPSI) and Li ionic conductivity at room temperature with its atomic-level mechanism. By successively applying three rigorous conceptual approaches, we identify that the LPSI has a similar symmetry class as Li10GeP2S12 (LGPS) material and estimate the Li ionic conductivity to be 0.3 mS cm(-1) with an activation energy of 0.20 eV, similar to the experimental value of 0.63 mS cm(-1). Iodine ions provide an additional path for Li ion diffusion, but a strong Li-I attractive interaction degrades the Li ionic transport. Calculated density of states (DOS) for LPSI indicate that electrochemical instability can be substantially improved by incorporating iodine at the Li metallic anode via forming a LiI compound. Our methods propose the computational design concept for a sulfide-based solid electrolyte with heteroatom doping for high-voltage Li ion batteries.

Local Symmetry Effects in Actinide 4f X-ray Absorption in Oxides

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

Butorin, Sergei M.; Modin, Anders; Vegelius, Johan R.

2016-03-23

A systematic X-ray absorption study at actinide N 6,7 (4f → 6d transitions) edges was performed for light-actinide oxides including data obtained for the first time for NpO 2, PuO 2, and UO 3. The measurements were supported by ab initio calculations based on local-density-approximation with added 5f-5f Coulomb interaction (LDA+U). Improved energy resolution compared to common experiments at actinide L 2,3 (2p → 6d transitions) edges allowed us to resolve the major structures of the unoccupied 6d density of states (DOS) and estimate the crystal-field splittings in the 6d shell directly from the spectra of light-actinide dioxides. The measurementsmore » demonstrated an enhanced sensitivity of the N 6,7 spectral shape to changes in the compound crystal structure. Finally, for nonstoichiometric NpO 2-x, the filling of the entire band gap with Np 6d states was observed thus supporting a phase coexistence of Np metal and stoichiometric NpO 2 which is in agreement with the tentative Np-O phase diagram.« less

Fermi surfaces, spin-mixing parameter, and colossal anisotropy of spin relaxation in transition metals from ab initio theory

NASA Astrophysics Data System (ADS)

Zimmermann, Bernd; Mavropoulos, Phivos; Long, Nguyen H.; Gerhorst, Christian-Roman; Blügel, Stefan; Mokrousov, Yuriy

2016-04-01

The Fermi surfaces and Elliott-Yafet spin-mixing parameter (EYP) of several elemental metals are studied by ab initio calculations. We focus first on the anisotropy of the EYP as a function of the direction of the spin-quantization axis [B. Zimmermann et al., Phys. Rev. Lett. 109, 236603 (2012), 10.1103/PhysRevLett.109.236603]. We analyze in detail the origin of the gigantic anisotropy in 5 d hcp metals as compared to 5 d cubic metals by band structure calculations and discuss the stability of our results against an applied magnetic field. We further present calculations of light (4 d and 3 d ) hcp crystals, where we find a huge increase of the EYP anisotropy, reaching colossal values as large as 6000 % in hcp Ti. We attribute these findings to the reduced strength of spin-orbit coupling, which promotes the anisotropic spin-flip hot loops at the Fermi surface. In order to conduct these investigations, we developed an adapted tetrahedron-based method for the precise calculation of Fermi surfaces of complicated shape and accurate Fermi-surface integrals within the full-potential relativistic Korringa-Kohn-Rostoker Green function method.

Silicate Melts of the Protolunar Disk and the Formation of the Magma Ocean from AB Initio Simulations

NASA Astrophysics Data System (ADS)

Caracas, R.; Stewart, S. T.

2018-05-01

We employ large-scale first-principles molecular dynamics simulations to understand the physical and chemical behavior of the evolution of the molten protolunar disk from its formation all the way to the crystallization of the magma ocean.

Ab Initio Path Integral Molecular Dynamics Study of the Nuclear Quantum Effect on Out-of-Plane Ring Deformation of Hydrogen Maleate Anion.

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

Ab initio path integral molecular dynamics (PIMD) simulation was performed to understand the nuclear quantum effect on the out-of-plane ring deformation of hydrogen maleate anion and investigate the existence of a stable structure with ring deformation, which was suggested in experimental observation (Fillaux et al., Chem. Phys. 1999, 120, 387-403). The isotope effect and the temperature effect are studied as well. We first investigated the nuclear quantum effect on the proton transfer. In static calculation and classical ab initio molecular dynamics simulations, the proton in the hydrogen bond is localized to either oxygen atom. On the other hand, the proton is located at the center of two oxygen atoms in quantum ab initio PIMD simulations. The nuclear quantum effect washes out the barrier of proton transfer. We next examined the nuclear quantum effect on the motion of hydrogen maleate anion. Principal component analysis revealed that the out-of-plane ring bending modes have dominant contribution to the entire molecular motion. In quantum ab initio PIMD simulations, structures with ring deformation were the global minimum for the deuterated isotope at 300 K. We analyzed the out-of-plane ring bending mode further and found that there are three minima along a ring distortion mode. We successfully found a stable structure with ring deformation of hydrogen maleate for the first time, to our knowledge, using theoretical calculation. The structures with ring deformation found in quantum simulation of the deuterated isotope allowed the proton transfer to occur more frequently than the planar structure. Static ab initio electronic structure calculation found that the structures with ring deformation have very small proton transfer barrier compared to the planar structure. We suggest that the "proton transfer driven" mechanism is the origin of stabilization for the structure with out-of-plane ring deformation.

Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.

Exotic behavior and crystal structures of calcium under pressure

PubMed Central

Oganov, Artem R.; Ma, Yanming; Xu, Ying; Errea, Ion; Bergara, Aitor; Lyakhov, Andriy O.

2010-01-01

Experimental studies established that calcium undergoes several counterintuitive transitions under pressure: fcc → bcc → simple cubic → Ca-IV → Ca-V, and becomes a good superconductor in the simple cubic and higher-pressure phases. Here, using ab initio evolutionary simulations, we explore the behavior of Ca under pressure and find a number of new phases. Our structural sequence differs from the traditional picture for Ca, but is similar to that for Sr. The β-tin (I41/amd) structure, rather than simple cubic, is predicted to be the theoretical ground state at 0 K and 33–71 GPa. This structure can be represented as a large distortion of the simple cubic structure, just as the higher-pressure phases stable between 71 and 134 GPa. The structure of Ca-V, stable above 134 GPa, is a complex host-guest structure. According to our calculations, the predicted phases are superconductors with Tc increasing under pressure and reaching approximately 20 K at 120 GPa, in good agreement with experiment. PMID:20382865

Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.

PubMed

Patil, Amol Baliram; Mahadeo Bhanage, Bhalchandra

2016-09-21

Room temperature ionic liquids (ILs), especially protic ionic liquids (PILs), are used in many areas of the chemical sciences. Ionicity, the extent of proton transfer, is a key parameter which determines many physicochemical properties and in turn the suitability of PILs for various applications. The spectrum of computational chemistry techniques applied to investigate ionic liquids includes classical molecular dynamics, Monte Carlo simulations, ab initio molecular dynamics, Density Functional Theory (DFT), CCSD(t) etc. At the other end of the spectrum is another computational approach: modern ab initio Valence Bond Theory (VBT). VBT differs from molecular orbital theory based methods in the expression of the molecular wave function. The molecular wave function in the valence bond ansatz is expressed as a linear combination of valence bond structures. These structures include covalent and ionic structures explicitly. Modern ab initio valence bond theory calculations of representative primary and tertiary ammonium protic ionic liquids indicate that modern ab initio valence bond theory can be employed to assess the acidity and ionicity of protic ionic liquids a priori.

Synthesis, Crystal Structures, Magnetic Properties, and Theoretical Investigation of a New Series of NiII-LnIII-WV Heterotrimetallics: Understanding the SMM Behavior of Mixed Polynuclear Complexes.

PubMed

Vieru, Veacheslav; Pasatoiu, Traian D; Ungur, Liviu; Suturina, Elizaveta; Madalan, Augustin M; Duhayon, Carine; Sutter, Jean-Pascal; Andruh, Marius; Chibotaru, Liviu F

2016-12-05

The polynuclear compounds containing anisotropic metal ions often exhibit efficient barriers for blocking of magnetization at fairly arbitrary geometries. However, at variance with mononuclear complexes, which usually become single-molecule magnets (SMM) under the sole requirement of a highly axial crystal field at the metal ion, the factors influencing the SMM behavior in polynuclear complexes, especially, with weakly axial magnetic ions, still remain largely unrevealed. As an attempt to clarify these conditions, we present here the synthesis, crystal structures, magnetic behavior, and ab initio calculations for a new series of Ni II -Ln III -W V trimetallics, [(CN) 7 W(CN)Ni(H 2 O)(valpn)Ln(H 2 O) 4 ]·H 2 O (Ln = Y 1, Eu 2, Gd 3, Tb 4, Dy 5, Lu 6). The surprising finding is the absence of the magnetic blockage even for compounds involving strongly anisotropic Dy III and Tb III metal ions. This is well explained by ab initio calculations showing relatively large transversal components of the g-tensor in the ground exchange Kramers doublets of 1 and 4 and large intrinsic tunneling gaps in the ground exchange doublets of 3 and 5. In order to get more insight into this behavior, another series of earlier reported compounds with the same trinuclear [W V Ni II Ln III ] core structure, [(CN) 7 W(CN)Ni(dmf)(valdmpn)Ln(dmf) 4 ]·H 2 O (Ln = Gd III 7, Tb III 8a, Dy III 9, Ho III 10), [(CN) 7 W(CN)Ni(H 2 O)(valdmpn)Tb(dmf) 2.5 (H 2 O) 1.5 ]·H 2 O·0.5dmf 8b, and [(CN) 7 W(CN)Ni(H 2 O)(valdmpn)Er(dmf) 3 (H 2 O) 1 ]·H 2 O·0.5dmf 11, has been also investigated theoretically. In this series, only 8b exhibits SMM behavior which is confirmed by the present ab initio calculations. An important feature for the entire series is the strong ferromagnetic coupling between Ni(II) and W(V), which is due to an almost perfect trigonal dodecahedron geometry of the octacyano wolframate fragment. The reason why only 8b is an SMM is explained by positive zero-field splitting on the nickel site, precluding magnetization blocking in complexes with fewer axial Ln ions. Further analysis has shown that, in the absence of ZFS on Ni ion, all compounds in the two series (except those containing Y and Gd) would be SMMs. The same situation arises for perfectly axial ZFS on Ni(II) with the main anisotropy axis parallel to the main magnetic axis of Ln(III) ions. In all other cases the ZFS on Ni(II) will worsen the SMM properties. The general conclusion is that the design of efficient SMMs on the basis of such complexes should involve isotropic or weekly anisotropic metal ions, such as Mn(II), Fe(III), etc., along with strongly axial lanthanides.

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

Osiry, H.; Cano, A.; Reguera, L.

The pentacyanonitrosylferrate complex anion, [Fe(CN){sub 5}NO]{sup 2−}, forms an insoluble solid with Hg(I) ion, of formula unit Hg{sub 2}[Fe(CN){sub 5}NO]·2H{sub 2}O, whose crystal structure and related properties are unknown. This contribution reports the preparation of that compound by the precipitation method and its structural study from X-ray powder patterns complemented with spectroscopic information from IR, Raman, and UV–vis techniques. The crystal structure was solved ab initio and then refined using the Rietveld method. The solid crystallizes with a triclinic unit cell, in the P−1 space group, with cell parameters a=10.1202(12), b=10.1000(13), c=7.4704(11) Å; α=110.664(10), β=110.114(10), γ=104.724(8) °. Within the unitmore » cell, two formula units are accommodated (Z=2). It adopts a layered structure related with the coordination of the equatorial CN groups at their N end to the Hg atoms while the axial CN ligand remains unlinked. Within the layers neighboring Hg{sub 2}[Fe(CN){sub 5}NO] building units remain linked through four relatively strong Hg–Hg interactions, with an interatomic distance of 2.549(3) Å. The charge donation from the equatorial CN groups through their 5σ orbitals results into an increase for the electron density on the Hg atoms, which strengths the Hg–Hg bond. In the Raman spectrum, that metal–metal bond is detected as a stretching vibration band at 167 cm{sup −1}. The available free volume between neighboring layers accommodates two water molecules, which are stabilized within the framework through hydrogen bonds with the N end of the unlinked axial CN group. The removal of these weakly bonded water molecules results in structural disorder for the material 3D framework. - Graphical abstract: Assembling of Hg{sub 2}[Fe(CN){sub 5}NO] units through Hg–Hg interactions. - Highlights: • Homometallic Hg–Hg interactions in metal nitroprusside. • 2D structure supported on metal–metal interactions. • Crystal structure and related properties for mercury (I) nitroprusside. • IR and UV–vis spectral features for mercury (I) nitroprusside.« less

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.

Elucidation of conformational states, dynamics, and mechanism of binding in human κ-opioid receptor complexes.

PubMed

Leonis, Georgios; Avramopoulos, Aggelos; Salmas, Ramin Ekhteiari; Durdagi, Serdar; Yurtsever, Mine; Papadopoulos, Manthos G

2014-08-25

Opioid G protein-coupled receptors (GPCRs) have been implicated in modulating pain, addiction, psychotomimesis, mood and memory, among other functions. We have employed the recently reported crystal structure of the human κ-opioid receptor (κ-OR) and performed molecular dynamics (MD), free energy, and ab initio calculations to elucidate the binding mechanism in complexes with antagonist JDTic and agonist SalA. The two systems were modeled in water and in DPPC lipid bilayers, in order to investigate the effect of the membrane upon conformational dynamics. MD and Atoms in Molecules (AIM) ab initio calculations for the complexes in water showed that each ligand was stabilized inside the binding site of the receptor through hydrogen bond interactions that involved residues Asp138 (with JDTic) and Gln115, His291, Leu212 (with SalA). The static description offered by the crystal structure was overcome to reveal a structural rearrangement of the binding pocket, which facilitated additional interactions between JDTic and Glu209/Tyr139. The role of Glu209 was emphasized, since it belongs to an extracellular loop that covers the binding site of the receptor and is crucial for ligand entrapment. The above interactions were retained in membrane complexes (SalA forms additional hydrogen bonds with Tyr139/312), except the Tyr139 interaction, which is abolished in the JDTic complex. For the first time, we report that JDTic alternates between a "V-shape" (stabilized via a water-mediated intramolecular interaction) and a more extended conformation, a feature that offers enough suppleness for effective binding. Moreover, MM-PBSA calculations showed that the more efficient JDTic binding to κ-OR compared to SalA (ΔGJDTic = -31.6 kcal mol(-1), ΔGSalA = -9.8 kcal mol(-1)) is attributed mostly to differences in electrostatic contributions. Importantly, our results are in qualitative agreement with the experiments (ΔGJDTic,exp = -14.4 kcal mol(-1), ΔGSalA,exp = -10.8 kcal mol(-1)). This study provides previously unattainable information on the dynamics of human κ-OR and insight on the rational design of drugs with improved pharmacological properties.

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors.

PubMed

Won, Jonghun; Lee, Gyu Rie; Park, Hahnbeom; Seok, Chaok

2018-06-07

The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by the observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed. A new metric for evaluating similarity of the target loop to templates was introduced for template selection. An ab initio loop sampling method was also developed to treat cases without highly similar templates. The ab initio method is based on the previously developed fragment assembly and loop closure method. A new sampling component that takes advantage of secondary structure prediction was added. In addition, a conserved disulfide bridge restraining ECL2 conformation was predicted and analytically incorporated into sampling, reducing the effective dimension of the conformational search space. The sampling method was combined with an existing energy function for comparison with previously reported loop structure prediction methods, and the benchmark test demonstrated outstanding performance.

2-Pyridinium propanol hydrogen squarate: experimental and computational study of a nonlinear optical material.

PubMed

Korkmaz, Ufuk; Bulut, Ahmet

2015-02-05

The experimental and theoretical investigation of a novel organic nonlinear optical (NLO) squarate salt of 2-pyridinium propanol hydrogen squarate (1), C8H12ON(+)·C4HO4(-), were reported in this study. The crystal structure of the title compound was found to crystallize in the triclinic P-1 space group. In the asymmetric unit each squaric acid molecules have donated one H atom to the pyridines N1 and N2 atoms of a 2-pyridine propanol molecule, forming the salt (1). The X-ray analysis clearly indicated that the crystal packing has shown the hydrogen bonding ring pattern of D2(2)(10) (α-dimer) through N-H⋯O interactions. The structural and vibrational properties of the compound were also studied by computational methods of ab initio performed on the compound at DFT/B3LYP/6-31++G(d,p) (2) and HF/6-31++G(d,p) (3) level of theory. The calculation results on the basis of two models for both the optimized molecular structure and vibrational properties for the 1 are presented and compared with the X-ray analysis result. The molecular electrostatic potential (MEP), electronic absorption spectra, frontier molecular orbitals (FMOs), conformational flexibility and non-linear optical properties (NLO) of the title compound were also studied at the 2 level and the results are reported. In order to evaluate the suitability for NLO applications thermal analysis (TG, DTA and DTG) data of 1 were also obtained. Copyright © 2014 Elsevier B.V. All rights reserved.

Synthesis, spectroscopic characterization and crystallographic behavior of a biologically relevant novel indole-fused heterocyclic compound - Experimental and theoretical (DFT) studies

NASA Astrophysics Data System (ADS)

Sharma, Sakshi; Brahmachari, Goutam; Banerjee, Bubun; Nurjamal, Khondekar; Kumar, Abhishek; Srivastava, Ambrish Kumar; Misra, Neeraj; Pandey, Sarvesh Kumar; Rajnikant; Gupta, Vivek K.

2016-08-01

The present communication deals with the eco-friendly synthesis, spectral properties and X-ray crystal structure of an indole derivative - Ethyl 2'-amino-3'-cyano-6'-methyl-5-nitro-2-oxospiro [indoline-3,4'-pyran]-5'-carboxylate. The title compound was synthesized in 87% yield. The crystal structure of the molecule is stabilized by intermolecular Nsbnd H … N, Nsbnd H … O and Csbnd H … π interactions. The molecule is organized in the crystal lattice forming sheet like structure. To interpret the experimental data, ab initio computations of the vibrational frequencies were carried out using the Gaussian 09 program followed by the full optimizations done using Density Functional Theory (DFT) at B3LYP/6-31 + G(d,p) level. The combined use of experiments and computations allowed a firm assignment of the majority of observed bands for the compound. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap were presented. The electronic and charge transfer properties have been explained on the basis of highest occupied molecular orbitals (HOMOs), lowest unoccupied molecular orbitals (LUMOs) and density of states (DOS). From the optimized geometry of the molecule, molecular electrostatic potential (MEP) distribution, frontier molecular orbitals (FMOs) of the title compound have been calculated in the ground state theoretically. The theoretical results showed good agreement with the experimental values. First hyperpolarizability values have been calculated to describe the nonlinear optical (NLO) property of the synthesized compound.

Electronic Structure and Thermoelectric Properties of Transition Metal Monosilicides

NASA Astrophysics Data System (ADS)

Pshenay-Severin, D. A.; Ivanov, Yu. V.; Burkov, A. T.; Novikov, S. V.; Zaitsev, V. K.; Reith, H.

2018-06-01

We present theoretical and experimental results on electronic structure and thermoelectric properties of cobalt monosilicide (CoSi) and of Co1- x M x Si diluted alloys (M = Fe and Ni) at temperatures from 2 K to 800 K. CoSi crystallizes into a non-centrosymmetric cubic B20 structure, which suggests the possibility of a topologically non-trivial electronic structure. We show that the electronic structure of CoSi exhibits linear band crossings in close vicinity to Fermi energy, confirming the possibility of non-trivial topology. The proximity of the linear-dispersion bands to Fermi energy implies their important contribution to the electronic transport. Calculation of thermopower of CoSi, using ab initio band structure and the constant relaxation time approximation, is carried out. It reveals that many body corrections to the electronic spectrum are important in order to obtain qualitative agreement of theoretical and experimental temperature dependences of thermopower. Phonon dispersion and lattice thermal conductivity are calculated. The phonons give a major contribution to the thermal conductivity of the compound below room temperature.

3D structural fluctuation of IgG1 antibody revealed by individual particle electron tomography

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

Zhang, Xing; Zhang, Lei; Tong, Huimin

2015-05-05

Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, wemore » derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding protein dynamics and functions.« less

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

NASA Astrophysics Data System (ADS)

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

2009-11-01

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

Applying the Coupled-Cluster Ansatz to Solids and Surfaces in the Thermodynamic Limit

NASA Astrophysics Data System (ADS)

Gruber, Thomas; Liao, Ke; Tsatsoulis, Theodoros; Hummel, Felix; Grüneis, Andreas

2018-04-01

Modern electronic structure theories can predict and simulate a wealth of phenomena in surface science and solid-state physics. In order to allow for a direct comparison with experiment, such ab initio predictions have to be made in the thermodynamic limit, substantially increasing the computational cost of many-electron wave-function theories. Here, we present a method that achieves thermodynamic limit results for solids and surfaces using the "gold standard" coupled cluster ansatz of quantum chemistry with unprecedented efficiency. We study the energy difference between carbon diamond and graphite crystals, adsorption energies of water on h -BN, as well as the cohesive energy of the Ne solid, demonstrating the increased efficiency and accuracy of coupled cluster theory for solids and surfaces.

X-ray absorption near edge structure/electron energy loss near edge structure calculation using the supercell orthogonalized linear combination of atomic orbitals method

NASA Astrophysics Data System (ADS)

Ching, Wai-Yim; Rulis, Paul

2009-03-01

Over the last eight years, a large number of x-ray absorption near edge structure (XANES) and/or electron energy loss near edge structure (ELNES) spectroscopic calculations for complex oxides and nitrides have been performed using the supercell-OLCAO (orthogonalized linear combination of atomic orbitals) method, obtaining results in very good agreement with experiments. The method takes into account the core-hole effect and includes the dipole matrix elements calculated from ab initio wavefunctions. In this paper, we describe the method in considerable detail, emphasizing the special advantages of this method for large complex systems. Selected results are reviewed and several hitherto unpublished results are also presented. These include the Y K edge of Y ions segregated to the core of a Σ31 grain boundary in alumina, O K edges of water molecules, C K edges in different types of single walled carbon nanotubes, and the Co K edge in the cyanocobalamin (vitamin B12) molecule. On the basis of these results, it is argued that the interpretation of specific features of the calculated XANES/ELNES edges is not simple for complex material systems because of the delocalized nature of the conduction band states. The long-standing notion of the 'fingerprinting' technique for spectral interpretation of experimental data is not tenable. A better approach is to fully characterize the structure under study, using either crystalline data or accurate ab initio modeling. Comparison between calculated XANES/ELNES spectra and available measurements enables us to ascertain the validity of the modeled structure. For complex crystals or structures, it is necessary to use the weighted sum of the spectra from structurally nonequivalent sites for comparison with the measured data. Future application of the supercell-OLCAO method to complex biomolecular systems is also discussed.

Ab-initio investigation of Rb substitution in KTP single crystal

NASA Astrophysics Data System (ADS)

Ghoohestani, Marzieh; Arab, Ali; Hashemifar, S. Javad; Sadeghi, Hossein

2018-01-01

The effects of rubidium doping on the structural, electronic, and optical properties of KTiOPO4 (KTP) are investigated in the framework of density functional theory. The equilibrium structural parameters of KTP and RbTiOPO4 (RTP) are calculated within the local density and Perdew-Burke-Ernzerhof (PBE), Wu-Cohen, and PBEsol formulation of generalized gradient approximations. We discuss that PBEsol predicts better equilibrium parameters for the KTP alloy. In addition, the variation of lattice constants and Ti-O-Ti bond angles are evaluated as a function of rubidium concentration. The modern modified Becke-Johnson functional is applied for more accurate band gap determination in the pure and alloyed KTP/RTP compounds. The phenomenological pseudoinversion parameter is calculated for a qualitative understanding of the effect of impurity on a non-linear optical response of KTP. We also analyze the behavior of the dielectric function, dispersive refractive indices, and birefringence of KTP/RTP alloys.

Stability limits and transformation pathways of α-quartz under high pressure

NASA Astrophysics Data System (ADS)

Hu, Q. Y.; Shu, J.-F.; Yang, W. G.; Park, C.; Chen, M. W.; Fujita, T.; Mao, H.-K.; Sheng, H. W.

2017-03-01

Ubiquitous on Earth, α-quartz plays an important role in modern science and technology. However, despite extensive research in the past, the mechanism of the polymorphic transitions of α-quartz at high pressures remains poorly understood. Here, combining in situ single-crystal x-ray diffraction experiment and advanced ab initio modeling, we report two stability limits and competing transition pathways of α-quartz under high pressure. Under near-equilibrium compression conditions at room temperature, α-quartz transits to a new P 2 /c silica phase via a structural intermediate. If the thermally activated transition is kinetically suppressed, the ultimate stability of α-quartz is controlled by its phonon instability and α-quartz collapses into a different crystalline phase. Our studies reveal that pressure-induced solid-state transformation of α-quartz undergoes a succession of structural stability limits, due to thermodynamic and mechanical catastrophes, and exhibits a hierarchy of transition pathways contingent upon kinetic conditions.

Factors Influencing the Mechanical Properties of Formamidinium Lead Halides and Related Hybrid Perovskites.

PubMed

Sun, Shijing; Isikgor, Furkan H; Deng, Zeyu; Wei, Fengxia; Kieslich, Gregor; Bristowe, Paul D; Ouyang, Jianyong; Cheetham, Anthony K

2017-10-09

The mechanical properties of formamidinium lead halide perovskites (FAPbX 3 , X=Br or I) grown by inverse-temperature crystallization have been studied by nanoindentation. The measured Young's moduli (9.7-12.3 GPa) and hardnesses (0.36-0.45 GPa) indicate good mechanical flexibility and ductility. The effects of hydrogen bonding were evaluated by performing ab initio molecular dynamics on both formamidinium and methylammonium perovskites and calculating radial distribution functions. The structural and chemical factors influencing these properties are discussed by comparison with corresponding values in the literature for other hybrid perovskites, including double perovskites. Our results reveal that bonding in the inorganic framework and hydrogen bonding play important roles in determining elastic stiffness. The influence of the organic cation becomes more important for structures at the limit of their perovskite stability, indicated by high tolerance factors. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Shi, X. M.; Wang, X. D., E-mail: wangxd@zju.edu.cn, E-mail: jiangjz@zju.edu.cn; Yu, Q.

The atomic structures of Al{sub 89}Y{sub 11}, Al{sub 90}Y{sub 6.5}La{sub 3.5}, and Al{sub 82.8}Y{sub 6.07}Ni{sub 8}La{sub 3.13} metallic glasses have been studied by using high energy X-ray diffraction, X-ray absorption fine structure combined with the ab initio molecular dynamics and reverse Monte Carlo simulations. It is demonstrated that the partial replacement of Y atoms by La has limited improvement of the glass forming ability (GFA), although La atoms reduce the ordering around Y atoms and also the fractions of icosahedron-like polyhedra centered by Al atoms. In contrast, Ni atoms can significantly improve the GFA, which are inclined to locate inmore » the shell of polyhedra centered by Al, Y, and La atoms, mainly forming Ni-centered icosahedron-like polyhedra to enhance the spatial connectivity between clusters and suppress the crystallization.« less

Ordered microporous layered lanthanide 1,3,5-benzenetriphosphonates pillared with cationic organic molecules.

PubMed

Araki, Takahiro; Kondo, Atsushi; Maeda, Kazuyuki

2015-04-13

Novel isomorphous pillared-layer-type crystalline lanthanide 1,3,5-benzenetriphosphonates were prepared with bpy and dbo as organic pillars (LnBP-bpy and LnBP-dbo; Ln: Ce, Pr, and Nd). Ab initio crystal structure solution using synchrotron X-ray powder diffraction data revealed that the organic pillars do not exist as neutral coordinating ligands but as cationic molecules. Especially the LnBP-dbo phases have ordered interlayer space filled with water molecules between the dbo pillars, and the interlayer water is successfully removed by heating under vacuum with slightly distorted but basically retained pillared layer structures. Microporosity of the materials is confirmed by adsorption of nitrogen, carbon dioxide, and hydrogen gases. Such microporous layered metal phosphonates pillared with cationic molecules should be unprecedented and should offer new strategies to design ordered microporous materials. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Towards accurate ab initio predictions of the vibrational spectrum of methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.

2002-01-01

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

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

Eremin, N. N., E-mail: neremin@geol.msu.ru; Grechanovsky, A. E.; Marchenko, E. I.

Semi-empirical and ab initio theoretical investigation of crystal structure geometry, interatomic distances, phase densities and elastic properties for some CaAl{sub 2}O{sub 4} phases under pressures up to 200 GPa was performed. Two independent simulation methods predicted the appearance of a still unknown super-dense CaAl{sub 2}O{sub 4} modification. In this structure, the Al coordination polyhedron might be described as distorted one with seven vertices. Ca atoms were situated inside polyhedra with ten vertices and Ca–O distances from 1.96 to 2.49 Å. It became the densest modification under pressures of 170 GPa (density functional theory prediction) or 150 GPa (semi-empirical prediction). Bothmore » approaches indicated that this super-dense CaAl{sub 2}O{sub 4} modification with a “stuffed α-PbO{sub 2}” type structure could be a probable candidate for mutual accumulation of Ca and Al in the lower mantle. The existence of this phase can be verified experimentally using high pressure techniques.« less

High-pressure structural and vibrational properties of monazite-type BiPO4, LaPO4, CePO4, and PrPO4

NASA Astrophysics Data System (ADS)

Errandonea, D.; Gomis, O.; Rodríguez-Hernández, P.; Muñoz, A.; Ruiz-Fuertes, J.; Gupta, M.; Achary, S. N.; Hirsch, A.; Manjon, F. J.; Peters, L.; Roth, G.; Tyagi, A. K.; Bettinelli, M.

2018-02-01

Monazite-type BiPO4, LaPO4, CePO4, and PrPO4 have been studied under high pressure by ab initio simulations and Raman spectroscopy measurements in the pressure range of stability of the monazite structure. A good agreement between experimental and theoretical Raman-active mode frequencies and pressure coefficients has been found which has allowed us to discuss the nature of the Raman-active modes. Besides, calculations have provided us with information on how the crystal structure is modified by pressure. This information has allowed us to determine the equation of state and the isothermal compressibility tensor of the four studied compounds. In addition, the information obtained on the polyhedral compressibility has been used to explain the anisotropic axial compressibility and the bulk compressibility of monazite phosphates. Finally, we have carried out a systematic discussion on the high-pressure behavior of the four studied phosphates in comparison to results of previous studies.

Finite temperature effects on the X-ray absorption spectra of energy related materials

NASA Astrophysics Data System (ADS)

Pascal, Tod; Prendergast, David

2014-03-01

We elucidate the role of room-temperature-induced instantaneous structural distortions in the Li K-edge X-ray absorption spectra (XAS) of crystalline LiF, Li2SO4, Li2O, Li3N and Li2CO3 using high resolution X-ray Raman spectroscopy (XRS) measurements and first-principles density functional theory calculations within the eXcited electron and Core Hole (XCH) approach. Based on thermodynamic sampling via ab-initio molecular dynamics (MD) simulations, we find calculated XAS in much better agreement with experiment than those computed using the rigid crystal structure alone. We show that local instantaneous distortion of the atomic lattice perturbs the symmetry of the Li 1 s core-excited-state electronic structure, broadening spectral line-shapes and, in some cases, producing additional spectral features. This work was conducted within the Batteries for Advanced Transportation Technologies (BATT) Program, supported by the U.S. Department of Energy Vehicle Technologies Program under Contract No. DE-AC02-05CH11231.

Ab initio theory and modeling of water.

PubMed

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

2017-10-10

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

Ab initio theory and modeling of water

PubMed Central

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

2017-01-01

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

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

Local structure order in Pd 78Cu 6Si 16 liquid

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

Yue, G. Q.; Zhang, Y.; Sun, Y.

2015-02-05

The short-range order (SRO) in Pd 78Cu 6Si 16 liquid was studied by high energy x-ray diffraction and ab initio molecular dynamics (MD) simulations. The calculated pair correlation functions at different temperatures agree well with the experimental results. The partial pair correlation functions from ab intio MD simulations indicate that Si atoms prefer to be uniformly distributed while Cu atoms tend to aggregate. By performing structure analysis using Honeycutt-Andersen index, Voronoi tessellation, and atomic cluster alignment method, we show that the icosahedron and face-centered cubic SRO increase upon cooling. The dominant SRO is the Pd-centered Pd 9Si 2 motif, namelymore » the structure of which motif is similar to the structure of Pd-centered clusters in the Pd 9Si 2 crystal. The study further confirms the existence of trigonal prism capped with three half-octahedra that is reported as a structural unit in Pd-based amorphous alloys. The majority of Cu-centered clusters are icosahedra, suggesting that the presence of Cu is benefit to promote the glass forming ability.« less

Cumulant Green's function calculations of plasmon satellites in bulk sodium: Influence of screening and the crystal environment

NASA Astrophysics Data System (ADS)

Zhou, Jianqiang Sky; Gatti, Matteo; Kas, J. J.; Rehr, J. J.; Reining, Lucia

2018-01-01

We present ab initio calculations of the photoemission spectra of bulk sodium using different flavors of the cumulant expansion approximation for the Green's function. In particular, we study the dispersion and intensity of the plasmon satellites. We show that the satellite spectrum is much more sensitive to many details than the quasiparticle spectrum, which suggests that the experimental investigation of satellites could yield additional information beyond the usual studies of the band structure. In particular, a comparison to the homogeneous electron gas shows that the satellites are influenced by the crystal environment, although the crystal potential in sodium is weak. Moreover, the temperature dependence of the lattice constant is reflected in the position of the satellites. Details of the screening also play an important role; in particular, the contribution of transitions from 2 s and 2 p semicore levels influences the satellites, but not the quasiparticle. Moreover, inclusion of contributions to the screening beyond the random-phase approximation has an effect on the satellites. Finally, we elucidate the importance of the coupling of electrons and holes by comparing the results of the time-ordered and the retarded cumulant expansion approximations. Again, we find small but noticeable differences. Since all the small effects add up, our most advanced calculation yields a satellite position which is improved with respect to previous calculations by almost 1 eV. This stresses the fact that the calculation of satellites is much more delicate than the calculation of a quasiparticle band structure.

Transition to collapsed tetragonal phase in CaFe 2As 2 single crystals as seen by 57Fe Mössbauer spectroscopy

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

Bud'ko, Sergey L.; Ma, Xiaoming; Tomić, Milan

Temperature dependent measurements of 57Fe Mössbauer spectra on CaFe 2As 2 single crystals in the tetragonal and collapsed tetragonal phases are reported. Clear features in the temperature dependencies of the isomer shift, relative spectra area, and quadrupole splitting are observed at the transition from the tetragonal to the collapsed tetragonal phase. From the temperature dependent isomer shift and spectral area data, an average stiffening of the phonon modes in the collapsed tetragonal phase is inferred. The quadrupole splitting increases by ~25% on cooling from room temperature to ~100 K in the tetragonal phase and is only weakly temperature dependent atmore » low temperatures in the collapsed tetragonal phase, in agreement with the anisotropic thermal expansion in this material. In order to gain microscopic insight about these measurements, we perform ab initio density functional theory calculations of the electric field gradient and the electron density of CaFe 2As 2 in both phases. By comparing the experimental data with the calculations we are able to fully characterize the crystal structure of the samples in the collapsed-tetragonal phase through determination of the As z coordinate. Furthermore, based on the obtained temperature dependent structural data we are able to propose charge saturation of the Fe-As bond region as the mechanism behind the stabilization of the collapsed-tetragonal phase at ambient pressure.« less

Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

NASA Astrophysics Data System (ADS)

Castro-Palacios, Juan Carlos; Rubayo-Soneira, Jesús; Ishii, Keisaku; Yamashita, Koichi

2007-04-01

The intermolecular potentials for the NO(XΠ2)-Kr and NO(AΣ+2)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1A'2 state [NO(XΠ2)-Kr ] and the multireference singles and doubles configuration interaction method for the excited 2A'2 state [NO(AΣ+2)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic results. A general overall view of the results suggests that, when the Kr-NO interaction takes place inside the matrix, potentials are rather symmetric and less repulsive than those for the triatomic system. pectroscopy, yields a mean absolute deviation of about 5cm-1 over the 22 levels. The dissociation energy with respect to the lowest vibrational energy is calculated within 30cm-1 of the experimental value of 12953±8cm-1. The reported agreement of the theoretical spectrum and dissociation energy with experiment is contingent upon the inclusion of the effects of core-generated electron correlation, spin-orbit coupling, and scalar relativity. The Dunham analysis [Phys. Rev. 41, 721 (1932)] of the spectrum is found to be very accurate. New values are given for the spectroscopic constants.

Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

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

2015-05-01

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 (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) 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.

On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials.

PubMed

Noel, Yves; D'arco, Philippe; Demichelis, Raffaella; Zicovich-Wilson, Claudio M; Dovesi, Roberto

2010-03-01

Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two-dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono- and bi-electronic integrals that enter into the Fock (Kohn-Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M x 2M matrix. The efficiency and accuracy of the computational scheme is documented. (c) 2009 Wiley Periodicals, Inc.

ns2np4 (n = 4, 5) lone pair triplets whirling in M*F2E3 (M* = Kr, Xe): Stereochemistry and ab initio analyses

NASA Astrophysics Data System (ADS)

Galy, Jean; Matar, Samir F.

2017-02-01

The stereochemistry of ns2np4 (n = 4, 5) lone pair LP characterizing noble gas Kr and Xe (labeled M*) in M*F2 difluorides is examined within coherent crystal chemistry and ab initio visualizations. M*2+ in such oxidation state brings three lone pairs (E) and difluorides are formulated M*F2E3. The analyses use electron localization function (ELF) obtained within density functional theory calculations showing the development of the LP triplets whirling {E3} quantified in the relevant chemical systems. Detailed ELF data analyses allowed showing that in α KrF2E3 and isostructural XeF2E3 difluorides the three E electronic clouds merge or hybridize into a torus and adopt a perfect gyration circle with an elliptical section, while in β KrF2 the network architecture deforms the whole torus into an ellipsoid shape. Original precise metrics are provided for the torus in the different compounds under study. In KrF2 the geometric changes upon β → α phase transition is schematized and mechanisms for the transformation with temperature or pressure are proposed. The results are further highlighted by electronic band structure calculations which show similar features of equal band gaps of 3 eV in both α and β KrF2 and a reorganization of frontier orbitals due to the different orientations of the F-Kr-F linear molecule in the two tetragonal structures.

Experimental evidence of new tetragonal polymorphs of silicon formed through ultrafast laser-induced confined microexplosion

DOE PAGES

Rapp, L.; Haberl, B.; Pickard, C. J.; ...

2015-06-29

Ordinary materials can transform into novel phases with new crystal structures at extraordinary high pressure and temperature applied under both equilibrium and non-equilibrium conditions 1-6. The recently developed method of ultra-short laser-induced confined microexplosions 7-9 extends the range of possible new phases by initiating a highly non-equilibrium plasma state deep inside a bulk material 7-12. Ultra-high quenching rates can help to overcome kinetic barriers to the formation of new metastable phases, while the surrounding pristine crystal confines the affected material and preserves it for further study 10-12. Here we demonstrate that ultra-rapid pressure release from a completely disordered plasma statemore » in silicon produces several new metastable end phases quenched to ambient conditions. Their structure is determined from comparison to an ab initio random structure search which revealed six new energetically competitive potential phases, four tetragonal and two monoclinic ones. We show the presence of bt8 and st12, which have been predicted theoretically previously 13-15, but have not been observed in nature or in laboratory experiments. Additionally, the presence of the as yet unidentified silicon phase, Si-VIII and two of our other predicted tetragonal phases are highly likely within laser-affected zones. These findings pave the way for new materials with novel and exotic properties.« less

Discovery of a Red-Emitting Li3RbGe8O18:Mn4+ Phosphor in the Alkali-Germanate System: Structural Determination and Electronic Calculations.

PubMed

Singh, Satendra Pal; Kim, Minseuk; Park, Woon Bae; Lee, Jin-Woong; Sohn, Kee-Sun

2016-10-17

A solid-state combinatorial chemistry approach, which used the A-Ge-O (A = Li, K, Rb) system doped with a small amount of Mn 4+ as an activator, was adopted in a search for novel red-emitting phosphors. The A site may have been composed of either a single alkali metal ion or of a combination of them. This approach led to the discovery of a novel phosphor in the above system with the chemical formula Li 3 RbGe 8 O 18 :Mn 4+ . The crystal structure of this novel phosphor was solved via direct methods, and subsequent Rietveld refinement revealed a trigonal structure in the P3̅1m space group. The discovered phosphor is believed to be novel in the sense that neither the crystal structure nor the chemical formula matches any of the prototype structures available in the crystallographic information database (ICDD or ICSD). The measured photoluminescence intensity that peaked at a wavelength of 667 nm was found to be much higher than the best intensity obtained among all the existing A 2 Ge 4 O 9 (A = Li, K, Rb) compounds in the alkali-germanate system. An ab initio calculation based on density function theory (DFT) was conducted to verify the crystal structure model and compare the calculated value of the optical band gap with the experimental results. The optical band gap obtained from diffuse reflectance measurement (5.26 eV) and DFT calculation (4.64 eV) results were in very good agreement. The emission wavelength of this phosphor that exists in the deep red region of the electromagnetic spectrum may be very useful for increasing the color gamut of LED-based display devices such as ultrahigh-definition television (UHDTV) as per the ITU-R BT.2020-2 recommendations and also for down-converter phosphors that are used in solar-cell applications.

Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.

PubMed

Simkovic, Felix; Thomas, Jens M H; Keegan, Ronan M; Winn, Martyn D; Mayans, Olga; Rigden, Daniel J

2016-07-01

For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.

Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds

PubMed Central

Simkovic, Felix; Thomas, Jens M. H.; Keegan, Ronan M.; Winn, Martyn D.; Mayans, Olga; Rigden, Daniel J.

2016-01-01

For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions (‘decoys’), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue–residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing. PMID:27437113

High pressure luminescence of Nd3+ in YAlO3 perovskite nanocrystals: A crystal-field analysis

NASA Astrophysics Data System (ADS)

Hernández-Rodríguez, Miguel A.; Muñoz-Santiuste, Juan E.; Lavín, Víctor; Lozano-Gorrín, Antonio D.; Rodríguez-Hernández, Plácida; Muñoz, Alfonso; Venkatramu, Vemula; Martín, Inocencio R.; Rodríguez-Mendoza, Ulises R.

2018-01-01

Pressure-induced energy blue- and red-shifts of the 4F3/2 → 4I9/2,11/2 near-infrared emission lines of Nd3+ ions in YAlO3 perovskite nano-particles have been measured from ambient conditions up to 29 GPa. Different positive and negative linear pressure coefficients have been calibrated for the emission lines and related to pressure-induced changes in the interactions between those Nd3+ ions and their twelve oxygen ligands at the yttrium site. Potentiality of the simple overlap model, combined with ab initio structural calculations, in the description of the effects of these interactions on the energy levels and luminescence properties of the optically active Nd3+ ion is emphasized. Simulations show how the energies of the 4f3 ground configuration and the barycenters of the multiplets increase with pressure, whereas the Coulomb interaction between f-electrons decreases and the crystal-field strength increases. All these effects combined explain the wavelength blue-shifts of some near-infrared emission lines of Nd3+ ions. Large pressure rates of various emission lines suggest that a YAlO3 perovskite nano-crystal can be a potential candidate for near-infrared optical pressure sensors.

Complete titanium substitution by boron in a tetragonal prism: exploring the complex boride series Ti(3-x)Ru(5-y)Ir(y)B(2+x) (0 ≤ x ≤ 1 and 1 < y < 3) by experiment and theory.

PubMed

Fokwa, Boniface P T; Hermus, Martin

2011-04-18

Polycrystalline samples and single crystals of four members of the new complex boride series Ti(3-x)Ru(5-y)Ir(y)B(2+x) (0 ≤ x ≤ 1 and 1 < y < 3) were synthesized by arc-melting the elements in a water-cooled copper crucible under an argon atmosphere. The new silvery phases were structurally characterized by powder and single-crystal X-ray diffraction as well as energy- and wavelength-dispersive X-ray spectroscopy analyses. They crystallize with the tetragonal Ti(3)Co(5)B(2) structure type in space group P4/mbm (No. 127). Tetragonal prisms of Ru/Ir atoms are filled with titanium in the boron-poorest phase (Ti(3)Ru(2.9)Ir(2.1)B(2)). Gradual substitution of titanium by boron then results in the successive filling of this site by a Ti/B mixture en route to the complete boron occupation, leading to the boron-richest phase (Ti(2)Ru(2.8)Ir(2.2)B(3)). Furthermore, both ruthenium and iridium share two sites in these structures, but a clear Ru/Ir site preference is found. First-principles density functional theory calculations (Vienna ab initio simulation package) on appropriate structural models (using a supercell approach) have provided more evidence on the stability of the boron-richest and -poorest phases, and the calculated lattice parameters corroborate very well with the experimentally found ones. Linear muffin-tin orbital atomic sphere approximation calculations further supported these findings through crystal orbital Hamilton population bonding analyses, which also show that the Ru/Ir-B and Ru/Ir-Ti heteroatomic interactions are mainly responsible for the structural stability of these compounds. Furthermore, some stable and unstable phases of this complex series could be predicted using the rigid-band model. According to the density of states analyses, all phases should be metallic conductors, as was expected from these metal-rich borides.

Microscopic origin of entropy-driven polymorphism in hybrid organic-inorganic perovskite materials

NASA Astrophysics Data System (ADS)

Butler, Keith T.; Svane, Katrine; Kieslich, Gregor; Cheetham, Anthony K.; Walsh, Aron

2016-11-01

Entropy is a critical, but often overlooked, factor in determining the relative stabilities of crystal phases. The importance of entropy is most pronounced in softer materials, where small changes in free energy can drive phase transitions, which has recently been demonstrated in the case of organic-inorganic hybrid-formate perovskites. In this Rapid Communication we demonstrate the interplay between composition and crystal structure that is responsible for the particularly pronounced role of entropy in determining polymorphism in hybrid organic-inorganic materials. Using ab initio based lattice dynamics, we probe the origins and effects of vibrational entropy of four archetype perovskite (A B X3 ) structures. We consider an inorganic material (SrTiO3), an A -site hybrid-halide material (CH3NH3) PbI3 , a X -site hybrid material KSr (BH4)3 , and a mixed A - and X -site hybrid-formate material (N2H5) Zn (HCO2)3 , comparing the differences in entropy between two common polymorphs. The results demonstrate the importance of low-frequency intermolecular modes in determining the phase stability in these materials. The understanding gained allows us to propose a general principle for the relative stability of different polymorphs of hybrid materials as temperature is increased.

Evidence for a Peierls phase-transition in a three-dimensional multiple charge-density waves solid

PubMed Central

Mansart, Barbara; Cottet, Mathieu J. G.; Penfold, Thomas J.; Dugdale, Stephen B.; Tediosi, Riccardo; Chergui, Majed; Carbone, Fabrizio

2012-01-01

The effect of dimensionality on materials properties has become strikingly evident with the recent discovery of graphene. Charge ordering phenomena can be induced in one dimension by periodic distortions of a material’s crystal structure, termed Peierls ordering transition. Charge-density waves can also be induced in solids by strong coulomb repulsion between carriers, and at the extreme limit, Wigner predicted that crystallization itself can be induced in an electrons gas in free space close to the absolute zero of temperature. Similar phenomena are observed also in higher dimensions, but the microscopic description of the corresponding phase transition is often controversial, and remains an open field of research for fundamental physics. Here, we photoinduce the melting of the charge ordering in a complex three-dimensional solid and monitor the consequent charge redistribution by probing the optical response over a broad spectral range with ultrashort laser pulses. Although the photoinduced electronic temperature far exceeds the critical value, the charge-density wave is preserved until the lattice is sufficiently distorted to induce the phase transition. Combining this result with ab initio electronic structure calculations, we identified the Peierls origin of multiple charge-density waves in a three-dimensional system for the first time. PMID:22451898

Understanding lattice thermal conductivity in thermoelectric clathrates: A density functional theory study on binary Si-based type-I clathrates

NASA Astrophysics Data System (ADS)

Euchner, Holger; Pailhès, Stéphane; Giordano, Valentina M.; de Boissieu, Marc

2018-01-01

Despite their crystalline nature, thermoelectric clathrates exhibit a strongly reduced lattice thermal conductivity. While the reason for this unexpected behavior is known to lie in the peculiarities of the complex crystal structure and the interplay of the underlying guest-host framework, their respective roles are still not fully disentangled and understood. Our ab initio study of the most simple type-I clathrate phase, the binary compound Ba8Si46 and its derivatives Ba8 -xSi46 seeks to identify these mechanisms and provides insight into their origin. Indeed, the strongly decreased lattice thermal conductivity in thermoelectric clathrates is a consequence of a reduction of the acoustic phonon bandwidth, a lowering of the acoustic phonon group velocities, and the amplification of three-phonon-scattering processes. While the complexity of the crystal structure is demonstrated not to be the leading factor, the reasons are manifold. A modified Si-Si interaction causes a first decrease of the sound velocity, whereas the presence of flat Ba modes results in an additional lowering. These modes correspond to confined Bloch states that are localized on the Ba atoms and significantly increase the scattering phase space and, together with an increased anharmonicity of the interatomic interactions, strongly affect the phonon lifetimes.

Direct band gap silicon crystals predicted by an inverse design method

NASA Astrophysics Data System (ADS)

Oh, Young Jun; Lee, In-Ho; Lee, Jooyoung; Kim, Sunghyun; Chang, Kee Joo

2015-03-01

Cubic diamond silicon has an indirect band gap and does not absorb or emit light as efficiently as other semiconductors with direct band gaps. Thus, searching for Si crystals with direct band gaps around 1.3 eV is important to realize efficient thin-film solar cells. In this work, we report various crystalline silicon allotropes with direct and quasi-direct band gaps, which are predicted by the inverse design method which combines a conformation space annealing algorithm for global optimization and first-principles density functional calculations. The predicted allotropes exhibit energies less than 0.3 eV per atom and good lattice matches, compared with the diamond structure. The structural stability is examined by performing finite-temperature ab initio molecular dynamics simulations and calculating the phonon spectra. The absorption spectra are obtained by solving the Bethe-Salpeter equation together with the quasiparticle G0W0 approximation. For several allotropes with the band gaps around 1 eV, photovoltaic efficiencies are comparable to those of best-known photovoltaic absorbers such as CuInSe2. This work is supported by the National Research Foundation of Korea (2005-0093845 and 2008-0061987), Samsung Science and Technology Foundation (SSTF-BA1401-08), KIAS Center for Advanced Computation, and KISTI (KSC-2013-C2-040).

Experimental and ab Initio Study of Catena(bis(μ2-iodo)-6-methylquinoline-copper(I)) under Pressure: Synthesis, Crystal Structure, Electronic, and Luminescence Properties.

PubMed

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).

Photoluminescent SBA-16 Rhombic Dodecahedral Particles: Assembly, Characterization, and ab Initio Modeling.

PubMed

Ruso, Juan M; Pardo, Victor; Sartuqui, Javier; Gravina, Noel; D'Elía, Noelia L; Pieroni, Olga I; Messina, Paula V

2015-06-17

Nowadays, the use of polyhedral instead of spherical particles as building blocks of engineering new materials has become an area of particular effort in the scientific community. Therefore, fabricating in a reproducible manner large amounts of uniform crystal-like particles is a huge challenge. In this work we report a low reagent-consuming binary surfactant templated method mediated by a hydrothermal treatment as a facile and controllable route for the synthesis of crystal-like rombdodecahedral particles exhibiting SBA-16 mesoporosity. It was determined that the hydrothermal treatment conditions were a key point upon the final material morphology, surface area, microporosity, wall thickness, and mesopore width. As a consequence of their internal mesoporosity order, rhombic dodecahedral synthesized particles exhibited highly efficient ultraviolet absorptions and photoluminescence emissions at room temperature. Conducting experimental and theoretical comparative studies allowed us to infer that the presence of intrinsic defects confined into an ordered mesoporous structure plays a very important role in semiconductor materials. The information presented here is expected to be useful, giving new, accurate information, for the construction of novel technological devices.

Experimental and ab initio studies on sub-lattice ordering and magnetism in Co{sub 2}Fe(Ge{sub 1−x}Si{sub x}) alloys

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

Deka, Bhargab; Kundu, Ashis; Ghosh, Subhradip

2015-10-07

Crystallographic and magnetic properties of bulk Co{sub 2}Fe(Ge{sub 1−x}Si{sub x}) alloys with 0 ≤ x ≤ 1, synthesized by arc melting method, have been studied. Co{sub 2}FeSi alloy has been found to crystallize with L2{sub 1} structure, but the super-lattice peaks are absent in the X-ray diffraction patterns of alloys containing high Ge concentration. Unit cell volume of this series of alloys decreased from 185.2 to 178.5 Å{sup 3} as Si content was increased from 0 to 1.00. All alloy compositions exhibit ferromagnetic behavior with a high Curie temperature (T{sub C}). T{sub C} showed a systematic variation with x. A comparison between the valuesmore » of saturation magnetization (M{sub s}) and effective moment per magnetic atom p{sub c} estimated from the temperature dependent susceptibility data above T{sub C}, shows that the alloys have half-metallic character. The alloy with x = 0 follows Slater-Pauling (S-P) rule with M{sub s} of 5.99μ{sub B}. However, M{sub s} for the alloy with x = 1.00 was found to be 5.42μ{sub B}, which is lower than the value of 6.0μ{sub B} predicted by S-P rule. Since atomic disorder is known to affect the M{sub s} and electronic structure of these alloys, ab initio calculations were carried out to explain the deviation in observed M{sub s} from S-P rule prediction and the half-metallic character of the alloys. Ab initio calculations reveal that alloys with L2{sub 1} structure have M{sub s} value as predicted by S-P rule. However, introduction of 12.5% DO{sub 3} disorder, which occurs due to swapping of Co and Fe atoms in the unit cell, decreases M{sub s} of alloys with x > 0 from the S-P prediction to values obtained experimentally. The results analyzed from the view point of electronic structure of the alloys in different ordered states bring out the influence of disorder on the observed magnetic properties of these technologically important alloys.« less

Crystal structures of Boro-AFm and sBoro-AFt phases

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

Champenois, Jean-Baptiste; Mesbah, Adel; Clermont Universite, ENSCCF, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand

2012-10-15

Crystal structures of boron-containing AFm (B-AFm) and AFt (B-AFt) phases have been solved ab-initio and refined from X-ray powder diffraction. {sup 11}B NMR and Raman spectroscopies confirm the boron local environment in both compounds: three-fold coordinated in B-AFm corresponding to HBO{sub 3}{sup 2-} species, and four-fold coordinated in B-AFt corresponding to B (OH){sub 4}{sup -} species. B-AFm crystallizes in the rhombohedral R3{sup Macron }c space group and has the 3CaO{center_dot}Al{sub 2}O{sub 3}{center_dot}CaHBO{sub 3}{center_dot}12H{sub 2}O (4CaO{center_dot}Al{sub 2}O{sub 3}{center_dot}1/2B{sub 2}O{sub 3}{center_dot}12.5H{sub 2}O, C{sub 4}AB{sub 1/2}H{sub 12.5}) general formulae with planar trigonal HBO{sub 3}{sup 2-} anions weakly bonded at the centre of themore » interlayer region. One HBO{sub 3}{sup 2-} anion is statistically distributed with two weakly bonded water molecules on the same crystallographic site. B-AFt crystallizes in the trigonal P3cl space group and has the 3CaO{center_dot}Al{sub 2}O{sub 3}{center_dot}Ca(OH){sub 2}{center_dot}2Ca(B (OH){sub 4}){sub 2}{center_dot}24H{sub 2}O (6CaO{center_dot}Al{sub 2}O{sub 3}{center_dot}2B{sub 2}O{sub 3}{center_dot}33H{sub 2}O, C{sub 6}AB{sub 2}H{sub 33}) general formulae with tetrahedral B (OH){sub 4}{sup -} anions located in the channel region of the structure. All tetrahedral anions are oriented in a unique direction, leading to a hexagonal c lattice parameter about half that of ettringite.« less

Ab initio structures and polarizabilities of sodium clusters

NASA Astrophysics Data System (ADS)

Kronik, Leeor; Vasiliev, Igor; Jain, Manish; Chelikowsky, James R.

2001-09-01

We present quantitative ab initio calculations for Na cluster structures and polarizabilities, for all cluster sizes up to 20 atoms. Our calculations are performed by combining an ab initio core-corrected pseudopotential and a gradient-corrected density functional within a real space approach. We find the cluster bonding to be very floppy and catalog a host of low-energy quasi-degenerate isomers for all second-decade clusters. The existence of these isomers results in a band of polarizability values for each cluster size even at zero temperature. This eliminates any finer structure in the polarizability curve. We further show that the experimental polarizability values are consistently underestimated by calculations at zero temperature. By computing the effects of structure expansion and distortion due to a finite temperature we arrive at a quantitative agreement between theory and experiment.

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

PubMed Central

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian

2017-01-01

Abstract Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Results: We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28453681

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

PubMed

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

2017-05-01

Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

Electronic structure, magnetism, and antisite disorder in CoFeCrGe and CoMnCrAl quaternary Heusler alloys

DOE PAGES

Enamullah, .; Venkateswara, Y.; Gupta, Sachin; ...

2015-12-10

In this study, we present a combined theoretical and experimental study of two quaternary Heusler alloys CoFeCrGe (CFCG) and CoMnCrAl (CMCA), promising candidates for spintronics applications. Magnetization measurement shows the saturation magnetization and transition temperature to be 3 μ B, 866 K and 0.9 μ B, 358 K for CFCG and CMCA respectively. The magnetization values agree fairly well with our theoretical results and also obey the Slater-Pauling rule, a prerequisite for half metallicity. A striking difference between the two systems is their structure; CFCG crystallizes in fully ordered Y-type structure while CMCA has L2 1 disordered structure. The antisitemore » disorder adds a somewhat unique property to the second compound, which arises due to the probabilistic mutual exchange of Al positions with Cr/Mn and such an effect is possibly expected due to comparable electronegativities of Al and Cr/Mn. Ab initio simulation predicted a unique transition from half metallic ferromagnet to metallic antiferromagnet beyond a critical excess concentration of Al in the alloy.« less

Accuracy of existing atomic potentials for the CdTe semiconductor compound

NASA Astrophysics Data System (ADS)

Ward, D. K.; Zhou, X. W.; Wong, B. M.; Doty, F. P.; Zimmerman, J. A.

2011-06-01

CdTe and CdTe-based Cd1-xZnxTe (CZT) alloys are important semiconductor compounds that are used in a variety of technologies including solar cells, radiation detectors, and medical imaging devices. Performance of such systems, however, is limited due to the propensity of nano- and micro-scale defects that form during crystal growth and manufacturing processes. Molecular dynamics simulations offer an effective approach to study the formation and interaction of atomic scale defects in these crystals, and provide insight on how to minimize their concentrations. The success of such a modeling effort relies on the accuracy and transferability of the underlying interatomic potential used in simulations. Such a potential must not only predict a correct trend of structures and energies of a variety of elemental and compound lattices, defects, and surfaces but also capture correct melting behavior and should be capable of simulating crystalline growth during vapor deposition as these processes sample a variety of local configurations. In this paper, we perform a detailed evaluation of the performance of two literature potentials for CdTe, one having the Stillinger-Weber form and the other possessing the Tersoff form. We examine simulations of structures and the corresponding energies of a variety of elemental and compound lattices, defects, and surfaces compared to those obtained from ab initio calculations and experiments. We also perform melting temperature calculations and vapor deposition simulations. Our calculations show that the Stillinger-Weber parameterization produces the correct lowest energy structure. This potential, however, is not sufficiently transferrable for defect studies. Origins of the problems of these potentials are discussed and insights leading to the development of a more transferrable potential suitable for molecular dynamics simulations of defects in CdTe crystals are provided.

Magnetic properties of vanadium doped CdTe: Ab initio calculations

NASA Astrophysics Data System (ADS)

Goumrhar, F.; Bahmad, L.; Mounkachi, O.; Benyoussef, A.

2017-04-01

In this paper, we are applying the ab initio calculations to study the magnetic properties of vanadium doped CdTe. This study is based on the Korringa-Kohn-Rostoker method (KKR) combined with the coherent potential approximation (CPA), within the local density approximation (LDA). This method is called KKR-CPA-LDA. We have calculated and plotted the density of states (DOS) in the energy diagram for different concentrations of dopants. We have also investigated the magnetic and half-metallic properties of this compound and shown the mechanism of exchange interaction. Moreover, we have estimated the Curie temperature Tc for different concentrations. Finally, we have shown how the crystal field and the exchange splittings vary as a function of the concentrations.

From Dimer to Crystal: Calculating the Cohesive Energy of Rare Gas Solids

ERIC Educational Resources Information Center

Halpern, Arthur M.

2012-01-01

An upper-level undergraduate project is described in which students perform high-level ab initio computational scans of the potential energy curves for Ne[subscript 2] and Ar[subscript 2] and obtain the respective Lennard-Jones (LJ) potential parameters [sigma] and [epsilon] for the dimers. Using this information, along with the summation of…

Visualization and processing of computed solid-state NMR parameters: MagresView and MagresPython.

PubMed

Sturniolo, Simone; Green, Timothy F G; Hanson, Robert M; Zilka, Miri; Refson, Keith; Hodgkinson, Paul; Brown, Steven P; Yates, Jonathan R

2016-09-01

We introduce two open source tools to aid the processing and visualisation of ab-initio computed solid-state NMR parameters. The Magres file format for computed NMR parameters (as implemented in CASTEP v8.0 and QuantumEspresso v5.0.0) is implemented. MagresView is built upon the widely used Jmol crystal viewer, and provides an intuitive environment to display computed NMR parameters. It can provide simple pictorial representation of one- and two-dimensional NMR spectra as well as output a selected spin-system for exact simulations with dedicated spin-dynamics software. MagresPython provides a simple scripting environment to manipulate large numbers of computed NMR parameters to search for structural correlations. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Magnetic properties of Zn0.9(Mn0.05,Ni0.05)O nanoparticle: Experimental and theoretical investigation

NASA Astrophysics Data System (ADS)

Mounkachi, O.; Lakhal, M.; Labrim, H.; Hamedoun, M.; Benyoussef, A.; El Kenz, A.; Loulidi, M.; Bhihi, M.

2012-06-01

The crystalline and magnetic properties of 5% Mn and 5% Ni co-doped nanocrystalline ZnO particles, obtained by the co-precipitation method, are performed. X-ray diffraction data revealed that Zn0.90Mn0.05Ni0.05O crystallizes in the monophasic wurtzite structure. DC magnetization measurement showed that the samples are paramagnetic at room temperature. However, a large increase in the magnetization is observed below 50 K. This behavior, along with the negative value of Weiss constant obtained from the linear fit of magnetic susceptibility data below room temperature, indicates ferrimagnetic behavior. The ferrimagnetic properties observed at low temperature are explained and confirmed from ab-initio calculations using the Korringa-Kohn-Rostoker method combined with the coherent potential approximation.

Bands dispersion and charge transfer in β-BeH2

NASA Astrophysics Data System (ADS)

Trivedi, D. K.; Galav, K. L.; Joshi, K. B.

2018-04-01

Predictive capabilities of ab-initio method are utilised to explore bands dispersion and charge transfer in β-BeH2. Investigations are carried out using the linear combination of atomic orbitals method at the level of density functional theory. The crystal structure and related parameters are settled by coupling total energy calculations with the Murnaghan equation of state. Electronic bands dispersion from PBE-GGA is reported. The PBE-GGA, and PBE0 hybrid functional, show that β-BeH2 is a direct gap semiconductor with 1.18 and 2.40 eV band gap. The band gap slowly decreases with pressure and beyond l00 GPa overlap of conduction and valence bands at the r point is observed. Charge transfer is studied by means of Mullikan population analysis.

Electronic and optical properties of Si and Ge nanocrystals: An ab initio study

NASA Astrophysics Data System (ADS)

Pulci, Olivia; Degoli, Elena; Iori, Federico; Marsili, Margherita; Palummo, Maurizia; Del Sole, Rodolfo; Ossicini, Stefano

2010-01-01

First-principles calculations within density functional theory and many-body perturbation theory have been carried out in order to investigate the structural, electronic and optical properties of undoped and doped silicon nanostructures. We consider Si nanoclusters co-doped with B and P. We find that the electronic band gap is reduced with respect to that of the undoped crystals, suggesting the possibility of impurity based engineering of electronic and optical properties of Si nanocrystals. Finally, motivated by recent suggestions concerning the chance of exploiting Ge dots for photovoltaic nanodevices, we present calculations of the electronic and optical properties of a Ge 35H 36 nanocrystal, and compare the results with those for the corresponding Si 35H 36 nanocrystals and the co-doped Si 33BPH 36.

Interplay between spin-orbit coupling and crystal-field effect in topological insulators

NASA Astrophysics Data System (ADS)

Lee, Hyungjun; Yazyev, Oleg V.

2015-07-01

Band inversion, one of the key signatures of time-reversal invariant topological insulators (TIs), arises mostly due to the spin-orbit (SO) coupling. Here, based on ab initio density-functional calculations, we report a theoretical investigation of the SO-driven band inversion in isostructural bismuth and antimony chalcogenide TIs from the viewpoint of its interplay with the crystal-field effect. We calculate the SO-induced energy shift of states in the top valence and bottom conduction manifolds and reproduce this behavior using a simple one-atom model adjusted to incorporate the crystal-field effect. The crystal-field splitting is shown to compete with the SO coupling, that is, stronger crystal-field splitting leads to weaker SO band shift. We further show how both these effects can be controlled by changing the chemical composition, whereas the crystal-field splitting can be tuned by means of uniaxial strain. These results provide a practical guidance to the rational design of novel TIs as well as to controlling the properties of existing materials.

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Ab initio study of collective excitations in a disparate mass molten salt.

PubMed

Bryk, Taras; Klevets, Ivan

2012-12-14

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

PubMed

Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

2015-02-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

Rational design of monocrystalline (InP)(y)Ge(5-2y)/Ge/Si(100) semiconductors: synthesis and optical properties.

PubMed

Sims, Patrick E; Chizmeshya, Andrew V G; Jiang, Liying; Beeler, Richard T; Poweleit, Christian D; Gallagher, James; Smith, David J; Menéndez, José; Kouvetakis, John

2013-08-21

In this work, we extend our strategy previously developed to synthesize functional, crystalline Si(5-2y)(AlX)y {X = N,P,As} semiconductors to a new class of Ge-III-V hybrid compounds, leading to the creation of (InP)(y)Ge(5-2y) analogues. The compounds are grown directly on Ge-buffered Si(100) substrates using gas source MBE by tuning the interaction between Ge-based P(GeH3)3 precursors and In atoms to yield nanoscale "In-P-Ge3" building blocks, which then confer their molecular structure and composition to form the target solids via complete elimination of H2. The collateral production of reactive germylene (GeH2), via partial decomposition of P(GeH3)3, is achieved by simple adjustment of the deposition conditions, leading to controlled Ge enrichment of the solid product relative to the stoichiometric InPGe3 composition. High resolution XRD, XTEM, EDX, and RBS indicate that the resultant monocrystalline (InP)(y)Ge(5-2y) alloys with y = 0.3-0.7 are tetragonally strained and fully coherent with the substrate and possess a cubic diamond-like structure. Molecular and solid-state ab initio density functional theory (DFT) simulations support the viability of "In-P-Ge3" building-block assembly of the proposed crystal structures, which consist of a Ge parent crystal in which the P atoms form a third-nearest-neighbor sublattice and "In-P" dimers are oriented to exclude energetically unfavorable In-In bonding. The observed InP concentration dependence of the lattice constant is closely reproduced by DFT simulation of these model structures. Raman spectroscopy and ellipsometry are also consistent with the "In-P-Ge3" building-block interpretation of the crystal structure, while the observation of photoluminescence suggests that (InP)(y)Ge(5-2y) may have important optoelectronic applications.

Topological Semimetals Studied by Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

2018-04-01

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

Investigations of mechanical, electronic, and magnetic properties of non-magnetic MgTe and ferro-magnetic Mg0.75 TM 0.25Te (TM = Fe, Co, Ni): An ab-initio calculation

NASA Astrophysics Data System (ADS)

Q, Mahmood; S, M. Alay-e.-Abbas; I, Mahmood; Mahmood, Asif; N, A. Noor

2016-04-01

The mechanical, electronic and magnetic properties of non-magnetic MgTe and ferro-magnetic (FM) Mg0.75 TM 0.25Te (TM = Fe, Co, Ni) in the zinc-blende phase are studied by ab-initio calculations for the first time. We use the generalized gradient approximation functional for computing the structural stability, and mechanical properties, while the modified Becke and Johnson local (spin) density approximation (mBJLDA) is utilized for determining the electronic and magnetic properties. By comparing the energies of non-magnetic and FM calculations, we find that the compounds are stable in the FM phase, which is confirmed by their structural stabilities in terms of enthalpy of formation. Detailed descriptions of elastic properties of Mg0.75 TM 0.25Te alloys in the FM phase are also presented. For electronic properties, the spin-polarized electronic band structures and density of states are computed, showing that these compounds are direct bandgap materials with strong hybridizations of TM 3d states and Te p states. Further, the ferromagnetism is discussed in terms of the Zener free electron model, RKKY model and double exchange model. The charge density contours in the (110) plane are calculated to study bonding properties. The spin exchange splitting and crystal field splitting energies are also calculated. The distribution of electron spin density is employed in computing the magnetic moments appearing at the magnetic sites (Fe, Co, Ni), as well as at the non-magnetic sites (Mg, Te). It is found that the p-d hybridization causes not only magnetic moments on the magnetic sites but also induces negligibly small magnetic moments at the non-magnetic sites.

Unravelling thermal emissivity spectra of the main minerals on Mercury's surface by comparison with ab initio calculated IR-HT vibrational frequencies

NASA Astrophysics Data System (ADS)

Stangarone, C.; Helbert, J.; Tribaudino, M.; Maturilli, A.; D'Amore, M.; Ferrari, S.; Prencipe, M.

2015-12-01

Spectral signatures of minerals are intimately related to the crystal structure; therefore they may represent a remote sensing model to determine surface composition of planetary bodies, by analysing their spectral reflectance and emission. However, one of the most critical point is data interpretation considering planetary surfaces, as Mercury, where the changes in spectral characteristics are induced by the high temperatures conditions (Helbert et al., 2013). The aim of this work is to interpret the experimental thermal emissivity spectra with an innovative approach: simulating IR spectra of the main mineral families that compose the surface of Mercury, focusing on pyroxenes (Sprague et al., 2002), both at room and high temperature, exploiting the accuracy of ab initio quantum mechanical calculations, by means of CRYSTAL14 code (Dovesi et al., 2014). The simulations will be compared with experimental emissivity measurements of planetary analogue samples at temperature up to 1000K, performed at Planetary Emissivity Laboratory (PEL) by Institute of Planetary Research (DLR, Berlin). Results will be useful to create a theoretical background to interpret HT-IR emissivity spectra that will be collected by the Mercury Radiometer and Thermal Infrared Spectrometer (MERTIS), a spectrometer developed by DLR that will be on board of the ESA BepiColombo Mercury Planetary Orbiter (MPO) scheduled for 2017. The goal is to point out the most interesting spectral features for a geological mapping of Mercury and other rocky bodies, simulating the environmental conditions of the inner planets of Solar System. Dovesi R., Saunders V. R., Roetti C., Orlando R., Zicovich-Wilson C. M., Pascale F., Civalleri B., Doll K., Harrison N. M., Bush I. J., D'Arco P., Llunell M., Causà M. & Noël Y. 2014. CRYSTAL14 User's Manual, University of Torino. Sprague, A. L., Emery, J. P., Donaldson, K. L., Russell, R. W., Lynch, D. K., & Mazuk, A. L. (2002). Mercury: Mid-infrared (3-13.5 μm) observations show heterogeneous composition, presence of intermediate and basic soil types, and pyroxene. Meteoritics & Planetary Science, 37(9), 1255-1268.

Palladium and platinum based solid and hollow nanoparticles: An ab-initio study of structural and electronic properties

NASA Astrophysics Data System (ADS)

Yildizhan, Gulsum; Caliskan, Serkan; Ozturk, Ramazan

2018-04-01

Nanoparticles composed of palladium and platinum are particularly interesting for catalytic purposes, for instance, selective hydrogenation and alcohol oxidation. The reactivity and selectivity of nanostructures are mostly based on the size and shape of the nanocrystals in catalytic reactions. In this work, we studied the structural stabilities of Pd and Pt based nanocubes and nanocages and adsorption strength of chemisorbed species on these nanostructures to investigate their structure dependent catalytic activities. Solid cubic and hollow cage like nanostructures of different sizes were designed with Pd and Pt atoms. The volume of the crystal cavity in nanocage structures was tuned by removing of atoms from solid cubic structure. The effect of size and shape on the formation energies and HOMO-LUMO energy gap of nanostructures were elucidated and correlated to structural stabilities, hardness-softness, electronegativity and electrophilicity index. The relationship between size and chemical reactivity clearly showed that increasing the number of atoms participating in a catalyst enhances the activity. For further understanding of the catalytic activity we employed 4-nitro thiophenol, as an S-donor representative molecule, to evaluate the adsorption characteristics of the nanostructures.

The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution.

PubMed

Hammel, Michal; Nemecek, Daniel; Keightley, J Andrew; Thomas, George J; Geisbrecht, Brian V

2007-12-01

The extracellular adherence protein (Eap) of Staphylococcus aureus participates in a wide range of protein-protein interactions that facilitate the initiation and dissemination of Staphylococcal disease. In this report, we describe the use of a multidisciplinary approach to characterize the solution structure of full-length Eap. In contrast to previous reports suggesting that a six-domain isoform of Eap undergoes multimerization, sedimentation equilibrium analytical ultracentrifugation data revealed that a four-domain isoform of Eap is a monomer in solution. In vitro proteolysis and solution small angle X-ray scattering studies both indicate that Eap adopts an extended conformation in solution, where the linkers connecting sequential EAP modules are solvent exposed. Construction of a low-resolution model of full-length Eap using a combination of ab initio deconvolution of the SAXS data and rigid body modeling of the EAP domain crystal structure suggests that full-length Eap may present several unique concave surfaces capable of participating in ligand binding. These results also raise the possibility that such surfaces may be held together by additional interactions between adjacent EAP modules. This hypothesis is supported by a comparative Raman spectroscopic analysis of full-length Eap and a stoichiometric solution of the individual EAP modules, which indicates the presence of additional secondary structure and a greater extent of hydrogen/deuterium exchange protection in full-length Eap. Our results provide the first insight into the solution structure of full-length Eap and an experimental basis for interpreting the EAP domain crystal structures within the context of the full-length molecule. They also lay a foundation for future studies into the structural and molecular bases of Eap-mediated protein-protein interactions with its many ligands.

The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution

PubMed Central

Hammel, Michal; Němeček, Daniel; Keightley, J. Andrew; Thomas, George J.; Geisbrecht, Brian V.

2007-01-01

The extracellular adherence protein (Eap) of Staphylococcus aureus participates in a wide range of protein–protein interactions that facilitate the initiation and dissemination of Staphylococcal disease. In this report, we describe the use of a multidisciplinary approach to characterize the solution structure of full-length Eap. In contrast to previous reports suggesting that a six-domain isoform of Eap undergoes multimerization, sedimentation equilibrium analytical ultracentrifugation data revealed that a four-domain isoform of Eap is a monomer in solution. In vitro proteolysis and solution small angle X-ray scattering studies both indicate that Eap adopts an extended conformation in solution, where the linkers connecting sequential EAP modules are solvent exposed. Construction of a low-resolution model of full-length Eap using a combination of ab initio deconvolution of the SAXS data and rigid body modeling of the EAP domain crystal structure suggests that full-length Eap may present several unique concave surfaces capable of participating in ligand binding. These results also raise the possibility that such surfaces may be held together by additional interactions between adjacent EAP modules. This hypothesis is supported by a comparative Raman spectroscopic analysis of full-length Eap and a stoichiometric solution of the individual EAP modules, which indicates the presence of additional secondary structure and a greater extent of hydrogen/deuterium exchange protection in full-length Eap. Our results provide the first insight into the solution structure of full-length Eap and an experimental basis for interpreting the EAP domain crystal structures within the context of the full-length molecule. They also lay a foundation for future studies into the structural and molecular bases of Eap-mediated protein–protein interactions with its many ligands. PMID:18029416

Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

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

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 factormore » shows the presence of liquid state in the considered alloys.« less

A Initio Studies of Polarisabilities of Ions in Crystals.

NASA Astrophysics Data System (ADS)

Tole, Philip

Available from UMI in association with The British Library. This thesis is concerned with the ab initio calculation of polarisabilities of ions in crystals. For a binary salt the Clausius-Mossotti equation relates the refractive index to the in-crystal polarisability of the ion-pair. However, there is no experimental means of separating the sum into anion and cation components. Theoretical models which use isolated ion polarisabilities to do this are physically unrealistic and have met with little success. A much better model has been developed using ab initio all-electron CHF calculations. The in-crystal environment is represented by a 'molecular' cluster embedded in a point-charge lattice. The physical features important to the success of the model are the nearest-neighbour overlap compression and the isotropic part of the electrostatic potential arising from the point -charge lattice. Calculations on simple first row alkali halides show the cation to be independent of these forces whereas the anion becomes, smaller, more bound and less polarisable in the crystal. When corrections for correlation are added the agreement with Clausius-Mossotti polarisabilities is at the 5% level or better. This implies a reduction in polarisability by factors of up to 2 with respect to the free ion. The polarisabilities for the anions in LiF, NaF, KF, LiCl, NaCl, KCl, LiBr, NaBr, KBr, CaF _2, BeO, MgO, CaO, Li_2O, Na_2O, K_2O, BeS, CaS, Li_2S, Na_2 S and K_2S were calculated. Anion polarisability is found to vary with lattice parameter but hardly at all with coordination number. Calculations on Be_2C show that in-crystal compression is sufficient to stabilise even C^{4 -}, which has a polarisability of over 20 au. Anions at the surface of LiF and MgO were also modelled. Because anisotropic overlap and electrostatic factors tend to cancel, the ion in 5-, 4- and 3-coordinate surface sites has a polarisability only a few per cent greater than in the bulk solid. Implications for active-site theories are discussed. A calculation of the geometric derivatives of the bromide polarisability in NaBr provides physical insight into models for simulating ionic melts. Calculations on NH_sp{4}{+} and CH_3NH_sp{3 }{+} show that of electronic properties of polyatomic cations also are independent of the crystal. CHF calculation of molecular polarisability was used to examine additivity of methyl-substituted alkanes, amines and ammonium cations, (CH_3)_ {x}CH_{4-x}, (CH_3)_{x} NH_{3-x} and (CH _3)_{x} NH_sp{4-x}{+} (x = 1...4). Calculations on polyatomic anions, OH^{-} and BH_sp{4}{-}, in sodium hydroxide and sodium borohydride environment show the same trends in electronic properties as those on monatomic anions.

Time-domain ab initio modeling of photoinduced dynamics at nanoscale interfaces.

PubMed

Wang, Linjun; Long, Run; Prezhdo, Oleg V

2015-04-01

Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics.

Involvement of conformational isomerism in the complexity of the crystal network of 1-(4-nitrophenyl)-1H-1,3-benzimidazole derivatives driven by C-H...A (A = NO2, Npy and π) and orthogonal Npy...NO2 and ONO...Csp2 interactions.

PubMed

García-Aranda, Mónica I; Gómez-Castro, Carlos Z; García-Báez, Efrén V; Gómez, Yolanda Gómez Y; Castrejón-Flores, José L; Padilla-Martínez, Itzia I

2018-04-01

A detailed structural analysis of the benzimidazole nitroarenes 1-(4-nitrophenyl)-1H-1,3-benzimidazole, C 13 H 9 N 3 O 2 , (I), 1-(4-nitrophenyl)-2-phenyl-1H-1,3-benzimidazole, C 19 H 13 N 3 O 2 , (II), and 2-(3-methylphenyl)-1-(4-nitrophenyl)-1H-1,3-benzimidazole, C 20 H 15 N 3 O 2 , (III), has been performed. They are nonplanar structures whose crystal arrangement is governed by Csp 2 -H...A (A = NO 2 , N py and π) hydrogen bonding. The inherent complexity of the supramolecular arrangements of compounds (I) (Z' = 2) and (II) (Z' = 4) into tapes, helices and sheets is the result of the additional participation of π-π NO2 and n-π* (n = O and N py ; π* = Csp 2 and N NO2 ) interactions that contribute to the stabilization of the equi-energetic conformations adopted by each of the independent molecules in the asymmetric unit. In contrast, compound (III) (Z' = 1) is self-paired, probably due to the effect of the steric demand of the methyl group on the crystal packing. Theoretical ab initio calculations confirmed that the presence of the arene ring at the benzimidazole 2-position increases the rotational barrier of the nitrobenzene ring and also supports the electrostatic nature of the orthogonal ONO...Csp 2 and N py ...NO 2 interactions.

Ab initio Design of Noncentrosymmetric Metals: Crystal Engineering in Oxide Heterostructures

DTIC Science & Technology

2015-07-29

electronic, magnetic, and optical properties of these materials are reported. Where available the experimental studies of these systems through...RevModPhys.86.1189 James M. Rondinelli, Emmanouil Kioupakis. Predicting and Designing Optical Properties of Inorganic Materials , Annual Review of Materials ...Advances in oxide materials : Preparation, properties , performance, at University of California, Santa Barbara California, USA (August 28, 2014

An ab initio molecular dynamics study of thermal decomposition of 3,6-di(azido)-1,2,4,5-tetrazine.

PubMed

Wu, Qiong; Zhu, Weihua; Xiao, Heming

2014-10-21

Ab initio molecular dynamics simulations were performed to study the thermal decomposition of isolated and crystal 3,6-di(azido)-1,2,4,5-tetrazine (DiAT). During unimolecular decomposition, the three different initiation mechanisms were observed to be N-N2 cleavage, ring opening, and isomerization, respectively. The preferential initial decomposition step is the homolysis of the N-N2 bond in the azido group. The release mechanisms of nitrogen gas are found to be very different in the early and later decomposition stages of crystal DiAT. In the early decomposition, DiAT decomposes very fast and drastically without forming any stable long-chains or heterocyclic clusters, and most of the nitrogen gases are released through rapid rupture of nitrogen-nitrogen and carbon-nitrogen bonds. But in the later decomposition stage, the release of nitrogen gas is inhibited due to low mobility, long distance from each other, and strong carbon-nitrogen bonds. To overcome the obstacles, the nitrogen gases are released through slow formation and disintegration of polycyclic networks. Our simulations suggest a new decomposition mechanism for the organic polyazido initial explosive at the atomistic level.

The elastic stability, bifurcation and ideal strength of gold under hydrostatic stress: an ab initio calculation.

PubMed

Wang, Hao; Li, Mo

2009-11-11

In this paper, we employ an ab initio density functional theory calculation to investigate the elastic stability of face-centered cubic Au under hydrostatic deformation. We identify the elastic stiffness constant B(ijkl) as the coefficient in the stress-strain relation for an arbitrary deformed state, and use it to test the stability condition. We show that this criterion bears the same physics as that proposed earlier by Frenkel and Orowan and agrees with the Born-Hill criterion. The results from those two approaches agree well with each other. We show that the stability limit, or instability, of the perfect Au crystal under hydrostatic expansion is not associated with the bulk stiffness modulus as predicted in the previous work; rather it is caused by a shear instability associated with the vanishing rhombohedral shear stiffness modulus. The deviation of the deformation mode from the primary hydrostatic loading path signals a bifurcation or symmetry breaking in the ideal crystal. The corresponding ideal hydrostatic strength for Au is 19.2 GPa at the Lagrangian expansion strain of ∼0.06. In the case of compression, Au remains stable over the entire pressure range in our calculation.

Ab initio velocity-field curves in monoclinic β-Ga2O3

NASA Astrophysics Data System (ADS)

Ghosh, Krishnendu; Singisetti, Uttam

2017-07-01

We investigate the high-field transport in monoclinic β-Ga2O3 using a combination of ab initio calculations and full band Monte Carlo (FBMC) simulation. Scattering rate calculation and the final state selection in the FBMC simulation use complete wave-vector (both electron and phonon) and crystal direction dependent electron phonon interaction (EPI) elements. We propose and implement a semi-coarse version of the Wannier-Fourier interpolation method [Giustino et al., Phys. Rev. B 76, 165108 (2007)] for short-range non-polar optical phonon (EPI) elements in order to ease the computational requirement in FBMC simulation. During the interpolation of the EPI, the inverse Fourier sum over the real-space electronic grids is done on a coarse mesh while the unitary rotations are done on a fine mesh. This paper reports the high field transport in monoclinic β-Ga2O3 with deep insight into the contribution of electron-phonon interactions and velocity-field characteristics for electric fields ranging up to 450 kV/cm in different crystal directions. A peak velocity of 2 × 107 cm/s is estimated at an electric field of 200 kV/cm.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

PubMed Central

Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

2015-01-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

NASA Astrophysics Data System (ADS)

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

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

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

Effects of molecular packing in organic crystals on singlet fission with ab initio many body perturbation theory

NASA Astrophysics Data System (ADS)

Haber, Jonah; Refaely-Abramson, Sivan; da Jornada, Felipe H.; Louie, Steven G.; Neaton, Jeffrey B.

Multi-exciton generation processes, in which multiple charge carriers are generated from a single photon, are mechanisms of significant interest for achieving efficiencies beyond the Shockley-Queisser limit of conventional p-n junction solar cells. One well-studied multiexciton process is singlet fission, whereby a singlet decays into two spin-correlated triplet excitons. Here, we use a newly developed computational approach to calculate singlet-fission coupling terms and rates with an ab initio Green's function formalism based on many-body perturbation theory (MBPT) within the GW approximation and the Bethe-Salpeter equation approach. We compare results for crystalline pentacene and TIPS-pentacene and explore the effect of molecular packing on the singlet fission mechanism. This work is supported by the Department of Energy.

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

Raman scattering tensors in thymine molecule from an ab initio MO calculation

NASA Astrophysics Data System (ADS)

Tsuboi, Masamichi; Kumakura, Akiko; Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ushizawa, Koichi; Ueda, Toyotoshi

1997-03-01

Ab initio SCF MO calculations have been made of the thymine molecule for the permanent polarizability and the polarizability derivatives with respect to the normal coordinates. The latter correspond to the components of the Raman tensors, and each of these tensors was brought into a visualized form by a transformation of the tensor axes into the principal system. For a comparison with such computational findings, a polarized Raman spectroscopic measurement has been made of a single crystal of thymine with 488.0 nm excitation. For most of the in-plane vibrations, calculated tensors were found to be well correlated with the observed Raman scattering anisotropy. On the basis of such correlations, discussions are given as for the polarizability oscillations caused by the atomic displacements in the molecule.

Quasi-2D silicon structures based on ultrathin Me2Si (Me = Mg, Ca, Sr, Ba) films

NASA Astrophysics Data System (ADS)

Migas, D. B.; Bogorodz, V. O.; Filonov, A. B.; Borisenko, V. E.; Skorodumova, N. V.

2018-04-01

By means of ab initio calculations with hybrid functionals we show a possibility for quasi-2D silicon structures originated from semiconducting Mg2Si, Ca2Si, Sr2Si and Ba2Si silicides to exist. Such a 2D structure is similar to the one of transition metal chalcogenides where silicon atoms form a layer in between of metal atoms aligned in surface layers. These metal surface atoms act as pseudo passivation species stabilizing crystal structure and providing semiconducting properties. Considered 2D Mg2Si, Ca2Si, Sr2Si and Ba2Si have band gaps of 1.14 eV, 0.69 eV, 0.33 eV and 0.19 eV, respectively, while the former one is also characterized by a direct transition with appreciable oscillator strength. Electronic states of the surface atoms are found to suppress an influence of the quantum confinement on the band gaps. Additionally, we report Sr2Si bulk in the cubic structure to have a direct band gap of 0.85 eV as well as sizable oscillator strength of the first direct transition.

Electron-density critical points analysis and catastrophe theory to forecast structure instability in periodic solids.

PubMed

Merli, Marcello; Pavese, Alessandro

2018-03-01

The critical points analysis of electron density, i.e. ρ(x), from ab initio calculations is used in combination with the catastrophe theory to show a correlation between ρ(x) topology and the appearance of instability that may lead to transformations of crystal structures, as a function of pressure/temperature. In particular, this study focuses on the evolution of coalescing non-degenerate critical points, i.e. such that ∇ρ(x c ) = 0 and λ 1 , λ 2 , λ 3 ≠ 0 [λ being the eigenvalues of the Hessian of ρ(x) at x c ], towards degenerate critical points, i.e. ∇ρ(x c ) = 0 and at least one λ equal to zero. The catastrophe theory formalism provides a mathematical tool to model ρ(x) in the neighbourhood of x c and allows one to rationalize the occurrence of instability in terms of electron-density topology and Gibbs energy. The phase/state transitions that TiO 2 (rutile structure), MgO (periclase structure) and Al 2 O 3 (corundum structure) undergo because of pressure and/or temperature are here discussed. An agreement of 3-5% is observed between the theoretical model and experimental pressure/temperature of transformation.

Stabilities and defect-mediated lithium-ion conduction in a ground state cubic Li 3 N structure

DOE PAGES

Nguyen, Manh Cuong; Hoang, Khang; Wang, Cai-Zhuang; ...

2016-01-07

A stable ground state structure with cubic symmetry of Li 3N (c-Li 3N) is found by ab initio initially symmetric random-generated crystal structure search method. Gibbs free energy, calculated within quasi-harmonic approximation, shows that c-Li 3N is the ground state structure for a wide range of temperature. The c-Li 3N structure has a negative thermal expansion coefficient at temperatures lower than room temperature, due mainly to two transverse acoustic phonon modes. This c-Li 3N phase is a semiconductor with an indirect band gap of 1.90 eV within hybrid density functional calculation. We also investigate the migration and energetics of nativemore » point defects in c-Li 3N, including lithium and nitrogen vacancies, interstitials, and anti-site defects. Lithium interstitials are found to have a very low migration barrier (~0.12 eV) and the lowest formation energy among all possible defects. Thus, the ionic conduction in c-Li 3N is expected to occur via an interstitial mechanism, in contrast to that in the well-known α-Li 3N phase which occurs via a vacancy mechanism.« less

Structure Based Virtual Screening Studies to Identify Novel Potential Compounds for GPR142 and Their Relative Dynamic Analysis for Study of Type 2 Diabetes

NASA Astrophysics Data System (ADS)

Kaushik, Aman C.; Kumar, Sanjay; Wei, Dong Q.; Sahi, Shakti

2018-02-01

GPR142 (G protein receptor 142) is a novel orphan GPCR (G protein coupled receptor) belonging to ‘Class A’ of GPCR family and expressed in beta cells of pancreas. In this study, we reported the structure based virtual screening to identify the hit compounds which can be developed as leads for potential agonists. The results were validated through induced fit docking, pharmacophore modeling and system biology approaches. Since, there is no solved crystal structure of GPR142, we attempted to predict the 3D structure followed by validation and then identification of active site using threading and ab initio methods. Also, structure based virtual screening was performed against a total of 1171519 compounds from different libraries and only top 20 best hit compounds were screened and analyzed. Moreover, the biochemical pathway of GPR142 complex with screened compound2 was also designed and compared with experimental data. Interestingly, compound2 showed an increase in insulin production via Gq mediated signaling pathway suggesting the possible role of novel GPR142 agonists in therapy against type 2 diabetes.

almaBTE : A solver of the space-time dependent Boltzmann transport equation for phonons in structured materials

NASA Astrophysics Data System (ADS)

Carrete, Jesús; Vermeersch, Bjorn; Katre, Ankita; van Roekeghem, Ambroise; Wang, Tao; Madsen, Georg K. H.; Mingo, Natalio

2017-11-01

almaBTE is a software package that solves the space- and time-dependent Boltzmann transport equation for phonons, using only ab-initio calculated quantities as inputs. The program can predictively tackle phonon transport in bulk crystals and alloys, thin films, superlattices, and multiscale structures with size features in the nm- μm range. Among many other quantities, the program can output thermal conductances and effective thermal conductivities, space-resolved average temperature profiles, and heat-current distributions resolved in frequency and space. Its first-principles character makes almaBTE especially well suited to investigate novel materials and structures. This article gives an overview of the program structure and presents illustrative examples for some of its uses. PROGRAM SUMMARY Program Title:almaBTE Program Files doi:http://dx.doi.org/10.17632/8tfzwgtp73.1 Licensing provisions: Apache License, version 2.0 Programming language: C++ External routines/libraries: BOOST, MPI, Eigen, HDF5, spglib Nature of problem: Calculation of temperature profiles, thermal flux distributions and effective thermal conductivities in structured systems where heat is carried by phonons Solution method: Solution of linearized phonon Boltzmann transport equation, Variance-reduced Monte Carlo

New insights into the application of the valence rules in Zintl phases—Crystal and electronic structures of Ba{sub 7}Ga{sub 4}P{sub 9}, Ba{sub 7}Ga{sub 4}As{sub 9}, Ba{sub 7}Al{sub 4}Sb{sub 9}, Ba{sub 6}CaAl{sub 4}Sb{sub 9}, and Ba{sub 6}CaGa{sub 4}Sb{sub 9}

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

He, Hua; Stoyko, Stanislav; Bobev, Svilen, E-mail: bobev@udel.edu

Crystals of three new ternary pnictides—Ba{sub 7}Al{sub 4}Sb{sub 9}, Ba{sub 7}Ga{sub 4}P{sub 9}, and Ba{sub 7}Ga{sub 4}As{sub 9} have been prepared by reactions of the respective elements in molten Al or Pb fluxes. Single-crystal X-ray diffraction studies reveal that the three phases are isotypic, crystallizing in the orthorhombic Ba{sub 7}Ga{sub 4}Sb{sub 9}-type structure (space group Pmmn, Pearson symbol oP40, Z=2), for which only the prototype is known. The structure is based on TrPn{sub 4} tetrahedra (Tr=Al, Ga; Pn=P, As, Sb), connected in an intricate scheme into 1D-ribbons. Long interchain Pn–Pn bonds (d{sub P–P}>3.0 Å; d{sub As–As}>3.1 Å; d{sub Sb–Sb}>3.3 Å)more » account for the realization of 2D-layers, separated by Ba{sup 2+} cations. Applying the classic valance rules to rationalize the bonding apparently fails, and Ba{sub 7}Ga{sub 4}Sb{sub 9} has long been known as a metallic Zintl phase. Earlier theoretical calculations, both empirical and ab-initio, suggest that the possible metallic properties originate from filled anti-bonding Pn–Pn states, and the special roles of the “cations” in this crystal structure. To experimentally probe this hypothesis, we sought to synthesize the ordered quaternary phases Ba{sub 6}CaTr{sub 4}Sb{sub 9} (Tr=Al, Ga). Single-crystal X-ray diffraction work confirms Ba{sub 6.145(3)}Ca{sub 0.855}Al{sub 4}Sb{sub 9} and Ba{sub 6.235(3)}Ca{sub 0.765}Ga{sub 4}Sb{sub 9}, with Ca atoms preferably substituting Ba on one of the three available sites. The nuances of the five crystal structures are discussed, and the chemical bonding in Ba{sub 7}Ga{sub 4}As{sub 9} is interrogated by tight-binding linear muffin-tin orbital calculations. - Graphical abstract: The new Zintl phases—Ba{sub 7}Al{sub 4}Sb{sub 9}, Ba{sub 7}Ga{sub 4}P{sub 9}, and Ba{sub 7}Ga{sub 4}As{sub 9}, and their quaternary variants Ba{sub 6}CaTr{sub 4}Sb{sub 9} (Tr=Al, Ga)—crystallize in the Ba{sub 7}Ga{sub 4}Sb{sub 9} structure type. The structures are based on TrPn{sub 4} tetrahedra (a perspective of the crystal structure is shown, as viewed along the c axis). - Highlights: • Ba{sub 7}Al{sub 4}Sb{sub 9}, Ba{sub 7}Ga{sub 4}P{sub 9}, and Ba{sub 7}Ga{sub 4}As{sub 9} are new compounds in the respective phase diagrams. • The quaternary phases Ba{sub 6}CaTr{sub 4}Sb{sub 9} (Tr=Al, Ga) show nearly ordered Ba/Ca distribution. • Very weak Pn–Pn bonds and pairing distortion are observed for Ba{sub 7}Ga{sub 4}Pn{sub 9} (Pn=P, As).« less

Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys

NASA Astrophysics Data System (ADS)

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

2014-04-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K 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 lead (l-Pb). 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 three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.

Ab initio studies of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine/1,3-dimethyl-2-imidazolidinone cocrystal under high pressure using dispersion corrected density functional theory

NASA Astrophysics Data System (ADS)

Gu, Bang-Ming; Lin, He; Zhu, Shun-Guan

2014-04-01

A detailed study of structural, electronic, and thermodynamic properties of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal under the hydrostatic pressure of 0-100 GPa was performed by using dispersion-corrected density functional theory (DFT-D) method. The calculated crystal structure is in reasonable agreement with the experimental data at the ambient pressure. Based on the analysis of lattice constants, bond lengths, bond angles, and dihedral angles under compression, it is found that HMX molecules in HMX/DMI cocrystal are seriously distorted. In addition, as the pressure increases, the band gap decreases gradually, which suggests that HMX/DMI cocrystal is becoming more metallic. Some important intermolecular interactions between HMX and DMI are also observed in the density of states spectrum. Finally, its thermodynamic properties were characterized, and the results show that HMX/DMI cocrystal is more easily formed in the low pressure.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

PubMed Central

Neumann, Marcus A.

2017-01-01

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations. PMID:28250956

Electronic structure and optical properties of CuAlO2 under biaxial strain.

PubMed

Ghosh, C K; Sarkar, D; Mitra, M K; Chattopadhyay, K K

2012-06-13

An ab initio calculation has been carried out to investigate the biaxial strain ( - 10.71% < ε < 9.13%) effect on elastic, electronic and optical properties of CuAlO(2). All the elastic constants (c(11), c(12), c(13), c(33)) except c(44) decrease (increase) during tensile (compressive) strain. The band gap is found to decrease in the presence of tensile as well as compressive strain. The relative decrease of the band gap is asymmetric with respect to the sign of the strain. Significant differences between the parallel and perpendicular components of the dielectric constant and the optical properties have been observed due to anisotropic crystal structure. It is further noticed that these properties are easily tunable by strain. Importantly, the collective oscillation of the valence electrons has been identified for light polarized perpendicular to the c-axis. From calculations, it is clear that the tensile strain can enhance the hole mobility as well as the transparency of CuAlO(2).

Electronic structure and optical properties of CuAlO2 under biaxial strain

NASA Astrophysics Data System (ADS)

Ghosh, C. K.; Sarkar, D.; Mitra, M. K.; Chattopadhyay, K. K.

2012-06-01

An ab initio calculation has been carried out to investigate the biaxial strain ( - 10.71% < ɛ < 9.13%) effect on elastic, electronic and optical properties of CuAlO2. All the elastic constants (c11, c12, c13, c33) except c44 decrease (increase) during tensile (compressive) strain. The band gap is found to decrease in the presence of tensile as well as compressive strain. The relative decrease of the band gap is asymmetric with respect to the sign of the strain. Significant differences between the parallel and perpendicular components of the dielectric constant and the optical properties have been observed due to anisotropic crystal structure. It is further noticed that these properties are easily tunable by strain. Importantly, the collective oscillation of the valence electrons has been identified for light polarized perpendicular to the c-axis. From calculations, it is clear that the tensile strain can enhance the hole mobility as well as the transparency of CuAlO2.

Observation of surface superstructure induced by systematic vacancies in the topological Dirac semimetal Cd3As2

NASA Astrophysics Data System (ADS)

Butler, Christopher J.; Tseng, Yi; Hsing, Cheng-Rong; Wu, Yu-Mi; Sankar, Raman; Wang, Mei-Fang; Wei, Ching-Ming; Chou, Fang-Cheng; Lin, Minn-Tsong

2017-02-01

The Dirac semimetal phase found in Cd3As2 is protected by a C4 rotational symmetry derived from a corkscrew arrangement of systematic Cd vacancies in its complicated crystal structure. It is therefore surprising that no microscopic observation, direct or indirect, of these systematic vacancies has so far been described. To this end, we revisit the cleaved (112) surface of Cd3As2 using a combined approach of scanning tunneling microscopy and ab initio calculations. We determine the exact position of the (112) plane at which Cd3As2 naturally cleaves, and describe in detail a structural periodicity found at the reconstructed surface, consistent with that expected to arise from the systematic Cd vacancies. This reconciles the current state of microscopic surface observations with those of crystallographic and theoretical models, and demonstrates that this vacancy superstructure, central to the preservation of the Dirac semimetal phase, survives the cleavage process and retains order at the surface.

Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

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

Geng, Hua Y., E-mail: huay.geng@gmail.com; Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate ismore » about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.« less

Magnetic Excitations in Polyoxotungstate-Supported Lanthanoid Single-Molecule Magnets: An Inelastic Neutron Scattering and ab Initio Study.

PubMed

Vonci, Michele; Giansiracusa, Marcus J; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

2017-01-03

Inelastic neutron scattering (INS) has been used to investigate the crystal field (CF) magnetic excitations of the analogs of the most representative lanthanoid-polyoxometalate single-molecule magnet family: Na 9 [Ln(W 5 O 18 ) 2 ] (Ln = Nd, Tb, Ho, Er). Ab initio complete active space self-consistent field/restricted active space state interaction calculations, extended also to the Dy analog, show good agreement with the experimentally determined low-lying CF levels, with accuracy better in most cases than that reported for approaches based only on simultaneous fitting to CF models of magnetic or spectroscopic data for isostructural Ln families. In this work we demonstrate the power of a combined spectroscopic and computational approach. Inelastic neutron scattering has provided direct access to CF levels, which together with the magnetometry data, were employed to benchmark the ab initio results. The ab initio determined wave functions corresponding to the CF levels were in turn employed to assign the INS transitions allowed by selection rules and interpret the observed relative intensities of the INS peaks. Ultimately, we have been able to establish the relationship between the wave function composition of the CF split Ln III ground multiplets and the experimentally measured magnetic and spectroscopic properties for the various analogs of the Na 9 [Ln(W 5 O 18 ) 2 ] family.

Charge Transport Properties of Durene Crystals from First-Principles.

PubMed

Motta, Carlo; Sanvito, Stefano

2014-10-14

We establish a rigorous computational scheme for constructing an effective Hamiltonian to be used for the determination of the charge carrier mobility of pure organic crystals at finite temperature, which accounts for van der Waals interactions, and it includes vibrational contributions from the entire phonon spectrum of the crystal. Such an approach is based on the ab initio framework provided by density functional theory and the construction of a tight-binding effective model via Wannier transformation. The final Hamiltonian includes coupling of the electrons to the crystals phonons, which are also calculated from density functional theory. We apply this methodology to the case of durene, a small π-conjugated molecule, which forms a high-mobility herringbone-stacked crystal. We show that accounting correctly for dispersive forces is fundamental for obtaining a high-quality phonon spectrum, in agreement with experiments. Then, the mobility as a function of temperature is calculated along different crystallographic directions and the phonons most responsible for the scattering are identified.

High thermoelectric performances of monolayer SnSe allotropes.

PubMed

Hu, Zi-Yu; Li, Kai-Yue; Lu, Yong; Huang, Yan; Shao, Xiao-Hong

2017-10-26

α-SnSe is one of the most promising thermoelectric materials with low thermal conductivity and a high power factor. Since the thermoelectric properties of a material have a strong dependence on its crystal structure, we study the energetic and thermoelectric properties of four new monolayer phases of SnSe (β, γ, δ and ε) together with α-SnSe using the ab initio density functional theory method. The calculated electronic structures show that all five phases are semiconductors with different band gaps. The α, β, γ, and δ phases have an indirect band gap with the hybridization of sp 2 orbitals, whereas the ε phase has a direct band with the hybridization of sp 3 orbitals. The thermoelectric transport properties and coefficients are obtained from the electronic structure using semi-classical Boltzmann theory, and the results indicate that the four new phases of SnSe (β, γ, δ and ε) all have better thermoelectric properties compared with the reported α phase. The predicted ZT value for the β-SnSe phase is 2.06 at 300 K, suggesting that it has great potential for novel thermoelectric applications.

Vibrational spectra and structure of benzil and its 18O- and d 10-labelled derivatives: a quantum chemical and experimental study

NASA Astrophysics Data System (ADS)

Kolev, Tsonko M.; Stamboliyska, Bistra A.

2002-12-01

Geometry and vibrational spectroscopic data of benzil-d 0 benzil-d 10 and benzil- 18O calculated at various levels of theory (RHF/6-31G*, B3LYP/6-31G*, BLYP/6-31G*) are reported. The theoretical results are discussed mainly in terms of the comparisons with infrared (4000-100 cm -1) and Raman (4000-50 cm -1) spectral data. The calculated isotopic frequency shifts, induced by the 18O- and d 10-labeling, are in a good agreement with the measured values. A complete vibrational assignment was made with the help of ab initio force field calculations. The data thus obtained were used for reassigning some vibrational frequencies. The results of the optimized molecular structure obtained on the basis of RHF and the DFT calculations are presented and compared with the experimental X-ray diffraction for the benzil-d 0 single crystal. It turns out that the best structural parameters are predicted by the B3LYP/6-31G* method.

Vibrational spectra and structure of benzil and its 18O- and d10-labelled derivatives: a quantum chemical and experimental study.

PubMed

Kolev, Tsonko M; Stamboliyska, Bistra A

2002-12-01

Geometry and vibrational spectroscopic data of benzil-d0 benzil-d10 and benzil-18O calculated at various levels of theory (RHF/6-31G*, B3LYP/6-31G*, BLYP/6-31G*) are reported. The theoretical results are discussed mainly in terms of the comparisons with infrared (4000-100 cm(-1)) and Raman (4000-50 cm(-1)) spectral data. The calculated isotopic frequency shifts, induced by the 18O- and d10-labeling, are in a good agreement with the measured values. A complete vibrational assignment was made with the help of ab initio force field calculations. The data thus obtained were used for reassigning some vibrational frequencies. The results of the optimized molecular structure obtained on the basis of RHF and the DFT calculations are presented and compared with the experimental X-ray diffraction for the benzil-d0 single crystal. It turns out that the best structural parameters are predicted by the B3LYP/6-31G* method.

Detection of Cu2Zn5SnSe8 and Cu2Zn6SnSe9 phases in co-evaporated Cu2ZnSnSe4 thin-films

NASA Astrophysics Data System (ADS)

Schwarz, Torsten; Marques, Miguel A. L.; Botti, Silvana; Mousel, Marina; Redinger, Alex; Siebentritt, Susanne; Cojocaru-Mirédin, Oana; Raabe, Dierk; Choi, Pyuck-Pa

2015-10-01

Cu2ZnSnSe4 thin-films for photovoltaic applications are investigated using combined atom probe tomography and ab initio density functional theory. The atom probe studies reveal nano-sized grains of Cu2Zn5SnSe8 and Cu2Zn6SnSe9 composition, which cannot be assigned to any known phase reported in the literature. Both phases are considered to be metastable, as density functional theory calculations yield positive energy differences with respect to the decomposition into Cu2ZnSnSe4 and ZnSe. Among the conceivable crystal structures for both phases, a distorted zinc-blende structure shows the lowest energy, which is a few tens of meV below the energy of a wurtzite structure. A band gap of 1.1 eV is calculated for both the Cu2Zn5SnSe8 and Cu2Zn6SnSe9 phases. Possible effects of these phases on solar cell performance are discussed.

Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

DOE PAGES

Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

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.

Quantum oscillations in the anomalous spin density wave state of FeAs

DOE PAGES

Campbell, Daniel J.; Eckberg, Chris; Wang, Kefeng; ...

2017-08-10

Quantum oscillations in the binary antiferromagnetic metal FeAs are presented and compared to theoretical predictions for the electronic band structure in the anomalous spin density wave state of this material. Demonstrating a method for growing single crystals out of Bi flux, we utilize the highest quality FeAs to perform torque magnetometry experiments up to 35 T, using rotations of field angle in two planes to provide evidence for one electron and one hole band in the magnetically ordered state. Finally, the resulting picture agrees with previous experimental evidence for multiple carriers at low temperatures, but the exact Fermi surface shapemore » differs from predictions, suggesting that correlations play a role in deviation from ab initio theory and cause up to a fourfold enhancement in the effective carrier mass.« less

Intrinsic quantum anomalous Hall effect in the kagome lattice Cs 2LiMn 3F 12

DOE PAGES

Xu, Gang; Lian, Biao; Zhang, Shou -Cheng

2015-10-27

In a kagome lattice, the time reversal symmetry can be broken by a staggered magnetic flux emerging from ferromagnetic ordering and intrinsic spin-orbit coupling, leading to several well-separated nontrivial Chern bands and intrinsic quantum anomalous Hall effect. Based on this idea and ab initio calculations, we propose the realization of the intrinsic quantum anomalous Hall effect in the single layer Cs 2Mn 3F 12 kagome lattice and on the (001) surface of a Cs 2LiMn 3F 12 single crystal by modifying the carrier coverage on it, where the band gap is around 20 meV. Furthermore, a simplified tight binding modelmore » based on the in-plane ddσ antibonding states is constructed to understand the topological band structures of the system.« less

The effect of long-range order on the elastic properties of Cu3Au

NASA Astrophysics Data System (ADS)

Wang, Gui-Sheng; Krisztina Delczeg-Czirjak, Erna; Hu, Qing-Miao; Kokko, Kalevi; Johansson, Börje; Vitos, Levente

2013-02-01

Ab initio calculations, based on the exact muffin-tin orbitals method are used to determine the elastic properties of Cu-Au alloys with Au/Cu ratio 1/3. The compositional disorder is treated within the coherent potential approximation. The lattice parameters and single-crystal elastic constants are calculated for different partially ordered structures ranging from the fully ordered L12 to the random face centered cubic lattice. It is shown that the theoretical elastic constants follow a clear trend with the degree of chemical order: namely, C11 and C12 decrease, whereas C44 remains nearly constant with increasing disorder. The present results are in line with the experimental findings that the impact of the chemical ordering on the fundamental elastic parameters is close to the resolution of the available experimental and theoretical tools.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

14N NQR lineshape in nanocrystals: An ab initio investigation of urea

PubMed Central

Gregorovič, Alan

2017-01-01

14N nuclear quadrupole resonance (NQR) lineshapes mostly contain information of low interest, although in nanocrystals they may display some unexpected behaviour. In this work, we present an ab initio computational study of the 14N NQR lineshapes in urea nanocrystals as a function of the nanocrystal size and geometry, focusing on the surface induced broadening of the lineshapes. The lineshapes were obtained through a calculation of the electric field gradient for each nitrogen site in the nanocrystal separately, taking into account the individual crystal field by embedding the molecule of interest in a suitable lattice of point multipoles representing other urea molecules in the nanocrystal. The small influence of distant molecules is found with a series expansion, using the in-crystal Sternheimer shieldings which we also calculated ab initio. We have considered nanocrystals with two geometries: a sphere and a cube, with characteristic sizes between 5 and 100 nm. Our calculations suggest that there is a dramatic difference between the linewidths for the two geometries. For spheres, we find a steep drop in linewidths at ∼10 nm; at 5 nm the linewidth is ∼11 kHz, whereas for sizes above 20 nm the linewidth is practically negligible (<100 Hz). For cubes, on the other hand, we find a steady 1/size decrease, from 12 kHz at 10 nm to 1.2 kHz at 100 nm. This analysis is important for 14N NQR spectroscopy of crystalline pharmaceuticals, where nanoparticles are increasingly more often embedded in some sort of matrix. Although this is only a theoretical analysis, we believe that this work can serve as a guidance for the forthcoming experimental analysis. PMID:28527464

Lithium cluster anions: photoelectron spectroscopy and ab initio calculations.

PubMed

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

2011-01-28

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

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

Zhao, D.; Ladipo, F.T.; Braddock-Wilking, J.

Low temperature crystal structures of (DABCO)H{sup +}Co(CO){sub 4}{sup -} (1) and (DABCO)H{sup +}Co(CO){sub 3}PPh{sub 3}{sup -} (2) (DABCO = 1,4-diazabicyclooctane) indicate that both salts exhibit N-H...Co hydrogen bonding. IR and NMR data indicate that these hydrogen bonded species persist in nonpolar solvents such as toluene, but exist as solvent separated ions in more polar solvents. Replacement of the axial CO ligand by PPh{sub 3} leads to a shortening of the N...Co separation in the solid state from 3.437(3) to 3.294(6) A. This change is accompanied by an increase in the angle between the equatorial carbonyl ligands. Thus, the crystallographic resultsmore » suggest a strengthening of the N-H...Co hydrogen bond upon increasing the basicity of the metal center, the first observation of this type in the solid state. This assertion is supported by variable-temperature {sup 1}H and {sup 13}C NMR data in toluene-d{sub 8} solution which, discussed in the light of ab initio calculations, indicate that the barrier to a fluxional process involving cleavage of the N-H...Co hydrogen bond is greater in 2 than in 1. The crystal structures of 1 and 2 have been determined by X-ray diffraction at 135(5) and 123(5) K, respectively. 19 refs., 2 figs., 5 tabs.« less

FAST TRACK COMMUNICATION: Pyroxenes: a new class of multiferroics

NASA Astrophysics Data System (ADS)

Jodlauk, S.; Becker, P.; Mydosh, J. A.; Khomskii, D. I.; Lorenz, T.; Streltsov, S. V.; Hezel, D. C.; Bohatý, L.

2007-10-01

Pyroxenes with the general formula AMSi2O6 (A = mono- or divalent metal, M = di- or trivalent metal) are shown to be a new class of multiferroic materials. In particular, we have found so far that NaFeSi2O6 becomes ferroelectric in a magnetically ordered state below ~6 K. Similarly, magnetically driven ferroelectricity is also detected in the Li homologues, LiFeSi2O6 (TC~18 K) and LiCrSi2O6 (TC~11 K). In all these monoclinic systems the electric polarization can be strongly modified by magnetic fields. Measurements of magnetic susceptibility, pyroelectric current and dielectric constants (and their dependence on magnetic field) are performed using a natural crystal of aegirine (NaFeSi2O6) and synthetic crystals of LiFeSi2O6 and LiCrSi2O6 grown from melt solution. For NaFeSi2O6 a temperature versus magnetic field phase diagram is proposed. Exchange constants are computed on the basis of ab initio band structure calculations. The possibility of a spiral magnetic structure caused by frustration to be the reason for the origin of the multiferroic behaviour is discussed. We propose that other pyroxenes may also be multiferroic, and that the versatility of this family offers an exceptional opportunity to study general conditions for and mechanisms of magnetically driven ferroelectricity.

(Na,□)5[MnO2]13 nanorods: a new tunnel structure for electrode materials determined ab initio and refined through a combination of electron and synchrotron diffraction data

PubMed Central

Mugnaioli, Enrico; Gemmi, Mauro; Merlini, Marco; Gregorkiewitz, Michele

2016-01-01

(Nax□1 − x)5[MnO2]13 has been synthesized with x = 0.80 (4), corresponding to Na0.31[MnO2]. This well known material is usually cited as Na0.4[MnO2] and is believed to have a romanèchite-like framework. Here, its true structure is determined, ab initio, by single-crystal electron diffraction tomography (EDT) and refined both by EDT data applying dynamical scattering theory and by the Rietveld method based on synchrotron powder diffraction data (χ2 = 0.690, R wp = 0.051, R p = 0.037, R F2 = 0.035). The unit cell is monoclinic C2/m, a = 22.5199 (6), b = 2.83987 (6), c = 14.8815 (4) Å, β = 105.0925 (16)°, V = 918.90 (4) Å3, Z = 2. A hitherto unknown [MnO2] framework is found, which is mainly based on edge- and corner-sharing octahedra and comprises three types of tunnels: per unit cell, two are defined by S-shaped 10-rings, four by egg-shaped 8-rings, and two by slightly oval 6-rings of Mn polyhedra. Na occupies all tunnels. The so-determined structure excellently explains previous reports on the electrochemistry of (Na,□)5[MnO2]13. The trivalent Mn3+ ions concentrate at two of the seven Mn sites where larger Mn—O distances and Jahn–Teller distortion are observed. One of the Mn3+ sites is five-coordinated in a square pyramid which, on oxidation to Mn4+, may easily undergo topotactic transformation to an octahedron suggesting a possible pathway for the transition among different tunnel structures. PMID:27910840

{bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

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

Richardson, S.L.; Martins, J.L.

1998-12-01

In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

Structure models: From shell model to ab initio methods. A brief introduction to microscopic theories for exotic nuclei

NASA Astrophysics Data System (ADS)

Bacca, Sonia

2016-04-01

A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.

Ab initio density functional theory investigation of structural and electronic properties of double-walled silicon carbide nanotubes

NASA Astrophysics Data System (ADS)

Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

2009-12-01

By using ab initio density functional theory, the structural and electronic properties of (n,n)@(11,11) double-walled silicon carbide nanotubes (SiCNTs) are investigated. Our calculations reveal the existence of an energetically favorable double-walled nanotube whose interwall distance is about 4.3 Å. Interwall spacing and curvature difference are found to be essential for the electronic states around the Fermi level.

Symplectic no-core configuration interaction framework for ab initio nuclear structure. II. Structure of rotational states

NASA Astrophysics Data System (ADS)

Caprio, Mark A.; McCoy, Anna E.; Dytrych, Tomas

2017-09-01

Rotational band structure is readily apparent as an emergent phenomenon in ab initio nuclear many-body calculations of light nuclei, despite the incompletely converged nature of most such calculations at present. Nuclear rotation in light nuclei can be analyzed in terms of approximate dynamical symmetries of the nuclear many-body problem: in particular, Elliott's SU (3) symmetry of the three-dimensional harmonic oscillator and the symplectic Sp (3 , R) symmetry of three-dimensional phase space. Calculations for rotational band members in the ab initio symplectic no-core configuration interaction (SpNCCI) framework allow us to directly examine the SU (3) and Sp (3 , R) nature of rotational states. We present results for rotational bands in p-shell nuclei. Supported by the US DOE under Award No. DE-FG02-95ER-40934 and the Czech Science Foundation under Grant No. 16-16772S.

Atomic structures of B20 FeGe thin films grown on the Si(111) surface

NASA Astrophysics Data System (ADS)

Kim, Wondong; Noh, Seungkyun; Yoon, Jisoo; Kim, Young Heon; Lee, Inho; Kim, Jae-Sung; Hwang, Chanyong

We investigated the growth and atomic structures of FeGe thin films on the Si (111) surface by using scanning tunneling microscopy (STM) and transmission electron microscopy (TEM). The 2 5nm- thick FeGe thin films were prepared on the clean Si(111) 7x7 surface by co-deposition of Fe and Ge from separated electron-beam evaporators. With direct deposition on the substrate at the temperature above 550 K, the surface of FeGe films was not smooth and consisted of coarse grains. By the combination of room-temperature annealing and post-annealing process around 800 K, the structure of FeGe thin films evolved into the well crystalized structures. Atom-resolved STM images revealed that there are at least four different surface terminations. We constructed atomic models for each surface terminations based on the bulk atomic arrangement of a B20 chiral structure and confirmed that the observed STM images are successfully reproduced by using computational simulations employing Vienna Ab Initio Simulation package (VASP) with a B20 chiral structure model. TEM cross-sectional images also support our atomic models by revealing clearly the characteristic zigzag features of B20 structures of FeGe(111) thin films.

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

Structure and energy of non-canonical basepairs: comparison of various computational chemistry methods with crystallographic ensembles.

PubMed

Panigrahi, Swati; Pal, Rahul; Bhattacharyya, Dhananjay

2011-12-01

Different types of non-canonical basepairs, in addition to the Watson-Crick ones, are observed quite frequently in RNA. Their importance in the three dimensional structure is not fully understood, but their various roles have been proposed by different groups. We have analyzed the energetics and geometry of 32 most frequently observed basepairs in the functional RNA crystal structures using different popular empirical, semi-empirical and ab initio quantum chemical methods and compared their optimized geometry with the crystal data. These basepairs are classified into three categories: polar, non-polar and sugar-mediated, depending on the types of atoms involved in hydrogen bonding. In case of polar basepairs, most of the methods give rise to optimized structures close to their initial geometry. The interaction energies also follow similar trends, with the polar ones having more attractive interaction energies. Some of the C-H...O/N hydrogen bond mediated non-polar basepairs are also found to be significantly stable in terms of their interaction energy values. Few polar basepairs, having amino or carboxyl groups not hydrogen bonded to anything, such as G:G H:W C, show large flexibility. Most of the non-polar basepairs, except A:G s:s T and A:G w:s C, are found to be stable; indicating C-H...O/N interaction also plays a prominent role in stabilizing the basepairs. The sugar mediated basepairs show variability in their structures, due to the involvement of flexible ribose sugar. These presumably indicate that the most of the polar basepairs along with few non-polar ones act as seed for RNA folding while few may act as some conformational switch in the RNA.

First-principles theory of iron up to earth-core pressures: Structural, vibrational, and elastic properties

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

Soederlind, P.; Moriarty, J.A.; Wills, J.M.

1996-06-01

{ital Ab} {ital initio} electronic-structure calculations, based on density-functional theory and a full-potential linear-muffin-tin-orbital method, have been used to predict crystal-structure phase stabilities, elastic constants, and Brillouin-zone-boundary phonons for iron under compression. Total energies for five crystal structures, bcc, fcc, bct, hcp, and dhcp, have been calculated over a wide volume range. In agreement with experiment and previous theoretical calculations, a magnetic bcc ground state is obtained at ambient pressure and a nonmagnetic hcp ground state is found at high pressure, with a predicted bcc {r_arrow} hcp phase transition at about 10 GPa. Also in agreement with very recent diamond-anvil-cellmore » experiments, a metastable dhcp phase is found at high pressure, which remains magnetic and consequently accessible at high temperature up to about 50 GPa. In addition, the bcc structure becomes mechanically unstable at pressures above 2 Mbar (200 GPa) and a metastable, but still magnetic, bct phase ({ital c}/{ital a} {approx_equal} 0.875) develops. For high-pressure nonmagnetic iron, fcc and hcp elastic constants and fcc phonon frequencies have been calculated to above 4 Mbar. These quantities rise smoothly with pressure, but an increasing tendency towards elastic anisotropy as a function of compression is observed, and this has important implications for the solid inner-core of the earth. The fcc elastic-constant and phonon data have also been used in combination with generalized pseudopotential theory to develop many-body interatomic potentials, from which high-temperature thermodynamic properties and melting can be obtained. In this paper, these potentials have been used to calculate full fcc and hcp phonon spectra and corresponding Debye temperatures as a function of compression. {copyright} {ital 1996 The American Physical Society.}« less

Electronic and magnetic properties of double perovskite Sr2CoUO6: Heisenberg model

NASA Astrophysics Data System (ADS)

Nid-bahami, A.; Ahmed, S. Sidi; Ait-Tamerd, M.; Zaari, H.; El Kenz, A.; Benyoussef, A.

2018-01-01

This work will be focused on the electronic and magnetic properties of Sr2CoUO6 (SCUO) using ab-initio calculations and Monte Carlo Simulation (MCS). Firstly, we calculate the exchange coupling and the crystal field, then, the electronic and magnetic properties will be studied, using the full-potential linearized augmented plane wave (FP-LAPW) method, as implemented in the Wien2k code. This method employing the generalized gradient approximation (GGA) for exchange-correlation term. The half-metallic ferromagnetic nature implies a potential application of this new compound in spintronics devices. Also, we have presented the results of the band structures and densities of states for the two up and down spin polarizations. The exchange coupling and the crystal field calculated are J = 0 . 567 meV and δ = 0 . 559meV, and total spin magnetic moments is 2.96 μB closed to experimental values 3 μB. Secondly, we have presented the results for the magnetization and the susceptibility as a function of temperature. Finally, we obtain the critical temperature T = 9 . 20 K by MCS in good agreement with the experimental value.

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

PubMed

Rana, Malay Kumar; Chandra, Amalendu

2013-05-28

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

Structural Investigation of Biological and Semiconductor Nanostructures with Nonlinear Multicontrast Microscopy

NASA Astrophysics Data System (ADS)

Cisek, Richard

Physical and functional properties of advanced nano-composite materials and biological structures are determined by self-organized atoms and molecules into nanostructures and in turn by microscopic organization of the nanostructures into assemblies of higher structural complexity. Therefore, microscopes are indispensable tools for structural investigations at various levels of organization. In this work, novel nonlinear optical microscopy methods were developed to non-invasively study structural organization at the nanoscopic and microscopic levels. Atomic organization of semiconductor nanowires, molecular organization of amylose biocrystallites in starch granules, and microscopic organization of several photosynthetic organisms was elucidated. The structure of ZnSe nanowires, key components in many modern nanodevices, was investigated using polarization harmonic generation microscopy. Based on nonlinear optical properties of the different crystal lattices, zinc blende and wurtzite nanowires were differentiated, and the three-dimensional orientation of the zinc blende nanowires could be found. The structure of starch granules, a model biocrystal, important in food as well as health sciences, was also investigated using polarization harmonic microscopy. The study was combined with ab initio calculations using the crystal structures of amylose A and B, revealing that second harmonic signals originate from the hydroxide and hydrogen bonds in the starch granules. Visualization of several photosynthetic organisms including the green algae, Chlamydomonas reinhardtii, two species of cyanobacteria, Leptolyngbya sp. and Anabaena sp., aggregates of light-harvesting pigment-protein complexes as well as chloroplasts from green plants were also explored, revealing that future nonlinear microscopy applications could include structural studies of cell walls, the Chlamydomonas eyespot, and photosynthetic membranes. In this study, several nonlinear optical microscopy modalities were developed for quantitative structural investigations of nano and micro-sized architectures. Non-invasive extraction of crystallographic information in microscopic samples will have a number of potential benefits, for example, in clinical applications, allowing observations of disease states inside tissues without the need for biopsy. Industrial nanotechnology will benefit from fast determination of nanostructures with nonlinear microscopy that will improve quality of nanodevices.

Atomistic determination of flexoelectric properties of crystalline dielectrics

NASA Astrophysics Data System (ADS)

Maranganti, R.; Sharma, P.

2009-08-01

Upon application of a uniform strain, internal sublattice shifts within the unit cell of a noncentrosymmetric dielectric crystal result in the appearance of a net dipole moment: a phenomenon well known as piezoelectricity. A macroscopic strain gradient on the other hand can induce polarization in dielectrics of any crystal structure, even those which possess a centrosymmetric lattice. This phenomenon, called flexoelectricity, has both bulk and surface contributions: the strength of the bulk contribution can be characterized by means of a material property tensor called the bulk flexoelectric tensor. Several recent studies suggest that strain-gradient induced polarization may be responsible for a variety of interesting and anomalous electromechanical phenomena in materials including electromechanical coupling effects in nonuniformly strained nanostructures, “dead layer” effects in nanocapacitor systems, and “giant” piezoelectricity in perovskite nanostructures among others. In this work, adopting a lattice dynamics based microscopic approach we provide estimates of the flexoelectric tensor for certain cubic crystalline ionic salts, perovskite dielectrics, III-V and II-VI semiconductors. We compare our estimates with experimental/theoretical values wherever available and also revisit the validity of an existing empirical scaling relationship for the magnitude of flexoelectric coefficients in terms of material parameters. It is interesting to note that two independent groups report values of flexoelectric properties for perovskite dielectrics that are orders of magnitude apart: Cross and co-workers from Penn State have carried out experimental studies on a variety of materials including barium titanate while Catalan and co-workers from Cambridge used theoretical ab initio techniques as well as experimental techniques to study paraelectric strontium titanate as well as ferroelectric barium titanate and lead titanate. We find that, in the case of perovskite dielectrics, our estimates agree to an order of magnitude with the experimental and theoretical estimates for strontium titanate. For barium titanate however, while our estimates agree to an order of magnitude with existing ab initio calculations, there exists a large discrepancy with experimental estimates. The possible reasons for the observed deviations are discussed.

Structural, vibrational, and quasiparticle band structure of 1,1-diamino-2,2-dinitroethelene from ab initio calculations

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

Appalakondaiah, S.; Vaitheeswaran, G., E-mail: gvaithee@gmail.com; Lebègue, S.

The effects of pressure on the structural and vibrational properties of the layered molecular crystal 1,1-diamino-2,2-dinitroethelene (FOX-7) are explored by first principles calculations. We observe significant changes in the calculated structural properties with different corrections for treating van der Waals interactions to Density Functional Theory (DFT), as compared with standard DFT functionals. In particular, the calculated ground state lattice parameters, volume and bulk modulus obtained with Grimme's scheme, are found to agree well with experiments. The calculated vibrational frequencies demonstrate the dependence of the intra and inter-molecular interactions on FOX-7 under pressure. In addition, we also found a significant incrementmore » in the N–H...O hydrogen bond strength under compression. This is explained by the change in bond lengths between nitrogen, hydrogen, and oxygen atoms, as well as calculated IR spectra under pressure. Finally, the computed band gap is about 2.3 eV with generalized gradient approximation, and is enhanced to 5.1 eV with the GW approximation, which reveals the importance of performing quasiparticle calculations in high energy density materials.« less

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

Xu, Gui -Liang; Sheng, Tian; Chong, Lina

Sodium-ion batteries (SIBs) have been considered as one of the promising power source candidates for the stationary storage industries owing to the much lower cost of sodium than lithium. It is well-known that the electrode materials largely determine the energy density of the battery systems. However, recent discoveries on the electrode materials showed that most of them present distinct lithium and sodium storage performance, which is not yet well understood. In this work, we performed a comparative understanding on the structural changes of porous cobalt oxide during its electrochemical lithiation and sodiation process by in operando synchrotron small angel X-raymore » scattering, X-ray diffraction, and X-ray absorption spectroscopy. It was found that compared to the lithiation process, the porous cobalt oxide undergoes less pore structure changes, oxidation state, and local structure changes as well as crystal structure evolution during its sodiation process, which is attributed to the intrinsic low sodiation activity of cobalt oxide as evidenced by ab initio molecular dynamics simulations. Moreover, it was indicated that the sodiation activity of metal sulfides is higher than that of metal oxides, indicating a better candidate for SIBs. Furthermore, such understanding is crucial for future design and improvement of high-performance electrode materials for SIBs.« less

Ab-initio study on the absorption spectrum of color change sapphire based on first-principles calculations with considering lattice relaxation-effect

NASA Astrophysics Data System (ADS)

Novita, Mega; Nagoshi, Hikari; Sudo, Akiho; Ogasawara, Kazuyoshi

2018-01-01

In this study, we performed an investigation on α-Al2O3: V3+ material, or the so-called color change sapphire, based on first-principles calculations without referring to any experimental parameter. The molecular orbital (MO) structure was estimated by the one-electron MO calculations using the discrete variational-Xα (DV-Xα) method. Next, the absorption spectra were estimated by the many-electron calculations using the discrete variational multi-electron (DVME) method. The effect of lattice relaxation on the crystal structures was estimated based on the first-principles band structure calculations. We performed geometry optimizations on the pure α-Al2O3 and with the impurity V3+ ion using Cambridge Serial Total Energy Package (CASTEP) code. The effect of energy corrections such as configuration dependence correction and correlation correction was also investigated in detail. The results revealed that the structural change on the α-Al2O3: V3+ resulted from the geometry optimization improved the calculated absorption spectra. By a combination of both the lattice relaxation-effect and the energy correction-effect improve the agreement to the experiment fact.

Synthesis and Magnetic Properties of Ni-DOPED ZnO Thin Films: Experimental and AB INITIO Study

NASA Astrophysics Data System (ADS)

Rouchdi, M.; Salmani, E.; Hat, A. El; Hassanain, N.; Mzerd, A.

Structural and magnetic properties of Zn1-xNixO thin films and diluted magnetic semiconductors have been investigated. This sample has been synthesized using a spray pyrolysis technique with a stoechiometric mixture of zinc acetate (C4H6O4Znṡ2H2O) and Nickel acetate (C4H6O4Niṡ 2H2O) on a heated glass substrate at 450∘C. The films were characterized by X-ray diffraction (XRD), UV-Vis spectrophotometry and Hall Effect measurements. These films of ZnO crystallized in the hexagonal Wurtzite structure. The optical study showed that the band-gap energy was increased, from 3.3eV to 3.5eV, with increasing the Ni concentration. The film resistivity was affected by Ni-doping, and the best resistivity value 1.15×10-2 (Ω cm) was obtained for the film doped with 2 at.% Ni. The electronic structure and optical properties of the Wurtzite structure Zn1-xNixO were obtained by first-principles calculations using the Korringa-Kohn-Rostoker method combined with the coherent potential approximation (CPA), as well as CPA confirm our results.

Epitaxially grown strained pentacene thin film on graphene membrane.

PubMed

Kim, Kwanpyo; Santos, Elton J G; Lee, Tae Hoon; Nishi, Yoshio; Bao, Zhenan

2015-05-06

Organic-graphene system has emerged as a new platform for various applications such as flexible organic photovoltaics and organic light emitting diodes. Due to its important implication in charge transport, the study and reliable control of molecular packing structures at the graphene-molecule interface are of great importance for successful incorporation of graphene in related organic devices. Here, an ideal membrane of suspended graphene as a molecular assembly template is utilized to investigate thin-film epitaxial behaviors. Using transmission electron microscopy, two distinct molecular packing structures of pentacene on graphene are found. One observed packing structure is similar to the well-known bulk-phase, which adapts a face-on molecular orientation on graphene substrate. On the other hand, a rare polymorph of pentacene crystal, which shows significant strain along the c-axis, is identified. In particular, the strained film exhibits a specific molecular orientation and a strong azimuthal correlation with underlying graphene. Through ab initio electronic structure calculations, including van der Waals interactions, the unusual polymorph is attributed to the strong graphene-pentacene interaction. The observed strained organic film growth on graphene demonstrates the possibility to tune molecular packing via graphene-molecule interactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fermi arc electronic structure and Chern numbers in the type-II Weyl semimetal candidate Mo x W 1 - x Te 2

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

Belopolski, Ilya; Xu, Su-Yang; Ishida, Yukiaki

2016-08-15

It has recently been proposed that electronic band structures in crystals can give rise to a previously overlooked type of Weyl fermion, which violates Lorentz invariance and, consequently, is forbidden in particle physics. It was further predicted that Mo x W 1 - x Te 2 may realize such a type-II Weyl fermion. Here, we first show theoretically that it is crucial to access the band structure above the Fermi level ε F to show a Weyl semimetal in Mo x W 1 - x Te 2 . Then, we study Mo x W 1 - x Te 2 bymore » pump-probe ARPES and we directly access the band structure > 0.2 eV above ε F in experiment. By comparing our results with ab initio calculations, we conclude that we directly observe the surface state containing the topological Fermi arc. We propose that a future study of Mo x W 1 - x Te 2 by pump-probe ARPES may directly pinpoint the Fermi arc. Our work sets the stage for the experimental discovery of the first type-II Weyl semimetal in Mo x W 1 - x Te 2 .« less

Lattice dynamics of solid N2 with an ab initio intermolecular potential

NASA Astrophysics Data System (ADS)

Luty, T.; van der Avoird, A.; Berns, R. M.

1980-11-01

We have performed harmonic and self-consistent phonon lattice dynamics calculations for α and γ N2 crystals using an intermolecular potential from ab initio calculations. This potential contains electrostatic (multipole) interactions, up to all R-9 terms inclusive, anisotropic dispersion interactions up to all R-10 terms inclusive, and anisotropic overlap interactions caused by charge penetration and exchange between the molecules. The lattice constants, cohesion energy, the frequencies of the translational phonon modes and the Grüneisen parameters for the librational modes are in good agreement with experimental values, confirming the quality of the potential. The frequencies of the librational modes and those of the mixed modes are less well reproduced, especially at temperatures near the α-β phase transition. Probably, the self-consistent phonon method used does not fully account for the anharmonicity in the librations.

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

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Ab initio study of the structure and dynamics of bulk liquid Fe

NASA Astrophysics Data System (ADS)

Marqués, M.; González, L. E.; González, D. J.

2015-10-01

Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.

Structural phase transition of BeTe: an ab initio molecular dynamics study.

PubMed

Alptekin, Sebahaddin

2017-08-11

Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure P T more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results. Graphical abstract The energy-volume relation and ZB phase for the BeTe.

Study of hydrogen bond polarized IR spectra of cinnamic acid crystals

NASA Astrophysics Data System (ADS)

Flakus, Henryk T.; Jabłońska, Magdalena

2004-11-01

This paper presents the results of investigation of the polarized IR spectra of cinnamic acid and of its deuterium derivative crystals. The spectra were measured by a transmission method, using polarized light, at the room temperature and at 77 K, for two different crystalline faces. Theoretical analysis of the results concerned linear dichroic effects, H/D isotopic and temperature effects, observed in the spectra of the hydrogen and of the deuterium bonds in cinnamic acid crystals, at the frequency ranges of the νO-H and the νO-D bands. The basic crystal spectral properties could be satisfactorily interpreted in a quantitative way for a centrosymmetric cyclic hydrogen bond dimer model. Such a model explains not only a two-branch structure of the νO-H and νO-D bands in crystalline spectra, but also some essential linear dichroic effects in the band frequency ranges, measured for isotopically diluted crystals. Model calculations, performed within the limits of the 'strong-coupling' model, allowed for quantitative interpretation and for understanding of the basic properties of the hydrogen bond IR spectra of cinnamic acid crystals, H/D isotopic, temperature and dichroic effects included. In the scope of our studies the mechanism of H/D isotopic 'self-organization' processes, taking place in the crystal hydrogen bond lattices, was also recognized. It was proved that for isotopically diluted crystalline samples of cinnamic acid, a non-random distribution of protons and deuterons occurs exclusively in the hydrogen bond dimers. Nevertheless, these co-operative interactions between the hydrogen bonds do not involve the adjacent hydrogen bond dimers in each unit cell. The two-branch fine structure pattern of the νO-H and νO-D bands was ascribed to the vibronic mechanism of vibrational dipole selection rule breaking in centrosymmetric hydrogen bond dimers. The observed in the spectra very high intensity of the forbidden transition sub-band in the analyzed νO-H and νO-D bands is a manifestation of an extremely effective symmetry rule breaking mechanism. It correlates with a relatively large excess electron charge on the cinnamic aid dimer carboxyl groups. This effect is a result of a partial withdrawal of the electron charge, from the conjugated π-bond systems of the styryl substituents, by the carboxyl groups. This statement has been supported by ab initio calculations.

Analysis of fcc metals fracture behaviour: Fracture behaviour of fcc metals: brittle/ductile behaviour criteria : with ab-initio, embedded atom and pseudopotential parameterization for Au, Ir and Al. analysis for Au, Ir and Al.

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.; Katsnelson, M. I.; Mryasov, Oleg N.; Freeman, A. J.; Trefilov, M. V.

1998-03-01

Theoretical analysis of the fracture behaviour of fcc Au, Ir and Al have been performed within various brittle/ductile criteria (BDC) with ab-initio, embedded atom (EAM), and pseudopotential parameterizations. We systematically examined several important aspects of the fracture behaviour: (i) dislocation structure, (ii) energetics of the cleavage decohesion and (iii) character of the interatomic interactions. Unit dislocation structures were analyzed within a two dimensional generalization of the Peierls-Nabarro model with restoring forces determined from ab-initio total energy calculations and found to be split with well defined highly mobile partials for all considered metals. We find from ab-initio and pseudopotential that in contrast with most of fcc metals, cleavage decohesion curve for Al appreciably differs from UBER relation. Finally, using ab-initio, EAM and pseudopotential parameterizations, we demonstrate that (i) Au (as a typical example of a ductile metal) is well described within existing BDC's, (ii) anomalous cleavage-like crack propagation of Ir is driven predominantly by it's high elastic modulus and (iii) Al is not described within BDC due to it's long-range interatomic interactions (and hence requires adjustments of the brittle/ductile criteria).

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

PubMed Central

Zhang, Yang

2014-01-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. PMID:23760925

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

PubMed

Zhang, Yang

2014-02-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials

NASA Astrophysics Data System (ADS)

Prahl, Ulrich; Bleck, Wolfgang; Saeed-Akbari, Alireza

This contribution reports the results of the collaborative research unit SFB 761 "Steel — ab initio", a cooperative project between RWTH Aachen University and the Max-Planck-Institute for Iron Research in Düsseldorf (MPIE) financed by the German Research Foundation (DFG). For the first time, it is exploited how ab initio approaches may lead to a detailed understanding and thus to a specific improvement of material development. The challenge lies in the combination of abstract natural science theories with rather engineering-like established concepts. Aiming at the technological target of the development of a new type of structural materials based on Fe-Mn-C alloys, the combination of ab initio and engineering methods is new, but could be followed quite successfully. Three major topics are treated in this research unit: a) development of a new method for material- and process-development based on ab initio calculations; b) design of a new class of structural materials with extraordinary property combinations; c) acceleration of development time and reduction of experimental efforts and complexity for material- and process-development. In the present work, an overview of the results of the first five years as well as an outlook for the upcoming three-year period is given.

Quenchable water-rich, aluminous post-stishovite: implications for seismic anomalies in the mid-mantle

NASA Astrophysics Data System (ADS)

Myhill, R.; Frost, D. J.; Panero, W. R.; Boffa Ballaran, T.; Miyajima, N.; Bureau, H.; Raepsaet, C.; Siersch, N.; Kohn, S. C.

2016-12-01

At mid-mantle pressures, stishovite undergoes a displacive phase transition to the calcium chloride structure. It has been argued that softening accompanying this phase transition leads to very low seismic velocities and that silica-rich materials in the lower mantle may therefore be effective scatterers of seismic energy. The post-stishovite phase is also a promising candidate for water storage in the lower mantle, as it is both stable at very high temperatures and isostructural with the high pressure hydrous phases delta-AlOOH and Phase H. Pure SiO2 post-stishovite is unquenchable, making ex-situ characterisation impossible. In this study, we exploit the stabilisation of the post-stishovite structure due to alumina incorporation to synthesise and quench large crystals of post-stishovite. Single crystals are characterised by X-ray diffraction, TEM and Raman spectroscopy, and water contents are analysed with elastic recoil detection and FTIR. We show that water contents in our post-stishovite crystals are consistent with an SiO2-AlOOH solid solution, containing 3-7 times more water per atom of aluminium than stishovite. Our results suggest that almost 1 wt % H2O could be incorporated into post-stishovite crystals in lower mantle mafic rocks. We use ab-initio simulations to investigate the effect of pressure on the mechanism of hydroxyl incorporation into aluminous stishovite and post-stishovite. Finally, we discuss the potential for post-stishovite to affect seismic velocities in the lower mantle. In addition to the scattering potential of the phase transition, patchy low velocity layers in the mid-mantle might represent regions where hydrous melts are reacting with post-stishovite. In the lowermost mantle, transformation of post-stishovite to seifertite could result in the formation of a hydrous melt that might explain seismologically observed ultra low velocity zones.

Unification of the phonon mode behavior in semiconductor alloys: Theory and ab initio calculations

NASA Astrophysics Data System (ADS)

Pagès, O.; Postnikov, A. V.; Kassem, M.; Chafi, A.; Nassour, A.; Doyen, S.

2008-03-01

We demonstrate how to overcome serious problems in understanding and classification of vibration spectra in semiconductor alloys, following from traditional use of the virtual crystal approximation (VCA). We show that such different systems as InGaAs (1- bond→1 -mode behavior), InGaP (modified 2-mode), and ZnTeSe (2- bond→1 -mode) obey, in fact, the same phonon mode behavior—hence probably a universal one—of a percolation type (1- bond→2 -mode). The change of paradigm from the “VCA insight” (an averaged microscopic one) to the “percolation insight” (a mesoscopic one) offers a promising link toward the understanding of alloy disorder. The discussion is supported by ab initio simulation of the phonon density of states at the zone center of representative supercells at intermediary composition (ZnTeSe) and at the impurity-dilute limits (all systems). In particular, we propose a simple ab initio “protocol” to estimate the basic input parameters of our semiempirical “percolation” model for the calculation of the 1- bond→2 -mode vibration spectra of zinc blende alloys. With this, the model turns self-sufficient.

An ab initio study of the conformational energy map of acetylcholine

NASA Astrophysics Data System (ADS)

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

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

Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations.

PubMed

Hagiwara, Yohsuke; Tateno, Masaru

2010-10-20

We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems. © 2010 IOP Publishing Ltd

An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

NASA Astrophysics Data System (ADS)

Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

2018-04-01

The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

PubMed

Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

2016-07-15

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

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.

Micro-, to nano-structural relationships in natural serpentines, derived from cationic substitutions.

NASA Astrophysics Data System (ADS)

Munoz, M.; Farges, F.; Andreani, M.; Ulrich, M.; Marcaillou, C.; Mathon, O.

2014-12-01

The understanding of the crystal chemistry of serpentine minerals (incl. antigorite, lizardite and chrysotile) is fundamental since serpentinization processes concern very large scientific domains: e.g., natural abiotic hydrogen production (Marcaillou et al., 2011), origins of life (Russell et al., 2010), fluid properties and mobility of metals in subduction zones (Kelley and Cottrell, 2009). This study aims at characterizing relations between the micro-, and nano-structures of the most abundant serpentine polytypes in the oceanic crust. Serpentine theoretical formula is Mg3Si2O5(OH)4 but several natural substitutions are possible and the formula may be written such as: (Mg,Fe2+,Fe3+,Al)3(Si,Al,Fe3+)2O5(OH)4; showing that Fe and Al may play an important role in the crystallization of serpentines. Preliminary crystal chemistry studies, suggest that, 1) the Al content alone cannot be directly correlated to serpentine polytypes (Andreani et al., 2008), 2) the amounts of tetrahedral iron can be significant in the presence of ferric iron (Marcaillou et al., 2011). Because magnetite is usually associated to serpentine, the Fe-speciation characterization of serpentine is delicate. Here, we provide the study of 33 magnetite-free serpentines containing various amounts of Fe and Al. The samples were characterized by SEM, Raman, XRF, as well as XANES, pre-edge, and EXAFS spectroscopy at the Fe K-edge. XANES experimental data were crosschecked and interpreted thanks to ab initio calculations and EXAFS shell-fitting. Also, preliminary 27Al-RMN data is presented. Results suggest relationships between the type and amount of substitution of trivalent cations in minerals, and the microstructures observed. Chrysotile incorporates less trivalent cations than other varieties, which tends to preserve the so-called misfit between the TO layers, and therefore the tubular structure of the mineral. Lizardites mainly involve Fe/Al Tschermak-type substitutions, while M-site vacancy charge-compensation mechanisms could be favored for antigorite crystals. ReferencesAndréani et al., 2008, European Journal of Mineralogy, 20, 159-171. Kelley and Cottrell, 2009, Science, 325, 605-607. Marcaillou et al., 2011, Earth And Planetary Science Letters, 303, 281-290. Russell et al., 2010, Geobiology, 8, 355-371.

Ab Initio Study of Interfacial Structure Transformation of Amorphous Carbon Catalyzed by Ti, Cr, and W Transition Layers.

PubMed

Li, Xiaowei; Li, Lei; Zhang, Dong; Wang, Aiying

2017-11-29

Amorphous carbon (a-C) films composited with transition layers exhibit the desirable improvement of adhesion strength between films and substrate, but the further understanding on the interfacial structure transformation of a-C structure induced by transition layers is still lacked. In this paper, using ab initio calculations, we comparatively studied the interfacial structure between Ti, Cr, or W transition layers and a-C film from the atomic scale, and demonstrated that the addition of Ti, Cr, or W catalyzed the graphitic transformation of a-C structure at different levels, which provided the theoretical guidance for designing a multilayer nanocomposite film for renewed application.

A new copper(II) chelate complex with tridentate ligand: Synthesis, crystal and molecular electronic structure of aqua-(diethylenetriamine-N, N‧, N‧‧)-copper(II) sulfate monohydrate and its fire retardant properties

NASA Astrophysics Data System (ADS)

Lavrenyuk, H.; Mykhalichko, O.; Zarychta, B.; Olijnyk, V.; Mykhalichko, B.

2015-09-01

The crystals of a new aqua-(diethylenetriamine-N, N‧, N‧‧)-copper(II) sulfate monohydrate have been synthesized by direct interaction of solid copper(II) sulfate pentahydrate with diethylenetriamine (deta). The crystal structure of [Cu(deta)H2O]SO4ṡH2O (1) has been determined by X-ray diffraction methods at 100 K and characterized using X-ray powder diffraction pattern: space group P 1 bar, a = 7.2819(4), b = 8.4669(4), c = 8.7020(3) Å, α = 83.590(3), β = 89.620(4), γ = 84.946(4)°, Z = 2. The environment of the Cu(II) atom is a distorted, elongated square pyramid which consists of three nitrogen atoms of the deta molecule and oxygen atom of the water molecule in the basal plane of the square pyramid (the average lengths of the in-plane Cu-N and Cu-O bonds are 2.00 Å). The apical position of the coordination polyhedron is occupied by complementary oxygen atom of the sulfate anion (the length of the axial Cu-O bond is 2.421(1) Å). The crystal packing is governed by strong hydrogen bonds of O-H⋯O and N-H⋯O types. The ab initio quantum-chemical calculations have been performed by the restricted Hartree-Fock method with a basis set 6-31∗G using the structural data of [Cu(deta)H2O]SO4ṡH2O. It has been ascertained that the degenerate d-orbitals of the Cu2+ ion split under the co-action of both the square-pyramidal coordination and the chelation. It is significant that visually observed crystals color (blue-violet) of the [Cu(deta)H2O]SO4ṡH2O complex is in good agreement with the calculated value of wavelength of visible light (λ = 5735 Å) which is closely related to the energy of the absorbed photon (Δ = 2.161 eV). Furthermore, the stereo-chemical aspect of influence of the CuSO4 upon combustibility of modified epoxy-amine polymers has been scrutinized.

CsSnI[subscript 3]: Semiconductor or Metal? High Electrical Conductivity and Strong Near-Infrared Photoluminescence from a Single Material. High Hole Mobility and Phase-Transitions

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

Chung, In; Song, Jung-Hwan; Im, Jino

CsSnI{sub 3} is an unusual perovskite that undergoes complex displacive and reconstructive phase transitions and exhibits near-infrared emission at room temperature. Experimental and theoretical studies of CsSnI{sub 3} have been limited by the lack of detailed crystal structure characterization and chemical instability. Here we describe the synthesis of pure polymorphic crystals, the preparation of large crack-/bubble-free ingots, the refined single-crystal structures, and temperature-dependent charge transport and optical properties of CsSnI{sub 3}, coupled with ab initio first-principles density functional theory (DFT) calculations. In situ temperature-dependent single-crystal and synchrotron powder X-ray diffraction studies reveal the origin of polymorphous phase transitions of CsSnI{submore » 3}. The black orthorhombic form of CsSnI{sub 3} demonstrates one of the largest volumetric thermal expansion coefficients for inorganic solids. Electrical conductivity, Hall effect, and thermopower measurements on it show p-type metallic behavior with low carrier density, despite the optical band gap of 1.3 eV. Hall effect measurements of the black orthorhombic perovskite phase of CsSnI{sub 3} indicate that it is a p-type direct band gap semiconductor with carrier concentration at room temperature of {approx} 10{sup 17} cm{sup -3} and a hole mobility of {approx} 585 cm{sup 2} V{sup -1} s{sup -1}. The hole mobility is one of the highest observed among p-type semiconductors with comparable band gaps. Its powders exhibit a strong room-temperature near-IR emission spectrum at 950 nm. Remarkably, the values of the electrical conductivity and photoluminescence intensity increase with heat treatment. The DFT calculations show that the screened-exchange local density approximation-derived band gap agrees well with the experimentally measured band gap. Calculations of the formation energy of defects strongly suggest that the electrical and light emission properties possibly result from Sn defects in the crystal structure, which arise intrinsically. Thus, although stoichiometric CsSnI{sub 3} is a semiconductor, the material is prone to intrinsic defects associated with Sn vacancies. This creates highly mobile holes which cause the materials to appear metallic.« less

Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

ERIC Educational Resources Information Center

Halpern, Arthur M.

2011-01-01

A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

Diffusion in liquid Germanium using ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.

1996-03-01

We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.

Ab-initio modeling of electromechanical coupling at Si surfaces

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

Hoppe, Sandra; Müller, Stefan, E-mail: stefan.mueller@tuhh.de; Michl, Anja

The electromechanical coupling at the silicon (100) and (111) surfaces was studied via density functional theory by calculating the response of the ionization potential and the electron affinity to different types of strain. We find a branched strain response of those two quantities with different coupling coefficients for negative and positive strain values. This can be attributed to the reduced crystal symmetry due to anisotropic strain, which partially lifts the degeneracy of the valence and conduction bands. Only the Si(111) electron affinity exhibits a monotonously linear strain response, as the conduction band valleys remain degenerate under strain. The strain responsemore » of the surface dipole is linear and seems to be dominated by volume changes. Our results may help to understand the mechanisms behind electromechanical coupling at an atomic level in greater detail and for different electronic and atomic structures.« less

Novel near-infrared emission from crystal defects in MoS2 multilayer flakes.

PubMed

Fabbri, F; Rotunno, E; Cinquanta, E; Campi, D; Bonnini, E; Kaplan, D; Lazzarini, L; Bernasconi, M; Ferrari, C; Longo, M; Nicotra, G; Molle, A; Swaminathan, V; Salviati, G

2016-10-04

The structural defects in two-dimensional transition metal dichalcogenides, including point defects, dislocations and grain boundaries, are scarcely considered regarding their potential to manipulate the electrical and optical properties of this class of materials, notwithstanding the significant advances already made. Indeed, impurities and vacancies may influence the exciton population, create disorder-induced localization, as well as modify the electrical behaviour of the material. Here we report on the experimental evidence, confirmed by ab initio calculations, that sulfur vacancies give rise to a novel near-infrared emission peak around 0.75 eV in exfoliated MoS 2 flakes. In addition, we demonstrate an excess of sulfur vacancies at the flake's edges by means of cathodoluminescence mapping, aberration-corrected transmission electron microscopy imaging and electron energy loss analyses. Moreover, we show that ripplocations, extended line defects peculiar to this material, broaden and redshift the MoS 2 indirect bandgap emission.

Negative-pressure-induced enhancement in a freestanding ferroelectric

NASA Astrophysics Data System (ADS)

Wang, Jin; Wylie-van Eerd, Ben; Sluka, Tomas; Sandu, Cosmin; Cantoni, Marco; Wei, Xian-Kui; Kvasov, Alexander; McGilly, Leo John; Gemeiner, Pascale; Dkhil, Brahim; Tagantsev, Alexander; Trodahl, Joe; Setter, Nava

2015-10-01

Ferroelectrics are widespread in technology, being used in electronics and communications, medical diagnostics and industrial automation. However, extension of their operational temperature range and useful properties is desired. Recent developments have exploited ultrathin epitaxial films on lattice-mismatched substrates, imposing tensile or compressive biaxial strain, to enhance ferroelectric properties. Much larger hydrostatic compression can be achieved by diamond anvil cells, but hydrostatic tensile stress is regarded as unachievable. Theory and ab initio treatments predict enhanced properties for perovskite ferroelectrics under hydrostatic tensile stress. Here we report negative-pressure-driven enhancement of the tetragonality, Curie temperature and spontaneous polarization in freestanding PbTiO3 nanowires, driven by stress that develops during transformation of the material from a lower-density crystal structure to the perovskite phase. This study suggests a simple route to obtain negative pressure in other materials, potentially extending their exploitable properties beyond their present levels.

High-temperature superconducting phase of HBr under pressure predicted by first-principles calculations

NASA Astrophysics Data System (ADS)

Gu, Qinyan; Lu, Pengchao; Xia, Kang; Sun, Jian; Xing, Dingyu

2017-08-01

The high pressure phases of HBr are explored with an ab initio crystal structure search. By taking into account the contribution of zero-point energy (ZPE), we find that the P 4 /n m m phase of HBr is thermodynamically stable in the pressure range from 150 to 200 GPa. The superconducting critical temperature (Tc) of P 4 /n m m HBr is evaluated to be around 73 K at 170 GPa, which is the highest record so far among binary halogen hydrides. Its Tc can be further raised to around 95K under 170 GPa if half of the bromine atoms in the P 4 /n m m HBr are substituted by the lighter chlorine atoms. Our study shows that, in addition to lower mass, higher coordination number, shorter bonds, and more highly symmetric environment for the hydrogen atoms are important factors to enhance the superconductivity in hydrides.

Breakdown of Magnetic Order in the Pressurized Kitaev Iridate β -Li2IrO3

NASA Astrophysics Data System (ADS)

Majumder, M.; Manna, R. S.; Simutis, G.; Orain, J. C.; Dey, T.; Freund, F.; Jesche, A.; Khasanov, R.; Biswas, P. K.; Bykova, E.; Dubrovinskaia, N.; Dubrovinsky, L. S.; Yadav, R.; Hozoi, L.; Nishimoto, S.; Tsirlin, A. A.; Gegenwart, P.

2018-06-01

Temperature-pressure phase diagram of the Kitaev hyperhoneycomb iridate β -Li2IrO3 is explored using magnetization, thermal expansion, magnetostriction, and muon spin rotation measurements, as well as single-crystal x-ray diffraction under pressure and ab initio calculations. The Néel temperature of β -Li2IrO3 increases with the slope of 0.9 K /GPa upon initial compression, but the reduction in the polarization field Hc reflects a growing instability of the incommensurate order. At 1.4 GPa, the ordered state breaks down upon a first-order transition, giving way to a new ground state marked by the coexistence of dynamically correlated and frozen spins. This partial freezing in the absence of any conspicuous structural defects may indicate the classical nature of the resulting pressure-induced spin liquid, an observation paralleled to the increase in the nearest-neighbor off-diagonal exchange Γ under pressure.

Novel near-infrared emission from crystal defects in MoS2 multilayer flakes

PubMed Central

Fabbri, F.; Rotunno, E.; Cinquanta, E.; Campi, D.; Bonnini, E.; Kaplan, D.; Lazzarini, L.; Bernasconi, M.; Ferrari, C.; Longo, M.; Nicotra, G.; Molle, A.; Swaminathan, V.; Salviati, G.

2016-01-01

The structural defects in two-dimensional transition metal dichalcogenides, including point defects, dislocations and grain boundaries, are scarcely considered regarding their potential to manipulate the electrical and optical properties of this class of materials, notwithstanding the significant advances already made. Indeed, impurities and vacancies may influence the exciton population, create disorder-induced localization, as well as modify the electrical behaviour of the material. Here we report on the experimental evidence, confirmed by ab initio calculations, that sulfur vacancies give rise to a novel near-infrared emission peak around 0.75 eV in exfoliated MoS2 flakes. In addition, we demonstrate an excess of sulfur vacancies at the flake's edges by means of cathodoluminescence mapping, aberration-corrected transmission electron microscopy imaging and electron energy loss analyses. Moreover, we show that ripplocations, extended line defects peculiar to this material, broaden and redshift the MoS2 indirect bandgap emission. PMID:27698425

3D hybrid carbon composed of multigraphene bridged by carbon chains

NASA Astrophysics Data System (ADS)

Liu, Lingyu; Hu, Meng; Liu, Chao; Shao, Cancan; Pan, Yilong; Ma, Mengdong; Wu, Yingju; Zhao, Zhisheng; Gao, Guoying; He, Julong

2018-01-01

The element carbon possesses various stable and metastable allotropes; some of them have been applied in diverse fields. The experimental evidences of both carbon chain and graphdiyne have been reported. Here, we reveal the mystery of an enchanting carbon allotrope with sp-, sp2-, and sp3-hybridized carbon atoms using a newly developed ab initio particle-swarm optimization algorithm for crystal structure prediction. This crystalline allotrope, namely m-C12, can be viewed as braided mesh architecture interwoven with multigraphene and carbon chains. The m-C12 meets the criteria for dynamic and mechanical stabilities and is energetically more stable than carbyne and graphdiyne. Analysis of the B/G and Poisson's ratio indicates that this allotrope is ductile. Notably, m-C12 is a superconducting carbon with Tc of 1.13 K, which is rare in the family of carbon allotropes.

Ab initio calculation of electronic structure and magnetic properties of R2Fe14BNx (R = Pr,Nd)

NASA Astrophysics Data System (ADS)

Tian, Guang; Zha, Liang; Yang, Wenyun; Qiao, Guanyi; Wang, Changsheng; Yang, Yingchang; Yang, Jinbo

2018-05-01

The site preference of N atom for R2Fe14BNx (R= Pr, Nd) and the interstitial nitrogen effect on the magnetic properties have been studied by the first-principles method. It was found that the nitrogen is more likely to occupy the 4e site for Pr2Fe14BNx compound, while 4f site for Nd2Fe14BNx. When N atoms entering some specific crystal sites (such as 2a and 4f), the total magnetic moments of these compounds are not reduced, but slightly increased. Although the doping of N may reduce the total magnetic moments of some R2Fe14B compounds in the cases of optimal occupancy, the volumetric effect caused by N doping can still change the electron density distributions of Fe near the Fermi level, improving the magnetic ordering temperature of such compounds.

Interstitial Fe in MgO

NASA Astrophysics Data System (ADS)

Mølholt, T. E.; Mantovan, R.; Gunnlaugsson, H. P.; Svane, A.; Masenda, H.; Naidoo, D.; Bharuth-Ram, K.; Fanciulli, M.; Gislason, H. P.; Johnston, K.; Langouche, G.; Ólafsson, S.; Sielemann, R.; Weyer, G.

2014-01-01

Isolated 57Fe atoms were studied in MgO single-crystals by emission Mössbauer spectroscopy following implantation of 57Mn decaying to 57Fe. Four Mössbauer spectral components were found corresponding to different Fe lattice positions and/or charge states. Two components represent Fe atoms substituting Mg as Fe2+ and Fe3+, respectively; a third component is due to Fe in a strongly implantation-induced disturbed region. The fourth component, which is the focus of this paper, can be assigned to Fe at an interstitial site. Comparison of its measured isomer shift with ab initio calculations suggests that the interstitial Fe is located on, or close to, the face of the rock-salt MgO structure. To harmonize such an assignment with the measured near-zero quadrupole interaction a local motion process (cage motion) of the Fe has to be stipulated. The relation of such a local motion as a starting point for long range diffusion is discussed.

Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF

PubMed Central

2014-01-01

We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157

Novel near-infrared emission from crystal defects in MoS2 multilayer flakes

NASA Astrophysics Data System (ADS)

Fabbri, F.; Rotunno, E.; Cinquanta, E.; Campi, D.; Bonnini, E.; Kaplan, D.; Lazzarini, L.; Bernasconi, M.; Ferrari, C.; Longo, M.; Nicotra, G.; Molle, A.; Swaminathan, V.; Salviati, G.

2016-10-01

The structural defects in two-dimensional transition metal dichalcogenides, including point defects, dislocations and grain boundaries, are scarcely considered regarding their potential to manipulate the electrical and optical properties of this class of materials, notwithstanding the significant advances already made. Indeed, impurities and vacancies may influence the exciton population, create disorder-induced localization, as well as modify the electrical behaviour of the material. Here we report on the experimental evidence, confirmed by ab initio calculations, that sulfur vacancies give rise to a novel near-infrared emission peak around 0.75 eV in exfoliated MoS2 flakes. In addition, we demonstrate an excess of sulfur vacancies at the flake's edges by means of cathodoluminescence mapping, aberration-corrected transmission electron microscopy imaging and electron energy loss analyses. Moreover, we show that ripplocations, extended line defects peculiar to this material, broaden and redshift the MoS2 indirect bandgap emission.

Topological Dirac line nodes and superconductivity coexist in SnSe at high pressure

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

Chen, Xuliang; Lu, Pengchao; Wang, Xuefei

2017-10-01

We report on the discovery of a pressure-induced topological and superconducting phase of SnSe, a material which attracts much attention recently due to its superior thermoelectric properties. In situ high-pressure electrical transport and synchrotron x-ray diffraction measurements show that the superconductivity emerges along with the formation of a CsCl-type structural phase of SnSe above around 27 GPa, with a maximum critical temperature of 3.2 K at 39 GPa. Based on ab initio calculations, this CsCl-type SnSe is predicted to be a Dirac line-node (DLN) semimetal in the absence of spin-orbit coupling, whose DLN states are protected by the coexistence ofmore » time-reversal and inversion symmetries. These results make CsCl-type SnSe an interesting model platform with simple crystal symmetry to study the interplay of topological physics and superconductivity.« less

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

NASA Astrophysics Data System (ADS)

Sharma, Abhiraj; Suryanarayana, Phanish

2018-05-01

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

Exploring proton transfer in 1,2,3-triazole-triazolium dimer with ab initio method

NASA Astrophysics Data System (ADS)

Li, Ailin; Yan, Tianying; Shen, Panwen

Ab initio calculations are utilized to search for transition state structures for proton transfer in the 1,2,3-triazole-triazolium complexes on the basis of optimized dimers. The result suggests six transition state structures for single proton transfer in the complexes, most of which are coplanar. The energy barriers, between different stable and transition states structures with zero point energy (ZPE) corrections, show that proton transfer occurs at room temperature with coplanar configuration that has the lowest energy. The results clearly support that reorientation gives triazole flexibility for proton transfer.

Structure of magnesium selenate enneahydrate, MgSeO4·9H2O, from 5 to 250 K using neutron time-of-flight Laue diffraction.

PubMed

Fortes, A Dominic; Alfè, Dario; Hernández, Eduardo R; Gutmann, Matthias J

2015-06-01

The complete structure of MgSeO4·9H2O has been refined from neutron single-crystal diffraction data obtained at 5, 100, 175 and 250 K. It is monoclinic, space group P2₁/c, Z = 4, with unit-cell parameters a = 7.222 (2), b = 10.484 (3), c = 17.327 (4) Å, β = 109.57 (2)°, and V = 1236.1 (6) Å(3) [ρ(calc) = 1770 (1) kg m(-3)] at 5 K. The structure consists of isolated [Mg(H2O)6](2+) octahedra, [SeO4](2-) tetrahedra and three interstitial lattice water molecules, all on sites of symmetry 1. The positions of the H atoms agree well with those inferred on the basis of geometrical considerations in the prior X-ray powder diffraction structure determination: no evidence of orientational disorder of the water molecules is apparent in the temperature range studied. Six of the nine water molecules are hydrogen bonded to one another to form a unique centrosymmetric dodecamer, (H2O)12. Raman spectra have been acquired in the range 170-4000 cm(-1) at 259 and 78 K; ab initio calculations, using density functional theory, have been carried out in order to aid in the analysis of the Raman spectrum as well as providing additional insights into the geometry and thermodynamics of the hydrogen bonds. Complementary information concerning the thermal expansion, crystal morphology and the solubility are also presented.

Electronic band structure effects in the stopping of protons in copper [Electronic band structure non-linear effects in the stopping of protons in copper

DOE PAGES

Quashie, Edwin E.; Saha, Bidhan C.; Correa, Alfredo A.

2016-10-05

Here, we present an ab initio study of the electronic stopping power of protons in copper over a wide range of proton velocities v = 0.02–10a.u. where we take into account nonlinear effects. Time-dependent density functional theory coupled with molecular dynamics is used to study electronic excitations produced by energetic protons. A plane-wave pseudopotential scheme is employed to solve the time-dependent Kohn-Sham equations for a moving ion in a periodic crystal. The electronic excitations and the band structure determine the stopping power of the material and alter the interatomic forces for both channeling and off-channeling trajectories. Our off-channeling results aremore » in quantitative agreement with experiments, and at low velocity they unveil a crossover region of superlinear velocity dependence (with a power of ~1.5) in the velocity range v = 0.07–0.3a.u., which we associate to the copper crystalline electronic band structure. The results are rationalized by simple band models connecting two separate regimes. We find that the limit of electronic stopping v → 0 is not as simple as phenomenological models suggest and it is plagued by band-structure effects.« less

Transformation Paths from Cubic to Low-Symmetry Structures in Heusler Ni2MnGa Compound.

PubMed

Zelený, Martin; Straka, Ladislav; Sozinov, Alexei; Heczko, Oleg

2018-05-08

In order to explain the formation of low-temperature phases in stoichiometric Ni 2 MnGa magnetic shape memory alloy, we investigate the phase transformation paths from cubic austenite with Heusler structure to low-symmetry martensitic structures. We used ab initio calculations combined with the generalized solid state nudged elastic band method to determine the minimum energy path and corresponding changes in crystal lattice. The four-, five-, and seven-layered modulated phases of martensite (4O, 10M, and 14M) are built as the relaxed nanotwinned non-modulated (NM) phase. Despite having a total energy larger than the other martensitic phases, the 10M phase will spontaneously form at 0 K, because there is no energy barrier on the path and the energy decreases with a large negative slope. Moreover, a similar negative slope in the beginning of path is found also for the transformation to the 6M premartensite, which appears as a local minimum on the path leading further to 10M martensite. Transformation paths to other structures exhibit more or less significant barriers in the beginning hindering such a transformation from austenite. These findings correspond to experiment and demonstrates that the kinetics of the transformation is decisive for the selection of the particular low-symmetry structure.

Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

PubMed

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.

Ab initio Computations of the Electronic, Mechanical, and Thermal Properties of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2

NASA Technical Reports Server (NTRS)

Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray

2011-01-01

Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.

Characterisation of irradiation-induced defects in ZnO single crystals

NASA Astrophysics Data System (ADS)

Prochazka, I.; Cizek, J.; Lukac, F.; Melikhova, O.; Valenta, J.; Havranek, V.; Anwand, W.; Skuratov, V. A.; Strukova, T. S.

2016-01-01

Positron annihilation spectroscopy (PAS) combined with optical methods was employed for characterisation of defects in the hydrothermally grown ZnO single crystals irradiated by 167 MeV Xe26+ ions to fluences ranged from 3×1012 to 1×1014 cm-2. The positron lifetime (LT), Doppler broadening as well as slow-positron implantation spectroscopy (SPIS) techniques were involved. The ab-initio theoretical calculations were utilised for interpretation of LT results. The optical transmission and photoluminescence measurements were conducted, too. The virgin ZnO crystal exhibited a single component LT spectrum with a lifetime of 182 ps which is attributed to saturated positron trapping in Zn vacancies associated with hydrogen atoms unintentionally introduced into the crystal during the crystal growth. The Xe ion irradiated ZnO crystals have shown an additional component with a longer lifetime of ≈ 360 ps which comes from irradiation-induced larger defects equivalent in size to clusters of ≈10 to 12 vacancies. The concentrations of these clusters were estimated on the basis of combined LT and SPIS data. The PAS data were correlated with irradiation induced changes seen in the optical spectroscopy experiments.

Electronic structure, bonding, charge distribution, and x-ray absorption spectra of the (001) surfaces of fluorapatite and hydroxyapatite from first principles

NASA Astrophysics Data System (ADS)

Rulis, Paul; Yao, Hongzhi; Ouyang, Lizhi; Ching, W. Y.

2007-12-01

Fluorapatite (FAP) and hydroxyapatite (HAP) are two very important bioceramic crystals. The (001) surfaces of FAP and HAP crystals are studied by ab initio density functional calculations using a supercell slab geometry. It is shown that in both crystals, the O-terminated (001) surface is more stable with calculated surface energies of 0.865 and 0.871J/m2 for FAP and HAP, respectively. In FAP, the two surfaces are symmetric. In HAP, the orientation of the OH group along the c axis reduces the symmetry such that the top and bottom surfaces are no longer symmetric. It is revealed that the atoms near the surface and subsurface are significantly relaxed especially in the case of HAP. The largest relaxations occurred via the lateral movements of the O ions at the subsurface level. The electronic structures of the surface models in the form of layer-by-layer resolved partial density of states for all the atoms show systematic variation from the surface region toward the bulk region. The calculated Mulliken effective charge on each type of atom and the bond order values between cations (Ca, P) and anions (O, F) show different charge transfers and bond strength variations from the bulk crystal values. Electron charge density calculations show that the surfaces of both FAP and HAP crystals are mostly positively charged due to the presence of Ca ions at the surface. The positively charged surfaces have implications for the absorption on apatite surfaces of water and other organic molecules in an aqueous environment which are an important part of its bioactivity. The x-ray absorption near-edge structure (XANES) spectra ( Ca-K , O-K , F-K , P-K , and P-L3 edges) of both the surface models and the bulk crystals are calculated and compared. The calculations use a supercell approach which takes into account the electron-core-hole interaction. It is shown that the site-specific XANES spectra show significant differences between atoms near the surface and in the bulk and are very sensitive to the local atomic environment of each atom. This information will be very valuable for characterizing the apatite materials and in the interpretation of experimental data. Comparisons of several sets of experimental data with the weighted sums of the calculated spectra at different sites for the same element show very good agreement.

Electronic structure and partial charge distribution of doxorubicin under different molecular environments

NASA Astrophysics Data System (ADS)

Poudel, Lokendra

Doxorubicin (trade name Adriamycin, abbreviated DOX) is a well-known an- thracyclic chemotherapeutic used in treating a variety of cancers including acute leukemia, lymphoma, multiple myeloma, and a range of stomach, lung, bladder, bone, breast, and ovarian cancers. The purpose of the present work is to study electronic structure, partial charge distribution and interaction energy of DOX under different environments. It provides a framework for better understanding of bioactivity of DOX with DNA. While in this work, we focus on DOX -- DNA interactions; the obtained knowledge could be translated to other drug -- target interactions or biomolecular interactions. The electronic structure and partial charge distribution of DOX in three dierent molecular environments: isolated, solvated, and intercalated into a DNA complex,were studied by rst principles density functional methods. It is shown that the addition of solvating water molecules to DOX and the proximity and interaction with DNA has a signicant impact on the electronic structure as well as the partial charge distribution. The calculated total partial charges for DOX in the three models are 0.0, +0.123 and -0.06 electrons for the isolated, solvated, and intercalated state, respectively. Furthermore, by using the more accurate ab initio partial charge values on every atom in the models, signicant improvement in estimating the DOX-DNA interaction energy is obtained in conjunction with the NAnoscale Molecular Dynamics (NAMD) code. The electronic structure of the DOX-DNA is further elucidated by resolving the total density of states (TDOS) into dierent functional groups of DOX, DNA, water, co-crystallized Spermine molecule, and Na ions. The surface partial charge distribution in the DOX-DNA is calculated and displayed graphically. We conclude that the presence of the solvent as well as the details of the interaction geometry matter greatly in the determination of the stability of the DOX complexion. Ab initio calculations on realistic models are an important step towards a more accurate description of biomolecular interaction and in the eventual understanding of long-range interactions in biomolecular systems.

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.

Concentration dependence of electrical resistivity of binary liquid alloy HgZn: Ab-initio study

NASA Astrophysics Data System (ADS)

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

2013-06-01

The electrical resistivity of HgZn liquid alloy has been made calculated using Troullier and Martins ab-initio pseudopotential as a function of concentration. Hard sphere diameters of Hg and Zn are obtained through the inter-ionic pair potential have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys.

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

NASA Astrophysics Data System (ADS)

Kibey, Sandeep A.

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

Electronic Structure and Properties of Berkelium Iodates.

PubMed

Silver, Mark A; Cary, Samantha K; Garza, Alejandro J; Baumbach, Ryan E; Arico, Alexandra A; Galmin, Gregory A; Chen, Kuan-Wen; Johnson, Jason A; Wang, Jamie C; Clark, Ronald J; Chemey, Alexander; Eaton, Teresa M; Marsh, Matthew L; Seidler, Kevin; Galley, Shane S; van de Burgt, Lambertus; Gray, Ashley L; Hobart, David E; Hanson, Kenneth; Van Cleve, Shelley M; Gendron, Frédéric; Autschbach, Jochen; Scuseria, Gustavo E; Maron, Laurent; Speldrich, Manfred; Kögerler, Paul; Celis-Barros, Cristian; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro; Ruf, Michael; Albrecht-Schmitt, Thomas E

2017-09-27

The reaction of 249 Bk(OH) 4 with iodate under hydrothermal conditions results in the formation of Bk(IO 3 ) 3 as the major product with trace amounts of Bk(IO 3 ) 4 also crystallizing from the reaction mixture. The structure of Bk(IO 3 ) 3 consists of nine-coordinate Bk III cations that are bridged by iodate anions to yield layers that are isomorphous with those found for Am III , Cf III , and with lanthanides that possess similar ionic radii. Bk(IO 3 ) 4 was expected to adopt the same structure as M(IO 3 ) 4 (M = Ce, Np, Pu), but instead parallels the structural chemistry of the smaller Zr IV cation. Bk III -O and Bk IV -O bond lengths are shorter than anticipated and provide further support for a postcurium break in the actinide series. Photoluminescence and absorption spectra collected from single crystals of Bk(IO 3 ) 4 show evidence for doping with Bk III in these crystals. In addition to luminescence from Bk III in the Bk(IO 3 ) 4 crystals, a broad-band absorption feature is initially present that is similar to features observed in systems with intervalence charge transfer. However, the high-specific activity of 249 Bk (t 1/2 = 320 d) causes oxidation of Bk III and only Bk IV is present after a few days with concomitant loss of both the Bk III luminescence and the broadband feature. The electronic structure of Bk(IO 3 ) 3 and Bk(IO 3 ) 4 were examined using a range of computational methods that include density functional theory both on clusters and on periodic structures, relativistic ab initio wave function calculations that incorporate spin-orbit coupling (CASSCF), and by a full-model Hamiltonian with spin-orbit coupling and Slater-Condon parameters (CONDON). Some of these methods provide evidence for an asymmetric ground state present in Bk IV that does not strictly adhere to Russel-Saunders coupling and Hund's Rule even though it possesses a half-filled 5f 7 shell. Multiple factors contribute to the asymmetry that include 5f electrons being present in microstates that are not solely spin up, spin-orbit coupling induced mixing of low-lying excited states with the ground state, and covalency in the Bk IV -O bonds that distributes the 5f electrons onto the ligands. These factors are absent or diminished in other f 7 ions such as Gd III or Cm III .

Calculation of x-ray scattering patterns from nanocrystals at high x-ray intensity

PubMed Central

Abdullah, Malik Muhammad; Jurek, Zoltan; Son, Sang-Kil; Santra, Robin

2016-01-01

We present a generalized method to describe the x-ray scattering intensity of the Bragg spots in a diffraction pattern from nanocrystals exposed to intense x-ray pulses. Our method involves the subdivision of a crystal into smaller units. In order to calculate the dynamics within every unit, we employ a Monte-Carlo-molecular dynamics-ab-initio hybrid framework using real space periodic boundary conditions. By combining all the units, we simulate the diffraction pattern of a crystal larger than the transverse x-ray beam profile, a situation commonly encountered in femtosecond nanocrystallography experiments with focused x-ray free-electron laser radiation. Radiation damage is not spatially uniform and depends on the fluence associated with each specific region inside the crystal. To investigate the effects of uniform and non-uniform fluence distribution, we have used two different spatial beam profiles, Gaussian and flattop. PMID:27478859

Thermal expansion in dispersion-bound molecular crystals

DOE PAGES

Ko, Hsin -Yu; DiStasio, Robert A.; Santra, Biswajit; ...

2018-05-18

In this paper, we explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within 2% of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I (≈ 40% more than classical thermalmore » expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. Finally, when predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.« less

Thermal expansion in dispersion-bound molecular crystals

NASA Astrophysics Data System (ADS)

Ko, Hsin-Yu; DiStasio, Robert A.; Santra, Biswajit; Car, Roberto

2018-05-01

We explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within 2 % of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I (≈40 % more than classical thermal expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. When predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.

Phase retrieval for crystalline specimens

NASA Astrophysics Data System (ADS)

Arnal, Romain A.; Millane, Rick P.

2017-09-01

The recent availability of ultra-bright and ultra-short X-rays pulses from new sources called x-ray free-electron lasers (XFELs) has introduced a new paradigm in X-ray crystallography. Called "diffraction-before-destruction," this paradigm addresses the main problems that plague crystallography using synchrotron sources. However, the phase problem of coherent diffraction imaging remains: one has to retrieve the phase of the measured diffraction amplitude in order to reconstruct the object. Fibrous and membrane proteins that crystallize in 1D and 2D crystals can now potentially be used for data collection with free-electron lasers. The crystallographic phase problem with such crystalline specimens is eased as the Fourier amplitude can be sampled more finely than at the Bragg sampling along one or two directions. Here we characterise uniqueness of the phase problem for different types of crystalline specimen. Simulated ab initio phase retrieval using iterative projection algorithms for 2D crystals is presented.

Thermal expansion in dispersion-bound molecular crystals

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

Ko, Hsin -Yu; DiStasio, Robert A.; Santra, Biswajit

In this paper, we explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within 2% of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I (≈ 40% more than classical thermalmore » expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. Finally, when predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.« less

Magnetic properties and stability of Cu3V2O8 compound in the different phases

NASA Astrophysics Data System (ADS)

Jezierski, Andrzej

2016-11-01

The magnetic and thermodynamic properties of Cu3V2O8 compound in four structures (P-1, P21/c, P21/m and Cmca) are reported. The calculations are performed by using the Full-Potential Local Orbital Minimum Basis (FPLO) and Vienna ab initio Simulation Package (VASP) methods. We have applied the local density approximation (LDA) with the generalized gradient corrections (GGA). The effect of electron correlations was also included in GGA+U approximation. The thermodynamic properties were obtained in the quasi-harmonic Debye-Grüneisen model using the equation of states (EOS) in the form of Poirier-Tarantola. Our ab-intio results indicate that α (P-1) phase is stable below 1.87 GPa, β (P21/c) exists in the region 1.87

Triple-twin domains in Mg doped GaN wurtzite nanowires: structural and electronic properties of this zinc-blende-like stacking

NASA Astrophysics Data System (ADS)

Arbiol, Jordi; Estradé, Sònia; Prades, Joan D.; Cirera, Albert; Furtmayr, Florian; Stark, Christoph; Laufer, Andreas; Stutzmann, Martin; Eickhoff, Martin; Gass, Mhairi H.; Bleloch, Andrew L.; Peiró, Francesca; Morante, Joan R.

2009-04-01

We report on the effect of Mg doping on the properties of GaN nanowires grown by plasma assisted molecular beam epitaxy. The most significant feature is the presence of triple-twin domains, the density of which increases with increasing Mg concentration. The resulting high concentration of misplaced atoms gives rise to local changes in the crystal structure equivalent to the insertion of three non-relaxed zinc-blende (ZB) atomic cells, which result in quantum wells along the wurtzite (WZ) nanowire growth axis. High resolution electron energy loss spectra were obtained exactly on the twinned (zinc-blende) and wurtzite planes. These atomically resolved measurements, which allow us to identify modifications in the local density of states, revealed changes in the band to band electronic transition energy from 3.4 eV for wurtzite to 3.2 eV in the twinned lattice regions. These results are in good agreement with specific ab initio atomistic simulations and demonstrate that the redshift observed in previous photoluminescence analyses is directly related to the presence of these zinc-blende domains, opening up new possibilities for band-structure engineering.

Magnetic and optical properties of carbon and silicon decorated free standing buckled germanene: A DFT approach

NASA Astrophysics Data System (ADS)

Dhar, Namrata; Jana, Debnarayan

2018-04-01

Ab initio magnetic and optical properties of group IV elements (carbon (C) and silicon (Si)) decorated free standing (FS) buckled germanene systems have been employed theoretically. Our study elucidates that, decoration of these elements in proper sites with suitable concentrations form dynamically stable configurations. Band structure is modified due to decoration of these atoms in Ge-nanosheet and pristine semi-metallic germanene undergoes to semiconductors with a finite amount of bandgap. Interestingly, this bandgap value meets closely the requirement of gap for field effect transistor (FET) applications. Moreover, significant magnetic moment is induced in non-magnetic germanene for C decorated structure and ground state in anti-ferromagnetic in nature for this structure. Along with magnetic property, optical properties like dielectric functions, optical absorption, electron energy loss spectra (EELS), refractive index and reflectivity of these systems have also been investigated. Maximum number of plasma frequencies appear for Si decorated configuration considering both parallel and perpendicular polarizations. In addition, birefringence characteristics of these configurations have also been studied as it is an important parameter in various applications of optical devices, liquid crystal displays, light modulators etc.

Theoretical investigation on the molecular structure, Infrared, Raman and NMR spectra of para-halogen benzenesulfonamides, 4-X-C 6H 4SO 2NH 2 (X = Cl, Br or F)

NASA Astrophysics Data System (ADS)

Karabacak, Mehmet; Çınar, Mehmet; Çoruh, Ali; Kurt, Mustafa

2009-02-01

In the present study, the structural properties of para-halogen benzenesulfonamides, 4-XC 6H 4SO 2NH 2 (4-chlorobenzenesulfonamide (I), 4-bromobenzenesulfonamide (II) and 4-fluorobenzenesulfonamide (III)) have been studied extensively utilizing ab initio Hartree-Fock (HF) and density functional theory (DFT) employing B3LYP exchange correlation. The vibrational frequencies were calculated and scaled values were compared with experimental values. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The effects of the halogen substituent on the characteristic benzenesulfonamides bands in the spectra are discussed. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecules were calculated using the Gauge-Invariant Atomic Orbital (GIAO) method. Finally, geometric parameters, vibrational bands and chemical shifts were compared with available experimental data of the molecules. The fully optimized geometries of the molecules were found to be consistent with the X-ray crystal structures. The observed and calculated frequencies and chemical shifts were found to be in very good agreement.

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

Quashie, Edwin E.; Saha, Bidhan C.; Correa, Alfredo A.

Here, we present an ab initio study of the electronic stopping power of protons in copper over a wide range of proton velocities v = 0.02–10a.u. where we take into account nonlinear effects. Time-dependent density functional theory coupled with molecular dynamics is used to study electronic excitations produced by energetic protons. A plane-wave pseudopotential scheme is employed to solve the time-dependent Kohn-Sham equations for a moving ion in a periodic crystal. The electronic excitations and the band structure determine the stopping power of the material and alter the interatomic forces for both channeling and off-channeling trajectories. Our off-channeling results aremore » in quantitative agreement with experiments, and at low velocity they unveil a crossover region of superlinear velocity dependence (with a power of ~1.5) in the velocity range v = 0.07–0.3a.u., which we associate to the copper crystalline electronic band structure. The results are rationalized by simple band models connecting two separate regimes. We find that the limit of electronic stopping v → 0 is not as simple as phenomenological models suggest and it is plagued by band-structure effects.« less

Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.

PubMed

Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R

2015-07-08

We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching.

Synthesis, PtS-type structure, and anomalous mechanics of the Cd(CN)2 precursor Cd(NH3)2[Cd(CN)4].

PubMed

Coates, Chloe S; Makepeace, Joshua W; Seel, Andrew G; Baise, Mia; Slater, Ben; Goodwin, Andrew L

2018-05-15

We report the nonaqueous synthesis of Cd(CN)2 by oxidation of cadmium metal with Hg(CN)2 in liquid ammonia. The reaction proceeds via an intermediate of composition Cd(NH3)2[Cd(CN)4], which converts to Cd(CN)2 on prolonged heating. Powder X-ray diffraction measurements allow us to determine the crystal structure of the previously-unreported Cd(NH3)2[Cd(CN)4], which we find to adopt a twofold interpenetrating PtS topology. We discuss the effect of partial oxidation on the Cd/Hg composition of this intermediate, as well as its implications for the reconstructive nature of the deammination process. Variable-temperature X-ray diffraction measurements allow us to characterise the anisotropic negative thermal expansion (NTE) behaviour of Cd(NH3)2[Cd(CN)4] together with the effect of Cd/Hg substitution; ab initio density functional theory (DFT) calculations reveal a similarly anomalous mechanical response in the form of both negative linear compressibility (NLC) and negative Poisson's ratios.

Ionic High-Pressure Form of Elemental Boron

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

Oganov, A.; Chen, J; Gatti, C

2009-01-01

This Letter presents the results of high-pressure experiments and ab initio evolutionary crystal structure predictions, and found a new boron phase that we named gamma-B28. This phase is comprised of icosahedral B12 clusters and B2 pairs in a NaCl-type arrangement, stable between 19 and 89 GPa, and exhibits evidence for charge transfer (for which our best estimate is delta approximately 0.48) between the constituent clusters to give (B2)delta+(B12)delta-. We have recently found that the same high-pressure boron phase may have given rise to the Bragg reflections reported by Wentorf in 1965 (ref. 1), although the chemical composition was not analysedmore » and the data (subsequently deleted from the Powder Diffraction File database) seems to not have been used to propose a structure model. We also note that although we used the terms 'partially ionic' and 'ionic' to emphasize the polar nature of the high-pressure boron phase and the influence this polarity has on several physical properties of the elemental phase, the chemical bonding in gamma-B28 is predominantly covalent.« less

Fermi-Surface Topological Phase Transition and Horizontal Order-Parameter Nodes in CaFe2As2 Under Pressure

PubMed Central

Gonnelli, R. S.; Daghero, D.; Tortello, M.; Ummarino, G. A.; Bukowski, Z.; Karpinski, J.; Reuvekamp, P. G.; Kremer, R. K.; Profeta, G.; Suzuki, K.; Kuroki, K.

2016-01-01

Iron-based compounds (IBS) display a surprising variety of superconducting properties that seems to arise from the strong sensitivity of these systems to tiny details of the lattice structure. In this respect, systems that become superconducting under pressure, like CaFe2As2, are of particular interest. Here we report on the first directional point-contact Andreev-reflection spectroscopy (PCARS) measurements on CaFe2As2 crystals under quasi-hydrostatic pressure, and on the interpretation of the results using a 3D model for Andreev reflection combined with ab-initio calculations of the Fermi surface (within the density functional theory) and of the order parameter symmetry (within a random-phase-approximation approach in a ten-orbital model). The almost perfect agreement between PCARS results at different pressures and theoretical predictions highlights the intimate connection between the changes in the lattice structure, a topological transition in the holelike Fermi surface sheet, and the emergence on the same sheet of an order parameter with a horizontal node line. PMID:27216477

Ab initio studies of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine/1,3-dimethyl-2-imidazolidinone cocrystal under high pressure using dispersion corrected density functional theory

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

Gu, Bang-Ming; Lin, He; Zhu, Shun-Guan, E-mail: zhusguan@yahoo.com

A detailed study of structural, electronic, and thermodynamic properties of 1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX)/1,3-dimethyl-2-imidazolidinone (DMI) cocrystal under the hydrostatic pressure of 0–100 GPa was performed by using dispersion-corrected density functional theory (DFT-D) method. The calculated crystal structure is in reasonable agreement with the experimental data at the ambient pressure. Based on the analysis of lattice constants, bond lengths, bond angles, and dihedral angles under compression, it is found that HMX molecules in HMX/DMI cocrystal are seriously distorted. In addition, as the pressure increases, the band gap decreases gradually, which suggests that HMX/DMI cocrystal is becoming more metallic. Some important intermolecular interactions between HMXmore » and DMI are also observed in the density of states spectrum. Finally, its thermodynamic properties were characterized, and the results show that HMX/DMI cocrystal is more easily formed in the low pressure.« less

Fermi-Surface Topological Phase Transition and Horizontal Order-Parameter Nodes in CaFe2As2 Under Pressure

NASA Astrophysics Data System (ADS)

Gonnelli, R. S.; Daghero, D.; Tortello, M.; Ummarino, G. A.; Bukowski, Z.; Karpinski, J.; Reuvekamp, P. G.; Kremer, R. K.; Profeta, G.; Suzuki, K.; Kuroki, K.

2016-05-01

Iron-based compounds (IBS) display a surprising variety of superconducting properties that seems to arise from the strong sensitivity of these systems to tiny details of the lattice structure. In this respect, systems that become superconducting under pressure, like CaFe2As2, are of particular interest. Here we report on the first directional point-contact Andreev-reflection spectroscopy (PCARS) measurements on CaFe2As2 crystals under quasi-hydrostatic pressure, and on the interpretation of the results using a 3D model for Andreev reflection combined with ab-initio calculations of the Fermi surface (within the density functional theory) and of the order parameter symmetry (within a random-phase-approximation approach in a ten-orbital model). The almost perfect agreement between PCARS results at different pressures and theoretical predictions highlights the intimate connection between the changes in the lattice structure, a topological transition in the holelike Fermi surface sheet, and the emergence on the same sheet of an order parameter with a horizontal node line.

Cd{sub 0.9375}Mn{sub 0.0625}S diluted magnetic semiconductor: A DFT study

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

Rani, Anita; Kaur, Kulwinder; Kumar, Ranjan, E-mail: ranianita64@gmail.com

We studied the spin polarized electronic band structures and magnetic properties of the diluted magnetic semiconductor Cd{sub 1-x}Mn{sub x}S in Zinc Blende phase (B3) with 0.0625 Mn by using ab initio method. The calculations were performed by using Density Functional Theory as implemented in the Spanish Initiative for Electronic Simulations with Thousands of Atoms code using local density approximation (LDA). Calculated electronic band structures and magnetic properties of Cd{sub 1-x}Mn{sub x}S are discussed in terms of contribution of Mn 3d{sup 5} 4s{sup 2}, Cd 4d{sup 10} 5s{sup 2}, S 3s{sup 2} 3p{sup 4} orbitals. The total magnetic moment is foundmore » to be 5.00 µb for Cd{sub 1−x}Mn{sub x}S at x=0.0625. This value indicate that Mn atom adds no hole carrier to the perfect CdS crystal. We found that Mn doped systems are ferromagnetic. Calculated results are in good agreement with previous studies.« less

Ab-Initio Calculation of Electronic Structure of Lead Halide Perovskites with Formamidinium Cation as an Active Material for Perovskite Solar Cells

NASA Astrophysics Data System (ADS)

Indari, E. D.; Wungu, T. D. K.; Hidayat, R.

2017-07-01

Organic lead halide perovskite material based solar cells show impressive power conversion efficiencies, which can reach above 19 percent for perovskite solar cell with methyl-ammonium cations. These efficiencies are originated from efficient photoexcitation and charge carrier transport and not observed in conventional perovskite crystals. In this preliminary research work, we therefore performed Density Functional Theory (DFT) calculation of formamidinium lead iodide (FAPI), an alternative to methyl-ammonium lead iodide (MAPI), to predict their electronic structure and density of state (DOS). The calculation result at the most stable lattice parameters show a good agreement with the experiment results. The obtained band gap energy is 1.307 eV. The valence band is dominantly formed by the 5p orbitals of I- anions, while the conduction band is dominantly formed by the 6p orbitals of Pb2+ cations. The DOS of valence band of this perovskite seems smaller compared to the case of methyl-ammonium lead iodide perovskite, which then may explain the observation of smaller power conversion efficiencies in perovskite solar cells with this formamidinium cations.

The complex ion structure of warm dense carbon measured by spectrally resolved x-ray scattering

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

Kraus, D.; Barbrel, B.; Falcone, R. W.

2015-05-15

We present measurements of the complex ion structure of warm dense carbon close to the melting line at pressures around 100 GPa. High-pressure samples were created by laser-driven shock compression of graphite and probed by intense laser-generated x-ray sources with photon energies of 4.75 keV and 4.95 keV. High-efficiency crystal spectrometers allow for spectrally resolving the scattered radiation. Comparing the ratio of elastically and inelastically scattered radiation, we find evidence for a complex bonded liquid that is predicted by ab-initio quantum simulations showing the influence of chemical bonds under these conditions. Using graphite samples of different initial densities we demonstrate the capability ofmore » spectrally resolved x-ray scattering to monitor the carbon solid-liquid transition at relatively constant pressure of 150 GPa. Showing first single-pulse scattering spectra from cold graphite of unprecedented quality recorded at the Linac Coherent Light Source, we demonstrate the outstanding possibilities for future high-precision measurements at 4th Generation Light Sources.« less

Higher-dimensional Wannier functions of multiparameter Hamiltonians

NASA Astrophysics Data System (ADS)

Hanke, Jan-Philipp; Freimuth, Frank; Blügel, Stefan; Mokrousov, Yuriy

2015-05-01

When using Wannier functions to study the electronic structure of multiparameter Hamiltonians H(k ,λ ) carrying a dependence on crystal momentum k and an additional periodic parameter λ , one usually constructs several sets of Wannier functions for a set of values of λ . We present the concept of higher-dimensional Wannier functions (HDWFs), which provide a minimal and accurate description of the electronic structure of multiparameter Hamiltonians based on a single set of HDWFs. The obstacle of nonorthogonality of Bloch functions at different λ is overcome by introducing an auxiliary real space, which is reciprocal to the parameter λ . We derive a generalized interpolation scheme and emphasize the essential conceptual and computational simplifications in using the formalism, for instance, in the evaluation of linear response coefficients. We further implement the necessary machinery to construct HDWFs from ab initio within the full potential linearized augmented plane-wave method (FLAPW). We apply our implementation to accurately interpolate the Hamiltonian of a one-dimensional magnetic chain of Mn atoms in two important cases of λ : (i) the spin-spiral vector q and (ii) the direction of the ferromagnetic magnetization m ̂. Using the generalized interpolation of the energy, we extract the corresponding values of magnetocrystalline anisotropy energy, Heisenberg exchange constants, and spin stiffness, which compare very well with the values obtained from direct first principles calculations. For toy models we demonstrate that the method of HDWFs can also be used in applications such as the virtual crystal approximation, ferroelectric polarization, and spin torques.

Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins

PubMed Central

2014-01-01

Background The advent of human genome sequencing project has led to a spurt in the number of protein sequences in the databanks. Success of structure based drug discovery severely hinges on the availability of structures. Despite significant progresses in the area of experimental protein structure determination, the sequence-structure gap is continually widening. Data driven homology based computational methods have proved successful in predicting tertiary structures for sequences sharing medium to high sequence similarities. With dwindling similarities of query sequences, advanced homology/ ab initio hybrid approaches are being explored to solve structure prediction problem. Here we describe Bhageerath-H, a homology/ ab initio hybrid software/server for predicting protein tertiary structures with advancing drug design attempts as one of the goals. Results Bhageerath-H web-server was validated on 75 CASP10 targets which showed TM-scores ≥0.5 in 91% of the cases and Cα RMSDs ≤5Å from the native in 58% of the targets, which is well above the CASP10 water mark. Comparison with some leading servers demonstrated the uniqueness of the hybrid methodology in effectively sampling conformational space, scoring best decoys and refining low resolution models to high and medium resolution. Conclusion Bhageerath-H methodology is web enabled for the scientific community as a freely accessible web server. The methodology is fielded in the on-going CASP11 experiment. PMID:25521245

Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)

NASA Astrophysics Data System (ADS)

Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik

2018-04-01

The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.

EXAFS and XANES investigation of the ETS-10 microporous titanosilicate.

PubMed

Prestipino, C; Solari, P L; Lamberti, C

2005-07-14

In this work, we report state-of-the-art analysis of both Ti K-edge high-resolution XANES and EXAFS data collected on the ETS-10 molecular sieve at the GILDA BM8 beamline of the ESRF facility. The interatomic distances and the angles obtained in our EXAFS study are in fair agreement with the single-crystal XRD data of Wang and Jacobson (Chem. Commun. 1999, 973) and with the recent ab initio periodic study of Damin et al. (J. Phys. Chem. B 2004, 108, 1328) Differently from previous EXAFS work (J. Phys. Chem. 1996, 100, 449), our study supports a model of ETS-10 where the Ti atoms are bonded with two equivalent axial oxygen atoms. This model is also able to reproduce the edge and the post-edge region of the XANES spectrum. Conversely, the weak but well-defined pre-edge peak at 4971.3 eV can be explained only by assuming that a fraction of Ti atoms are in a local geometry similar to that of the pentacoordinated Ti sites in the ETS-4 structure. These Ti atoms in ETS-10 should be the terminal of the -Ti-O-Ti-O-Ti- chains, of which the actual number is strongly increased by the high crystal defectivity (Ti vacancies).

Mechanical properties of non-centrosymmetric CePt3Si and CePt3B

NASA Astrophysics Data System (ADS)

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

2017-05-01

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

Determining the structure of tetragonal Y 2WO 6 and the site occupation of Eu 3+ dopant

NASA Astrophysics Data System (ADS)

Huang, Jinping; Xu, Jun; Li, Hexing; Luo, Hongshan; Yu, Xibin; Li, Yikang

2011-04-01

The compound Y 2WO 6 is prepared by solid state reaction at 750 °C using sodium chloride as mineralizer. Its structure is solved by ab-initio methods from X-ray powder diffraction data. This low temperature phase of yttrium tungstate crystallizes in tetragonal space group P4/ nmm (No. 129), Z=2, a=5.2596(2) Å, c=8.4158(4) Å. The tungsten atoms in the structure adopt an unusual [WO 6] distorted cubes coordination, connecting [YO 6] distorted cubes with oxygen vacancies at the O 2 layers while other yttrium ions Y 2 form [YO 8] cube coordination. Y 3+ ions occupy two crystallographic sites of 2 c ( C4v symmetry) and 2 a ( D2d symmetry) in the Y 2WO 6 host lattice. With Eu 3+ ions doped, the high resolution emission spectrum of Y 2WO 6:Eu 3+ suggests that Eu 3+ partly substituted for Y 3+ in these two sites. The result of the Rietveld structure refinement shows that the Eu 3+ dopants preferentially enter the 2 a site. The uniform cube coordination environment of Eu 3+ ions with the identical eight Eu-O bond lengths is proposed to be responsible for the intense excitation of long wavelength ultraviolet at 466-535 nm.

Excitonic states and defect physics of two-dimensional group-IV monochalcogenides.

NASA Astrophysics Data System (ADS)

Gomes, Lidia; Carvalho, Alexandra; Trevisanutto, Paolo; Rodin, Aleksandr; Neto, Antonio

Layered group-IV monochalcogenides have become an important group of materials within the ever-growing family of two-dimensional crystals. Among the binary IV-VI compounds, SnS, SnSe, GeS, and GeSe form a subgroup with orthorhombic structure which has shown exciting particularities and has been considered of high potential for numerous application. We give a brief overview of some important properties of the 2D form of this group and focus on recent results addressing the excitonic properties and the impact of the introduction of point defects on their structures. Vacancies and oxygen defects are modeled using first principles calculations. Energetic and structural analysis of five different models for chemisorbed oxygen atoms, reveals a better resistance of these materials to oxidation if compared to their isostructural partner, phosphorene. We also discuss a parallel work where quasi-particle band structure and excitonic properties of GeS and GeSe monolayers are investigated through ab initio GW and Bethe-Salpeter equation calculations. Within the main results, we show that the optical spectra of both materials are dominated by excitonic effects, however, GeS presents a remarkably larger binding energy of 1 eV. NRF-CRP award Novel 2D materials with tailored properties: beyond graphene (R-144-000-295-281) 1.

Simulation of Phonon Spectra in Three-Component Two-Dimensional Crystals of Refractory-Metal Dichalcogenides

NASA Astrophysics Data System (ADS)

Alexeev, A. Yu.; Krivosheeva, A. V.; Shaposhnikov, V. L.; Borisenko, V. E.

2017-09-01

A model for ab initio calculation of the phonon properties of three-component solid solutions of refractory-metal dichalcogenides was developed based on the assumption that displacements of the same type of chalcogen atoms and decoupled displacements of the metal atoms were identical. The calculated phonon frequencies at the Γ-point for monomolecular layers of MoS2-xSex and MoS2-xTex agreed with existing experimental Raman spectra.

Ab initio calculation of electron–phonon coupling in monoclinic β-Ga{sub 2}O{sub 3} crystal

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

Ghosh, Krishnendu, E-mail: kghosh3@buffalo.edu; Singisetti, Uttam, E-mail: uttamsin@buffalo.edu

2016-08-15

The interaction between electrons and vibrational modes in monoclinic β-Ga{sub 2}O{sub 3} is theoretically investigated using ab-initio calculations. The large primitive cell of β-Ga{sub 2}O{sub 3} gives rise to 30 phonon modes all of which are taken into account in transport calculation. The electron-phonon interaction is calculated under density functional perturbation theory and then interpolated using Wannier–Fourier interpolation. The long-range interaction elements between electrons and polar optical phonon (POP) modes are calculated separately using the Born effective charge tensor. The direction dependence of the long-range POP coupling in a monoclinic crystal is explored and is included in the transport calculations.more » Scattering rate calculations are done using the Fermi golden rule followed by solving the Boltzmann transport equation using the Rode's method to estimate low field mobility. A room temperature mobility of 115 cm{sup 2}/V s is observed. Comparison with recent experimentally reported mobility is done for a wide range of temperatures (30 K–650 K). It is also found that the POP interaction dominates the electron mobility under low electric field conditions. The relative contribution of the different POP modes is analyzed and the mode 21 meV POP is found to have the highest impact on low field electron mobility at room temperature.« less

Ab initio vel ex eventu

NASA Astrophysics Data System (ADS)

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

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

Macromolecular ab initio phasing enforcing secondary and tertiary structure.

PubMed

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.

Structural, electronic, magnetic, and transport properties of the equiatomic quaternary Heusler alloy CoRhMnGe: Theory and experiment

NASA Astrophysics Data System (ADS)

Rani, Deepika; Enamullah, Suresh, K. G.; Yadav, A. K.; Jha, S. N.; Bhattacharyya, D.; Varma, Manoj Raama; Alam, Aftab

2017-11-01

In this work, we present structural, electronic, magnetic, mechanical, and transport properties of equiatomic quaternary Heusler alloy, CoRhMnGe, using theoretical and experimental techniques. A detailed structural analysis is performed using x-ray diffraction and extended x-ray absorption fine structure spectroscopy. The alloy is found to crystallize in Y -type structure having space group F 4 ¯3 m (no. 216). The ab initio simulation predicts half-metallic ferromagnetic characteristics leading to large spin polarization. The calculated magnetization is found to be in fair agreement with experiment as well as those predicted by the Slater-Pauling rule, which is a prerequisite for half-metallicity. The magnetic transition temperature (TC) is found to be ˜760 K. Measured electrical resistivity in the temperature range 2-400 K also gives an indication of half-metallic behavior. Effect of hydrostatic pressure on electronic structure, magnetic, and mechanical properties are investigated in detail. The alloy is found to preserve half-metallic characteristics up to 30.27 GPa, beyond which it transits to metallic phase. No magnetic phase transition is found to occur in the whole range of pressure. The system also satisfies the Born-Huang criteria for mechanical stability up to a limited range of pressure. All these properties make the CoRhMnGe alloy promising for spintronics devices.

A fragmentation and reassembly method for ab initio phasing.

PubMed

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.

An ab initio study of the structure and dynamics of bulk liquid Ag and its liquid-vapor interface

NASA Astrophysics Data System (ADS)

Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique; Gonzalez Fernandez, David Jose

Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals collective density excitations with an associated dispersion relation which points to a small positive dispersion. Results are also reported at a slightly higher temperature in order to study the structure of the free liquid surface. The ionic density profile shows an oscillatory behaviour with two different wavelenghts, as the spacing between the outer and first inner layer is different from that between the other inner layers.

Experimental and ab initio molecular dynamics simulation studies of liquid Al60Cu40 alloy

NASA Astrophysics Data System (ADS)

Wang, S. Y.; Kramer, M. J.; Xu, M.; Wu, S.; Hao, S. G.; Sordelet, D. J.; Ho, K. M.; Wang, C. Z.

2009-04-01

X-ray diffraction and ab initio molecular dynamics simulation studies of molten Al60Cu40 have been carried out between 973 and 1323 K. The structures obtained from our simulated atomic models are fully consistent with the experimental results. The local structures of the models analyzed using Honeycutt-Andersen and Voronoi tessellation methods clearly demonstrate that as the temperatures of the liquid is lowered it becomes more ordered. While no one cluster-type dominates the local structure of this liquid, the most prevalent polyhedra in the liquid structure can be described as distorted icosahedra. No obvious correlations between the clusters observed in the liquid and known stable crystalline phases in this system were observed.

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

Li, H.K.; Science Center for Phase Diagram and Materials Design and Manufacture, Central South University, Changsha, Hunan 410083; Cai, G.M., E-mail: caigemei@csu.edu.cn

Two novel borate compounds MgInBO{sub 4} and MgIn{sub 7/8}B{sub 7/8}O{sub 29/8}, have been synthesized via solid-state reactions, and their crystal structures have been solved and refined from powder X-ray diffraction data. The compound MgInBO{sub 4}, which was obtained at 1190 °C, belongs to the warwickite family. It crystallizes in the Pnma space group (no. 62) with a=9.5443(1) Å, b=3.2771(1) Å, c=9.5228(1) Å, and Z=4. The fundamental building units are liner –Mg(In)O{sub 6}–[In(Mg)]{sub 2}O{sub 10}–Mg(In)O{sub 6}– chains and isolated BO{sub 3} triangles. The low-temperature phase, MgIn{sub 7/8}B{sub 7/8}O{sub 29/8}, whose crystal structure is solved ab initio by the charge-flipping method withmore » standard chemical formula MgInBO{sub 4}, was prepared at 1080 °C. It crystallizes in the P12{sub 1}/n1 space group (no. 14) with a=17.0976(1) Å, b=3.2504(1) Å, c=5.3387(1) Å, β=96.0829(3)°, and Z=4. The structure of MgIn{sub 7/8}B{sub 7/8}O{sub 29/8} contains [In(2)/Mg(2)]{sub 2}O{sub 10} groups, –MgO{sub 6}–InO{sub 6}– infinite ribbons and isolated BO{sub 3} triangles. The experiments and the differential thermal analysis (DTA) show the decompositions of MgInBO{sub 4} and MgIn{sub 7/8}B{sub 7/8}O{sub 29/8} happen at about 1220 °C and 1180 °C, respectively. The comparative crystal chemistry from MgIn{sub 7/8}B{sub 7/8}O{sub 29/8} to MgInBO{sub 4} has been discussed. Infrared spectra and UV–vis diffuse reflectance spectra of MgInBO{sub 4} and MgIn{sub 7/8}B{sub 7/8}O{sub 29/8} were measured. - Graphical abstract: The structural transformation from the monoclinic MgIn{sub 7/8}B{sub 7/8}O{sub 29/8} (P12{sub 1}/n1) to the orthorhombic MgInBO{sub 4} (Pnma). - Highlights: • Two novel borate compounds MgInBO{sub 4} and MgIn{sub 7/8}B{sub 7/8}O{sub 29/8} have been synthesized via solid-state reactions for the first time. • The crystal structures of MgInBO{sub 4} and MgIn{sub 7/8}B{sub 7/8}O{sub 29/8} have been solved and refined from powder X-ray diffraction data. • The possible crystal chemical analysis from MgIn{sub 7/8}B{sub 7/8}O{sub 29/8} to MgInBO{sub 4} is discussed. • Infrared spectra and UV–vis diffuse reflectance spectra of MgInBO{sub 4} and MgIn{sub 7/8}B{sub 7/8}O{sub 29/8} have been measured.« less