Lithium doping and vacancy effects on the structural, electronic and magnetic properties of hexagonal boron nitride sheet: A first-principles calculation

NASA Astrophysics Data System (ADS)

Fartab, Dorsa S.; Kordbacheh, Amirhossein Ahmadkhan

2018-06-01

The first-principles calculations based on spin-polarized density functional theory is carried out to investigate the structural, electronic and magnetic properties of a hexagonal boron nitride sheet (h-BNS) doped by one or two lithium atom(s). Moreover, a vacancy in the neighborhood of one Li-substituted atom is introduced into the system. All optimized structures indicate significant local deformations with Li atom(s) protruded to the exterior of the sheet. The defects considered at N site are energetically more favorable than their counterpart structures at B site. The spin-polarized impurity states appear within the bandgap region of the pristine h-BNS, which lead to a spontaneous magnetization with the largest magnetic moments of about 2 μB in where a single or two B atom(s) are replaced by Li atom(s). Furthermore, the Li substitution for a single B atom increases the density of holes compared to that of electrons forming a p-type semiconductor. More interestingly, the structure in which two Li are substituted two neighboring B atoms appears to show desired half-metallic behavior that may be applicable in spintronic. The results provide a way to enhance the conductivity and magnetism of the pristine h-BNS for potential applications in BN-based nanoscale devices.

A microscopic study investigating the structure of SnSe surfaces

NASA Astrophysics Data System (ADS)

Kim, Sang-ui; Duong, Anh-Tuan; Cho, Sunglae; Rhim, S. H.; Kim, Jungdae

2016-09-01

SnSe has been widely studied due to its many potential applications that take advantage of its excellent thermoelectric, photovoltaic, and optoelectronic properties. However, experimental investigations into the microscopic structure of SnSe remain largely unexplored. Herein, for the first time, the atomic and electronic structures of SnSe surfaces are studied by a home-built low temperature scanning tunneling microscope (STM) and density functional theory (DFT) calculations. The cleaved surface of SnSe is comprised of covalently bonded Se and Sn atoms in zigzag patterns. However, rectangular periodicity was observed in the atomic images of SnSe surfaces for filled and empty state probing. Detailed atomic structures are analyzed by DFT calculations, indicating that the bright extrusions of both filled and empty state images are mostly located at the positions of Sn atoms.

The effect of boron concentration on the structure and elastic properties of Ru-Ir alloys: first-principles calculations

NASA Astrophysics Data System (ADS)

Li, Xiaolong; Zhou, Zhaobo; Hu, Riming; Zhou, Xiaolong; Yu, Jie; Liu, Manmen

2018-04-01

The Phase stability, electronic structure, elastic properties and hardness of Ru-Ir alloys with different B concentration were investigated by first principles calculations. The calculated formation enthaplies and cohesive energies show that these compounds are all thermodynamically stable. Information on electronic structure indicates that they possess metallic characteristic and Ru-Ir-B alloys were composed of the Ru-B and Ir-B covalent bond. The elastic properties were calculated, which included bulk modulus, shear modulus, Young’s modulus, Poisson’s ratio and hardness. The calculated results reveal that the plastic of Ru-Ir-B alloys increase with the increase of the content of B atoms, but the hardness of Ru-Ir-B alloys have no substantial progress with the increase of the content of B atoms. However, it is interesting that the hardness of the Ru-Ir-B compound was improved obviously as the B content was higher than 18 atoms because of a phase structure transition.

First-principles study of structure, electronic properties and stability of tungsten adsorption on TiC(111) surface with disordered vacancies

NASA Astrophysics Data System (ADS)

Ilyasov, Victor V.; Pham, Khang D.; Zhdanova, Tatiana P.; Phuc, Huynh V.; Hieu, Nguyen N.; Nguyen, Chuong V.

2017-12-01

In this paper, we systematically investigate the atomic structure, electronic and thermodynamic properties of adsorbed W atoms on the polar Ti-terminated TixCy (111) surface with different configurations of adsorptions using first principle calculations. The bond length, adsorption energy, and formation energy for different reconstructions of the atomic structure of the W/TixCy (111) systems were established. The effect of the tungsten coverage on the electronic structure and the adsorption mechanism of tungsten atom on the TixCy (111) are also investigated. We also suggest the possible mechanisms of W nucleation on the TixCy (111) surface. The effective charges on W atoms and nearest-neighbor atoms in the examined reconstructions were identified. Additionally, we have established the charge transfer from titanium atom to tungsten and carbon atoms which determine by the reconstruction of the local atomic and electronic structures. Our calculations showed that the charge transfer correlates with the electronegativity of tungsten and nearest-neighbor atoms. We also determined the effective charge per atom of titanium, carbon atoms, and neighboring adsorbed tungsten atom in different binding configurations. We found that, with reduction of the lattice symmetry associated with titanium and carbon vacancies, the adsorption energy increases by 1.2 times in the binding site A of W/TixCy systems.

Modification of band gaps and optoelectronic properties of binary calcium chalcogenides by means of doping of magnesium atom(s) in rock-salt phase- a first principle based theoretical initiative

NASA Astrophysics Data System (ADS)

Debnath, Bimal; Sarkar, Utpal; Debbarma, Manish; Bhattacharjee, Rahul; Chattopadhyaya, Surya

2018-02-01

The band gaps and optoelectronic properties of binary calcium chalcogenide semiconductors have been modified theoretically by doping magnesium atom(s) into their respective rock-salt unit cells at some specific concentrations x = 0.0, 0.25, 0.50, 0.75 and 1.0 and confirmed such modifications by studying their structural, electronic and optical properties using DFT based FP-LAPW approach. The WC-GGA functional is used to calculate structural properties, while mBJ, B3LYP and WC-GGA are used for calculating electronic and optical properties. The concentration dependences of lattice parameter, bulk modulus and fundamental band gap for each alloy system exhibit nonlinearity. The atomic and orbital origin of different electronic states in the band structure of each compound are explored from its density of states (DOS). The microscopic origin of band gap bowing for each of the alloy systems is explored in terms of volume deformation, charge exchange and structural relaxation. The chemical bonds between the constituent atoms in each compound are found as ionic in nature. Optical properties of each specimen are calculated from its computed spectra of dielectric function, refractive index, extinction coefficient, normal incidence reflectivity, optical conductivity, optical absorption and energy loss function. Several calculated results have been compared with available experimental and other theoretical data.

Electronic structure and magnetic properties of Pr-Co intermetallics: ab initio FP-LAPW calculations and correlation with experiments

NASA Astrophysics Data System (ADS)

Bakkari, Karim; Fersi, Riadh; Kebir Hlil, El; Bessais, Lotfi; Thabet Mliki, Najeh

2018-03-01

First-principle calculations combining density functional theory and the full-potential linearized augmented plane wave (FP-LAPW) method are performed to investigate the electronic and magnetic structure of Pr2Co7 in its two polymorphic forms, (2:7 H) and (2:7 R), for the first time. This type of calculation was also performed for PrCo5 and PrCo2 intermetallics. We have computed the valence density of states separately for spin-up and spin-down states in order to investigate the electronic band structure. This is governed by the strong contribution of the partial DOS of 3d-Co bands compared to the partial DOS of the 4f-Pr bands. Such a high ferromagnetic state is discussed in terms of the strong spin polarization observed in the total DOS. The magnetic moments carried by the Co and Pr atoms located in several sites for all compounds are computed. These results mainly indicate that cobalt atoms make a dominant contribution to the magnetic moments. The notable difference in the atomic moments of Pr and Co atoms between different structural slabs is explained in terms of the magnetic characteristics of the PrCo2 and PrCo5 compounds and the local chemical environments of the Pr and Co atoms in different structural slabs of Pr2Co7. From spin-polarized calculations we have simulated the 3d and 4f band population to estimate the local magnetic moments. These results are in accordance with the magnetic moments calculated using the FP-LAPW method. In addition, the exchange interactions J ij are calculated and used as input for M(T) simulations. Involving the data obtained from the electronic structure calculations, the appropriate Padé Table is applied to simulate the magnetization M(T) and to estimate the mean-field Curie temperature. We report a fairly good agreement between the ab initio calculation of magnetization and Curie temperature with the experimental data.

Investigation on the neutral and anionic BxAlyH2 (x + y = 7, 8, 9) clusters using density functional theory combined with photoelectron spectroscopy.

PubMed

Ding, Li-Ping; Shao, Peng; Lu, Cheng; Zhang, Fang-Hui; Ding, Lei; Yuan, Tao Li

2016-08-17

The structure and bonding nature of neutral and negatively charged BxAlyH2 (x + y = 7, 8, 9) clusters are investigated with the aid of previously published experimental photoelectron spectra combined with the present density functional theory calculations. The comparison between the experimental photoelectron spectra and theoretical simulated spectra helps to identify the ground state structures. The accuracy of the obtained ground state structures is further verified by calculating their adiabatic electron affinities and vertical detachment energies and comparing them against available experimental data. The results show that the structures of BxAlyH2 transform from three-dimensional to planar structures as the number of boron atoms increases. Moreover, boron atoms tend to bind together forming Bn units. The hydrogen atoms prefer to bind with boron atoms rather than aluminum atoms. The analyses of the molecular orbital on the ground state structures further support the abovementioned results.

Characterization of local atomic structure in Co/Zn based ZIFs by XAFS

NASA Astrophysics Data System (ADS)

Podkovyrina, Yulia; Butova, Vera; Bulanova, Elena; Budnyk, Andriy; Kremennaya, Maria; Soldatov, Alexander; Lamberti, Carlo

2018-03-01

The local atomic structure in bimetallic Co/Zn zeolitic imidazolate frameworks (ZIFs) was studied using X-ray Absorption Fine Structure (XAFS) spectroscopy and theoretical calculations. The experimental Co K-edge and Zn K-edge XANES (X-ray Absorption Near Edge Structure) spectra of Zn1-xCoxC8H10N4 samples (x = 0.05, 0.25, 0.75) synthesized by microwave synthesis were compared with the data for the ZIF-67 (x=1) and ZIF-8 (x=0). Theoretical XANES spectra for the bimetallic ZIFs were calculated. It was shown that in bimetallic ZIFs the Co and Zn atoms have the similar local environment.

Structure and properties of microporous titanosilicate determined by first-principles calculations

NASA Astrophysics Data System (ADS)

Ching, W. Y.; Xu, Yong-Nian; Gu, Zong-Quan

1996-12-01

The structure of EST-10, a member of synthetic microporous titanosilicates, was recently determined by an ingenious combination of experimental and simulational techniques. However, the locations of the alkali atoms in the framework remain elusive and its electronic structure is totally unknown. Based on first-principles local density calculations, the possible locations of the alkali atoms are identified and its electronic structure and bonding fully elucidated. ETS-10 is a semiconductor with a direct band gap of 2.33 eV. The Na atoms are likely to locate inside the seven-member ring pore adjacent to the one-dimensional Ti-O-Ti-O- chain.

Effects of the c-Si/a-SiO2 interfacial atomic structure on its band alignment: an ab initio study.

PubMed

Zheng, Fan; Pham, Hieu H; Wang, Lin-Wang

2017-12-13

The crystalline-Si/amorphous-SiO 2 (c-Si/a-SiO 2 ) interface is an important system used in many applications, ranging from transistors to solar cells. The transition region of the c-Si/a-SiO 2 interface plays a critical role in determining the band alignment between the two regions. However, the question of how this interface band offset is affected by the transition region thickness and its local atomic arrangement is yet to be fully investigated. Here, by controlling the parameters of the classical Monte Carlo bond switching algorithm, we have generated the atomic structures of the interfaces with various thicknesses, as well as containing Si at different oxidation states. A hybrid functional method, as shown by our calculations to reproduce the GW and experimental results for bulk Si and SiO 2 , was used to calculate the electronic structure of the heterojunction. This allowed us to study the correlation between the interface band characterization and its atomic structures. We found that although the systems with different thicknesses showed quite different atomic structures near the transition region, the calculated band offset tended to be the same, unaffected by the details of the interfacial structure. Our band offset calculation agrees well with the experimental measurements. This robustness of the interfacial electronic structure to its interfacial atomic details could be another reason for the success of the c-Si/a-SiO 2 interface in Si-based electronic applications. Nevertheless, when a reactive force field is used to generate the a-SiO 2 and c-Si/a-SiO 2 interfaces, the band offset significantly deviates from the experimental values by about 1 eV.

Effects of the c-Si/a-SiO 2 interfacial atomic structure on its band alignment: an ab initio study

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

Zheng, Fan; Pham, Hieu H.; Wang, Lin-Wang

The crystalline-Si/amorphous-SiO 2 (c-Si/a-SiO 2) interface is an important system used in many applications, ranging from transistors to solar cells. The transition region of the c-Si/a-SiO 2 interface plays a critical role in determining the band alignment between the two regions. However, the question of how this interface band offset is affected by the transition region thickness and its local atomic arrangement is yet to be fully investigated. Here in this study, by controlling the parameters of the classical Monte Carlo bond switching algorithm, we have generated the atomic structures of the interfaces with various thicknesses, as well as containingmore » Si at different oxidation states. A hybrid functional method, as shown by our calculations to reproduce the GW and experimental results for bulk Si and SiO 2, was used to calculate the electronic structure of the heterojunction. This allowed us to study the correlation between the interface band characterization and its atomic structures. We found that although the systems with different thicknesses showed quite different atomic structures near the transition region, the calculated band offset tended to be the same, unaffected by the details of the interfacial structure. Our band offset calculation agrees well with the experimental measurements. This robustness of the interfacial electronic structure to its interfacial atomic details could be another reason for the success of the c-Si/a-SiO 2 interface in Si-based electronic applications. Nevertheless, when a reactive force field is used to generate the a-SiO 2 and c-Si/a-SiO 2 interfaces, the band offset significantly deviates from the experimental values by about 1 eV« less

Effects of the c-Si/a-SiO 2 interfacial atomic structure on its band alignment: an ab initio study

DOE PAGES

Zheng, Fan; Pham, Hieu H.; Wang, Lin-Wang

2017-11-13

The crystalline-Si/amorphous-SiO 2 (c-Si/a-SiO 2) interface is an important system used in many applications, ranging from transistors to solar cells. The transition region of the c-Si/a-SiO 2 interface plays a critical role in determining the band alignment between the two regions. However, the question of how this interface band offset is affected by the transition region thickness and its local atomic arrangement is yet to be fully investigated. Here in this study, by controlling the parameters of the classical Monte Carlo bond switching algorithm, we have generated the atomic structures of the interfaces with various thicknesses, as well as containingmore » Si at different oxidation states. A hybrid functional method, as shown by our calculations to reproduce the GW and experimental results for bulk Si and SiO 2, was used to calculate the electronic structure of the heterojunction. This allowed us to study the correlation between the interface band characterization and its atomic structures. We found that although the systems with different thicknesses showed quite different atomic structures near the transition region, the calculated band offset tended to be the same, unaffected by the details of the interfacial structure. Our band offset calculation agrees well with the experimental measurements. This robustness of the interfacial electronic structure to its interfacial atomic details could be another reason for the success of the c-Si/a-SiO 2 interface in Si-based electronic applications. Nevertheless, when a reactive force field is used to generate the a-SiO 2 and c-Si/a-SiO 2 interfaces, the band offset significantly deviates from the experimental values by about 1 eV« less

Atomic and electronic structure of the CdTe(111)B–(2√3 × 4) orthogonal surface

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

Bekenev, V. L., E-mail: bekenev@ipms.kiev.ua; Zubkova, S. M.

2017-01-15

The atomic and electronic structure of four variants of Te-terminated CdTe(111)B–(2√3 × 4) orthogonal polar surface (ideal, relaxed, reconstructed, and reconstructed with subsequent relaxation) are calculated ab initio for the first time. The surface is modeled by a film composed of 12 atomic layers with a vacuum gap of ~16 Å in the layered superlattice approximation. To close Cd dangling bonds on the opposite side of the film, 24 fictitious hydrogen atoms with a charge of 1.5 electrons each are added. Ab initio calculations are performed using the Quantum Espresso program based on density functional theory. It is demonstrated thatmore » relaxation leads to splitting of the four upper layers. The band energy structures and total and layer-by-layer densities of electronic states for the four surface variants are calculated and analyzed.« less

Atomic and electronic structures of Si(1 1 1)-(√3 x √3)R30°-Au and (6 × 6)-Au surfaces.

PubMed

Patterson, C H

2015-12-02

Si(1 1 1)-Au surfaces with around one monolayer of Au exhibit many ordered structures and structures containing disordered domain walls. Hybrid density functional theory (DFT) calculations presented here reveal the origin of these complex structures and tendency to form domain walls. The conjugate honeycomb chain trimer (CHCT) structure of the [Formula: see text]-Au phase contains Si atoms with non-bonding surface states which can bind Au atoms in pairs in interstices of the CHCT structure and make this surface metallic. Si adatoms adsorbed on the [Formula: see text]-Au surface induce a gapped surface through interaction with the non-bonding states. Adsorption of extra Au atoms in interstitial sites of the [Formula: see text]-Au surface is stabilized by interaction with the non-bonding orbitals and leads to higher coverage ordered structures including the [Formula: see text]-Au phase. Extra Au atoms bound in interstitial sites of the [Formula: see text]-Au surface result in top layer Si atoms with an SiAu4 butterfly wing configuration. The structure of a [Formula: see text]-Au phase, whose in-plane top atomic layer positions were previously determined by an electron holography technique (Grozea et al 1998 Surf. Sci. 418 32), is calculated using total energy minimization. The Patterson function for this structure is calculated and is in good agreement with data from an in-plane x-ray diffraction study (Dornisch et al 1991 Phys. Rev. B 44 11221). Filled and empty state scanning tunneling microscopy (STM) images are calculated for domain walls and the [Formula: see text]-Au structure. The [Formula: see text]-Au phase is 2D chiral and this is evident in computed and actual STM images. [Formula: see text]-Au and domain wall structures contain the SiAu4 motif with a butterfly wing shape. Chemical bonding within the Si-Au top layers of the [Formula: see text]-Au and [Formula: see text]-Au surfaces is analyzed and an explanation for the SiAu4 motif structure is given.

Chemical shielding properties for BN, BP, AlN, and AlP nanocones: DFT studies

NASA Astrophysics Data System (ADS)

Mirzaei, Mahmoud; Yousefi, Mohammad; Meskinfam, Masoumeh

2012-06-01

The properties of boron nitride (BN), boron phosphide (BP), aluminum nitride (AlN), and aluminum phosphide (AlP) nanocones were investigated by density functional theory (DFT) calculations. The investigated structures were optimized and chemical shielding (CS) properties including isotropic and anisotropic CS parameters were calculated for the atoms of the optimized structures. The magnitudes of CS parameters were observed to be mainly dependent on the bond lengths of considered atoms. The results indicated that the atoms could be divided into atomic layers due to the similarities of their CS properties for the atoms of each layer. The trend means that the atoms of each layer detect almost similar electronic environments. Moreover, the atoms at the apex and mouth of nanocones exhibit different properties with respect to the other atomic layers.

First-principles analysis of structural and opto-electronic properties of indium tin oxide

NASA Astrophysics Data System (ADS)

Tripathi, Madhvendra Nath; Shida, Kazuhito; Sahara, Ryoji; Mizuseki, Hiroshi; Kawazoe, Yoshiyuki

2012-05-01

Density functional theory (DFT) and DFT + U (DFT with on-site Coulomb repulsion corrections) calculations have been carried out to study the structural and opto-electronic properties of indium tin oxide (ITO) for both the oxidized and reduced environment conditions. Some of the results obtained by DFT calculations differ from the experimental observations, such as uncertain indication for the site preference of tin atom to replace indium atom at b-site or d-site, underestimation of local inward relaxation in the first oxygen polyhedra around tin atom, and also the improper estimation of electronic density of states and hence resulting in an inappropriate optical spectra of ITO. These discrepancies of theoretical outcomes with experimental observations in ITO arise mainly due to the underestimation of the cationic 4d levels within standard DFT calculations. Henceforth, the inclusion of on-site corrections within DFT + U framework significantly modifies the theoretical results in better agreement to the experimental observations. Within this framework, our calculations show that the indium b-site is preferential site over d-site for tin atom substitution in indium oxide under both the oxidized and reduced conditions. Moreover, the calculated average inward relaxation value of 0.16 Å around tin atom is in good agreement with the experimental value of 0.18 Å. Furthermore, DFT + U significantly modify the electronic structure and consequently induce modifications in the calculated optical spectra of ITO.

Reaction mechanism and kinetics of the degradation of terbacil initiated by OH radical - A theoretical study

NASA Astrophysics Data System (ADS)

Ponnusamy, S.; Sandhiya, L.; Senthilkumar, K.

2018-02-01

The reaction of terbacil with OH radical is studied by using electronic structure calculations. The reaction of terbacil with OH radical is found to proceed by H-atom abstraction, Cl-atom abstraction and OH addition reactions. The initially formed alkyl radical will undergo atmospheric transformation in the presence of molecular oxygen leading to the formation of peroxy radical. The reaction of peroxy radical with other atmospheric oxidants, such as HO2 and NO radicals is studied. The rate constant is calculated for the H-atom abstraction reactions over the temperature range of 200-1000 K. The results obtained from electronic structure calculations and kinetic study show that the H-atom abstraction reaction is more favorable. The calculated lifetime of terbacil is 24 h in normal atmospheric OH concentration. The rate constant calculated for H-atom abstraction reactions is 6 × 10-12, 4.4 × 10-12 and 3.2 × 10-12 cm3molecule-1s-1, respectively which is in agreement with the previous literature value of 1.9 × 10-12 cm3molecule-1s-1.

Efficient evaluation of atom tunneling combined with electronic structure calculations.

PubMed

Ásgeirsson, Vilhjálmur; Arnaldsson, Andri; Jónsson, Hannes

2018-03-14

Methodology for finding optimal tunneling paths and evaluating tunneling rates for atomic rearrangements is described. First, an optimal JWKB tunneling path for a system with fixed energy is obtained using a line integral extension of the nudged elastic band method. Then, a calculation of the dynamics along the path is used to determine the temperature at which it corresponds to an optimal Feynman path for thermally activated tunneling (instanton) and a harmonic approximation is used to estimate the transition rate. The method is illustrated with calculations for a modified two-dimensional Müller-Brown surface but is efficient enough to be used in combination with electronic structure calculations of the energy and atomic forces in systems containing many atoms. An example is presented where tunneling is the dominant mechanism well above room temperature as an H 3 BNH 3 molecule dissociates to form H 2 . Also, a solid-state example is presented where density functional theory calculations of H atom tunneling in a Ta crystal give close agreement with experimental measurements on hydrogen diffusion over a wide range in temperature.

DFT+U Study of Chemical Impurities in PuO 2

DOE PAGES

Hernandez, Sarah C.; Holby, Edward F.

2016-05-24

In this paper, we employ density functional theory to explore the effects of impurities in the fluorite crystal structure of PuO 2. The impurities that were considered are known impurities that exist in metallic δ-phase Pu, including H, C, Fe, and Ga. These impurities were placed at various high-symmetry sites within the PuO 2 structure including an octahedral interstitial site, an interstitial site with coordination to two neighboring O atoms, an O substitutional site, and a Pu substitutional site. Incorporation energies were calculated to be energetically unfavorable for all sites except the Pu substitutional site. When impurities were placed inmore » a Pu substitutional site, complexes incorporating the impurities and O formed within the PuO 2 structure. The observed defect-oxygen structures were OH, CO 3, FeO 5, and GaO 3. The presence of these defects led to distortion of the surrounding O atoms within the structure, producing long-range disorder of O atoms. In contrast, perturbations of Pu atoms had a relatively short-range effect on the relaxed structures. These effects are demonstrated via radial distribution functions for O and Pu vacancies. Calculated electronic structure revealed hybridization of the impurity atom with the O valence states and a relative decrease in the Pu 5f states. Minor differences in band gaps were observed for the defected PuO 2 structures containing H, C, and Ga. Finally, Fe-containing structures, however, were calculated to have a significantly decreased band gap, where the implementation of a Hubbard U parameter on the Fe 3d orbitals will maintain the calculated PuO 2 band gap.« less

Fine structure of heliumlike ions and determination of the fine structure constant.

PubMed

Pachucki, Krzysztof; Yerokhin, Vladimir A

2010-02-19

We report a calculation of the fine-structure splitting in light heliumlike atoms, which accounts for all quantum electrodynamical effects up to order alpha{5} Ry. For the helium atom, we resolve the previously reported disagreement between theory and experiment and determine the fine-structure constant with an accuracy of 31 ppb. The calculational results are extensively checked by comparison with the experimental data for different nuclear charges and by evaluation of the hydrogenic limit of individual corrections.

Identification of F impurities in F-doped ZnO by synchrotron X-ray absorption near edge structures

NASA Astrophysics Data System (ADS)

Na-Phattalung, Sutassana; Limpijumnong, Sukit; Min, Chul-Hee; Cho, Deok-Yong; Lee, Seung-Ran; Char, Kookrin; Yu, Jaejun

2018-04-01

Synchrotron X-ray absorption near edge structure (XANES) measurements of F K-edge in conjunction with first-principles calculations are used to identify the local structure of the fluorine (F) atom in F-doped ZnO. The ZnO film was grown by pulsed laser deposition with an Nd:YAG laser, and an oxyfluoridation method was used to introduce F ions into the ZnO films. The measured XANES spectrum of the sample was compared against the first-principles XANES calculations based on various models for local atomic structures surrounding F atoms. The observed spectral features are attributed to ZnF2 and FO defects in wurtzite bulk ZnO.

Structure and properties of microporous titanosilicate determined by first-principles calculations

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

Ching, W.Y.; Xu, Y.; Gu, Z.

1996-12-01

The structure of EST-10, a member of synthetic microporous titanosilicates, was recently determined by an ingenious combination of experimental and simulational techniques. However, the locations of the alkali atoms in the framework remain elusive and its electronic structure is totally unknown. Based on first-principles local density calculations, the possible locations of the alkali atoms are identified and its electronic structure and bonding fully elucidated. ETS-10 is a semiconductor with a direct band gap of 2.33 eV. The Na atoms are likely to locate inside the seven-member ring pore adjacent to the one-dimensional Ti-O-Ti-O- chain. {copyright} {ital 1996 The American Physicalmore » Society.}« less

Atomic structure of self-organizing iridium induced nanowires on Ge(001)

NASA Astrophysics Data System (ADS)

Kabanov, N. S.; Heimbuch, R.; Zandvliet, H. J. W.; Saletsky, A. M.; Klavsyuk, A. L.

2017-05-01

The atomic structure of self-organizing iridium (Ir) induced nanowires on Ge(001) is studied by density functional theory (DFT) calculations and variable-temperature scanning tunneling microscopy. The Ir induced nanowires are aligned in a direction perpendicular to the Ge(001) substrate dimer rows, have a width of two atoms and are completely kink-less. Density functional theory calculations show that the Ir atoms prefer to dive into the Ge(001) substrate and push up the neighboring Ge substrate atoms. The nanowires are composed of Ge atoms and not Ir atoms as previously assumed. The regions in the vicinity of the nanowires are very dynamic, even at temperatures as low as 77 K. Time-resolved scanning tunneling microscopy measurements reveal that this dynamics is caused by buckled Ge substrate dimers that flip back and forth between their two buckled configurations.

Colloquium: Laser probing of neutron-rich nuclei in light atoms

NASA Astrophysics Data System (ADS)

Lu, Z.-T.; Mueller, P.; Drake, G. W. F.; Nörtershäuser, W.; Pieper, Steven C.; Yan, Z.-C.

2013-10-01

The neutron-rich He6 and He8 isotopes exhibit an exotic nuclear structure that consists of a tightly bound He4-like core with additional neutrons orbiting at a relatively large distance, forming a halo. Recent experimental efforts have succeeded in laser trapping and cooling these short-lived, rare helium atoms and have measured the atomic isotope shifts along the He4-He6-He8 chain by performing laser spectroscopy on individual trapped atoms. Meanwhile, the few-electron atomic structure theory, including relativistic and QED corrections, has reached a comparable degree of accuracy in the calculation of the isotope shifts. In parallel efforts, also by measuring atomic isotope shifts, the nuclear charge radii of lithium and beryllium isotopes have been studied. The techniques employed were resonance ionization spectroscopy on neutral, thermal lithium atoms and collinear laser spectroscopy on beryllium ions. Combining advances in both atomic theory and laser spectroscopy, the charge radii of these light halo nuclei have now been determined for the first time independent of nuclear structure models. The results are compared with the values predicted by a number of nuclear structure calculations and are used to guide our understanding of the nuclear forces in the extremely neutron-rich environment.

First-principles study of hydrogen-bonded molecular conductor κ -H3(Cat-EDT-TTF/ST)2

NASA Astrophysics Data System (ADS)

Tsumuraya, Takao; Seo, Hitoshi; Kato, Reizo; Miyazaki, Tsuyoshi

2015-07-01

We theoretically study hydrogen-bonded molecular conductors synthesized recently, κ -H3(Cat-EDT-TTF) 2 and its diselena analog, κ -H3(Cat-EDT-ST) 2, by first-principles density functional theory calculations. In these crystals, two H(Cat-EDT-TTF/ST) units share a hydrogen atom with a short O-H-O hydrogen bond. The calculated band structure near the Fermi level shows a quasi-two-dimensional character with a rather large interlayer dispersion due to the absence of insulating layers, in contrast with conventional molecular conductors. We discuss effective low-energy models based on H(Cat-EDT-TTF/ST) units and its dimers, respectively, where the microscopic character of the orbitals composing them are analyzed. Furthermore, we find a stable structure which is different from the experimentally determined structure, where the shared hydrogen atom becomes localized to one of the oxygen atoms, in which charge disproportionation between the two types of H(Cat-EDT-TTF) units is associated. The calculated potential energy surface for the H atom is very shallow near the minimum points; therefore the probability of the H atom can be delocalized between the two O atoms.

Structural, electronic and magnetic properties of chevron-type graphene, BN and BC2N nanoribbons

NASA Astrophysics Data System (ADS)

Guerra, T.; Azevedo, S.; Kaschny, J. R.

2017-04-01

Graphene nanoribbons are predicted to be essential components in future nanoelectronics. The size, edge type, arrangement of atoms and width of nanoribbons drastically change their properties. Boronnitrogencarbon nanoribbons properties are not fully understood so far. In the present contribution it was investigated the structural, electronic and magnetic properties of chevron-type carbon, boron nitride and BC2N nanoribbons, using first-principles calculations. The results indicate that the structural stability is closely related to the discrepancies in the bond lengths, which can induce structural deformations and stress. Such nanoribbons present a wide range of electronic behaviors, depending on their composition and particularities of the atomic arrangement. A net magnetic moment is found for structures that present carbon atoms at the nanoribbon borders. Nevertheless, the calculated magnetic moment depends on the peculiarities of the symmetric arrangement of atoms and imbalance of carbon atoms between different sublattices. It was found that all structures which have a significant energy gap do not present magnetic moment, and vice-versa. Such result indicates the strong correlation between the electronic and magnetic properties of the chevron-type nanoribbons.

Defects in ion-implanted hcp-titanium: A first-principles study of electronic structures

NASA Astrophysics Data System (ADS)

Raji, Abdulrafiu T.; Mazzarello, Riccardo; Scandolo, Sandro; Nsengiyumva, Schadrack; Härting, Margit; Britton, David T.

2011-12-01

The electronic structures of hexagonal closed-packed (h.c.p) titanium containing a vacancy and krypton impurity atoms at various insertion sites are calculated by first-principles methods in the framework of the density-functional theory (DFT). The density of states (DOS) for titanium containing a vacancy defect shows resonance-like features. Also, the bulk electron density decreases from ˜0.15/Å 3 to ˜0.05/Å 3 at the vacancy centre. Electronic structure calculations have been performed to investigate what underlies the krypton site preference in titanium. The DOS of the nearest-neighbour (NN) titanium atoms to the octahedral krypton appears to be less distorted (relative to pure titanium) when compared to the NN titanium atoms to the tetrahedral krypton. The electronic density deformation maps show that polarization of the titanium atoms is stronger when the krypton atom is located at the tetrahedral site. Since krypton is a closed-shell atom, thus precluding any bonding with the titanium atoms, we may conclude that the polarization of the electrons in the vicinity of the inserted krypton atoms and the distortion of the DOS of the NN titanium atoms to the krypton serve to indicate which defect site is preferred when a krypton atom is inserted into titanium. Based on these considerations, we conclude that the substitutional site is the most favourable one, and the octahedral is the preferred interstitial site, in agreement with recent DFT calculations of the energetics of krypton impurity sites.

DIFFRACTION FROM MODEL CRYSTALS

USDA-ARS?s Scientific Manuscript database

Although calculating X-ray diffraction patterns from atomic coordinates of a crystal structure is a widely available capability, calculation from non-periodic arrays of atoms has not been widely applied to cellulose. Non-periodic arrays result from modeling studies that, even though started with at...

Theoretical Calculations of Atomic Data for Spectroscopy

NASA Technical Reports Server (NTRS)

Bautista, Manuel A.

2000-01-01

Several different approximations and techniques have been developed for the calculation of atomic structure, ionization, and excitation of atoms and ions. These techniques have been used to compute large amounts of spectroscopic data of various levels of accuracy. This paper presents a review of these theoretical methods to help non-experts in atomic physics to better understand the qualities and limitations of various data sources and assess how reliable are spectral models based on those data.

Atomic charges of sulfur in ionic liquids: experiments and calculations.

PubMed

Fogarty, Richard M; Rowe, Rebecca; Matthews, Richard P; Clough, Matthew T; Ashworth, Claire R; Brandt, Agnieszka; Corbett, Paul J; Palgrave, Robert G; Smith, Emily F; Bourne, Richard A; Chamberlain, Thomas W; Thompson, Paul B J; Hunt, Patricia A; Lovelock, Kevin R J

2017-12-14

Experimental near edge X-ray absorption fine structure (NEXAFS) spectra, X-ray photoelectron (XP) spectra and Auger electron spectra are reported for sulfur in ionic liquids (ILs) with a range of chemical structures. These values provide experimental measures of the atomic charge in each IL and enable the evaluation of the suitability of NEXAFS spectroscopy and XPS for probing the relative atomic charge of sulfur. In addition, we use Auger electron spectroscopy to show that when XPS binding energies differ by less than 0.5 eV, conclusions on atomic charge should be treated with caution. Our experimental data provides a benchmark for calculations of the atomic charge of sulfur obtained using different methods. Atomic charges were computed for lone ions and ion pairs, both in the gas phase (GP) and in a solvation model (SMD), with a wide range of ion pair conformers considered. Three methods were used to compute the atomic charges: charges from the electrostatic potential using a grid based method (ChelpG), natural bond orbital (NBO) population analysis and Bader's atoms in molecules (AIM) approach. By comparing the experimental and calculated measures of the atomic charge of sulfur, we provide an order for the sulfur atoms, ranging from the most negative to the most positive atomic charge. Furthermore, we show that both ChelpG and NBO are reasonable methods for calculating the atomic charge of sulfur in ILs, based on the agreement with both the XPS and NEXAFS spectroscopy results. However, the atomic charges of sulfur derived from ChelpG are found to display significant, non-physical conformational dependence. Only small differences in individual atomic charge of sulfur were observed between lone ion (GP) and ion pair IL(SMD) model systems, indicating that ion-ion interactions do not strongly influence individual atomic charges.

The atomic simulation environment-a Python library for working with atoms.

PubMed

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D; Jennings, Paul C; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W

2017-07-12

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

The atomic simulation environment—a Python library for working with atoms

NASA Astrophysics Data System (ADS)

Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

2017-07-01

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Influence of the plasma environment on atomic structure using an ion-sphere model

DOE PAGES

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

2015-09-03

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Influence of the plasma environment on atomic structure using an ion-sphere model

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

Belkhiri, Madeny Jean; Fontes, Christopher John; Poirier, Michel

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for themore » six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe 22+, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the MCDF value of B. Saha et al.« less

Defect formation energy and magnetic structure of shape memory alloys Ni-X-Ga (X=Mn, Fe, Co) by first principle calculation

NASA Astrophysics Data System (ADS)

Bai, J.; Raulot, J. M.; Zhang, Y. D.; Esling, C.; Zhao, X.; Zuo, L.

2010-09-01

The crystallographic and magnetic structures of the Ni2XGa (X=Mn, Fe, Co), are systematically investigated by means of the first-principles calculations within the framework of density functional theory using the VIENNA AB INITIO SOFTWARE PACKAGE. The formation energies of several kinds of defects (atomic exchange, antisite, vacancy) are estimated. The Ga atoms stabilize the cubic structure, and the effect of X atoms on the structural stability is opposite. For most cases of the site occupation, the excess atoms of the rich component directly occupy the site(s) of the deficient one(s), except for Ga-rich Ni-deficient type. The magnitude of the variation in Ni moments is much larger than that of Mn in defective Ni2XGa. The value of Ni magnetic moment sensitively depends on the distance between Ni and X. Excess Mn could be ferromagnetic or antiferromagnetic, depending on the distance between the neighboring Mn atoms.

Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

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

Gomez, Thomas; Nagayama, Taisuke; Fontes, Chris

Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods). Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numericalmore » complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange) part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. Here, this technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.« less

Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

DOE PAGES

Gomez, Thomas; Nagayama, Taisuke; Fontes, Chris; ...

2018-04-23

Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods). Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numericalmore » complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange) part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. Here, this technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.« less

Atomic and electronic structures of Si(1 1 1)-\\left(\\sqrt{\\mathbf{3}}\\times\\sqrt{\\mathbf{3}}\\right)\\text{R}\\mathbf{3}{{\\mathbf{0}}^{\\circ}} -Au and (6 × 6)-Au surfaces

NASA Astrophysics Data System (ADS)

Patterson, C. H.

2015-12-01

Si(1 1 1)-Au surfaces with around one monolayer of Au exhibit many ordered structures and structures containing disordered domain walls. Hybrid density functional theory (DFT) calculations presented here reveal the origin of these complex structures and tendency to form domain walls. The conjugate honeycomb chain trimer (CHCT) structure of the \\sqrt{3} -Au phase contains Si atoms with non-bonding surface states which can bind Au atoms in pairs in interstices of the CHCT structure and make this surface metallic. Si adatoms adsorbed on the \\sqrt{3} -Au surface induce a gapped surface through interaction with the non-bonding states. Adsorption of extra Au atoms in interstitial sites of the \\sqrt{3} -Au surface is stabilized by interaction with the non-bonding orbitals and leads to higher coverage ordered structures including the ≤ft(6× 6\\right) -Au phase. Extra Au atoms bound in interstitial sites of the \\sqrt{3} -Au surface result in top layer Si atoms with an SiAu4 butterfly wing configuration. The structure of a ≤ft(6× 6\\right) -Au phase, whose in-plane top atomic layer positions were previously determined by an electron holography technique (Grozea et al 1998 Surf. Sci. 418 32), is calculated using total energy minimization. The Patterson function for this structure is calculated and is in good agreement with data from an in-plane x-ray diffraction study (Dornisch et al 1991 Phys. Rev. B 44 11221). Filled and empty state scanning tunneling microscopy (STM) images are calculated for domain walls and the ≤ft(6× 6\\right) -Au structure. The ≤ft(6× 6\\right) -Au phase is 2D chiral and this is evident in computed and actual STM images. ≤ft(6× 6\\right) -Au and domain wall structures contain the SiAu4 motif with a butterfly wing shape. Chemical bonding within the Si-Au top layers of the \\sqrt{3} -Au and ≤ft(6× 6\\right) -Au surfaces is analyzed and an explanation for the SiAu4 motif structure is given.

Tight-binding calculation studies of vacancy and adatom defects in graphene

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

Zhang, Wei; Lu, Wen-Cai; Zhang, Hong-Xing

2016-02-19

Computational studies of complex defects in graphene usually need to deal with a larger number of atoms than the current first-principles methods can handle. We show a recently developed three-center tight-binding potential for carbon is very efficient for large scale atomistic simulations and can accurately describe the structures and energies of various defects in graphene. Using the three-center tight-binding potential, we have systematically studied the stable structures and formation energies of vacancy and embedded-atom defects of various sizes up to 4 vacancies and 4 embedded atoms in graphene. In conclusion, our calculations reveal low-energy defect structures and provide a moremore » comprehensive understanding of the structures and stability of defects in graphene.« less

The structural, electronic and optical properties of Au-ZnO interface structure from the first-principles calculation

NASA Astrophysics Data System (ADS)

Huo, Jin-Rong; Li, Lu; Cheng, Hai-Xia; Wang, Xiao-Xu; Zhang, Guo-Hua; Qian, Ping

2018-03-01

The interface structure, electronic and optical properties of Au-ZnO are studied using the first-principles calculation based on density functional theory (DFT). Given the interfacial distance, bonding configurations and terminated surface, we built the optimal interface structure and calculated the electronic and optical properties of the interface. The total density of states, partial electronic density of states, electric charge density and atomic populations (Mulliken) are also displayed. The results show that the electrons converge at O atoms at the interface, leading to a stronger binding of interfaces and thereby affecting the optical properties of interface structures. In addition, we present the binding energies of different interface structures. When the interface structure of Au-ZnO gets changed, furthermore, varying optical properties are exhibited.

Probing structure, thermochemistry, electron affinity, and magnetic moment of thulium-doped silicon clusters TmSi n (n = 3-10) and their anions with density functional theory.

PubMed

Huang, Xintao; Yang, Jucai

2017-12-26

The most stable structures and electronic properties of TmSi n (n = 3-10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi n and their anions can be regarded as substituting a Si atom of the ground state structure of Si n + 1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi n (n = 3-10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster. The NPA analyses indicated that the 4f electron of Tm atom in TmSi n (n = 3-10) and their anions do not participate in bonding. The total magnetic moments of TmSi n are mainly provided by the 4f electrons of Tm atom. The dissociation energy of Tm atom from the most stable structure of TmSi n and their anions has been calculated to examine relative stability.

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.

PubMed

Ionescu, Crina-Maria; Sehnal, David; Falginella, Francesco L; Pant, Purbaj; Pravda, Lukáš; Bouchal, Tomáš; Svobodová Vařeková, Radka; Geidl, Stanislav; Koča, Jaroslav

2015-01-01

Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form. Due to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC.

The Hyperfine Structure of the Ground State in the Muonic Helium Atoms

NASA Astrophysics Data System (ADS)

Aznabayev, D. T.; Bekbaev, A. K.; Korobov, V. I.

2018-05-01

Non-relativistic ionization energies 3He2+μ-e- and 4He2+μ-e- of helium-muonic atoms are calculated for ground states. The calculations are based on the variational method of the exponential expansion. Convergence of the variational energies is studied by an increasing of a number of the basis functions N. This allows to claim that the obtained energy values have 26 significant digits for ground states. With the obtained results we calculate hyperfine splitting of the muonic helium atoms.

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

NASA Technical Reports Server (NTRS)

Kahn, L. R.

1982-01-01

Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

Embedded-atom-method study of structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys

NASA Astrophysics Data System (ADS)

Asta, Mark; Morgan, Dane; Hoyt, J. J.; Sadigh, Babak; Althoff, J. D.; de Fontaine, D.; Foiles, S. M.

1999-06-01

Structural, thermodynamic, and atomic-transport properties of liquid Ni-Al alloys have been studied by Monte Carlo and molecular-dynamics simulations based upon three different embedded-atom method (EAM) interatomic potentials, namely those due to Foiles and Daw (FD) [J. Mater. Res. 2, 5 (1987)], Voter and Chen (VC) [in Characterization of Defects in Materials, edited by R. W. Siegel et al. MRS Symposia Proceedings. No. 82 (Materials Research Society, Pittsburgh, 1987), p.175] and Ludwig and Gumbsch (LG) [Model. Simul. Mater. Sci. Eng. 3, 533 (1995)]. We present detailed comparisons between calculated results and experimental data for structure factors, atomic volumes, enthalpies of mixing, activities, and viscosities. Calculated partial structure factors are found to be in semiquantitative agreement with published neutron scattering measurements for Ni20Al80 alloys, indicating that short-range order in the liquid phase is qualitatively well described. Calculated thermodynamic properties of mixing are found to agree very well with experimental data for Ni compositions greater than 75 atomic %, while for alloys richer in Al the magnitudes of the enthalpies and entropies of mixing are significantly underestimated. The VC and LG potentials give atomic densities and viscosities in good agreement with experiment for Ni-rich compositions, while FD potentials consistently underestimate both properties at all concentrations. The results of this study demonstrate that VC and LG potentials provide a realistic description of the thermodynamic and atomic transport properties for NixAl1-x liquid alloys with x>=0.75, and point to the limitations of EAM potentials for alloys richer in Al.

Yong-Ki Kim — His Life and Recent Work

NASA Astrophysics Data System (ADS)

Stone, Philip M.

2007-08-01

Dr. Kim made internationally recognized contributions in many areas of atomic physics research and applications, and was still very active when he was killed in an automobile accident. He joined NIST in 1983 after 17 years at the Argonne National Laboratory following his Ph.D. work at the University of Chicago. Much of his early work at Argonne and especially at NIST was the elucidation and detailed analysis of the structure of highly charged ions. He developed a sophisticated, fully relativistic atomic structure theory that accurately predicts atomic energy levels, transition wavelengths, lifetimes, and transition probabilities for a large number of ions. This information has been vital to model the properties of the hot interior of fusion research plasmas, where atomic ions must be described with relativistic atomic structure calculations. In recent years, Dr. Kim worked on the precise calculation of ionization and excitation cross sections of numerous atoms, ions, and molecules that are important in fusion research and in plasma processing for manufacturing semiconductor chips. Dr. Kim greatly advanced the state-of-the-art of calculations for these cross sections through development and implementation of highly innovative methods, including his Binary-Encounter-Bethe (BEB) theory and a scaled plane wave Born (scaled PWB) theory. His methods, using closed quantum mechanical formulas and no adjustable parameters, avoid tedious large-scale computations with main-frame computers. His calculations closely reproduce the results of benchmark experiments as well as large-scale calculations requiring hours of computer time. This recent work on BEB and scaled PWB is reviewed and examples of its capabilities are shown.

Ab initio calculations of ionic hydrocarbon compounds with heptacoordinate carbon.

PubMed

Wang, George; Rahman, A K Fazlur; Wang, Bin

2018-04-25

Ionic hydrocarbon compounds that contain hypercarbon atoms, which bond to five or more atoms, are important intermediates in chemical synthesis and may also find applications in hydrogen storage. Extensive investigations have identified hydrocarbon compounds that contain a five- or six-coordinated hypercarbon atom, such as the pentagonal-pyramidal hexamethylbenzene, C 6 (CH 3 ) 6 2+ , in which a hexacoordinate carbon atom is involved. It remains challenging to search for further higher-coordinated carbon in ionic hydrocarbon compounds, such as seven- and eight-coordinated carbon. Here, we report ab initio density functional calculations that show a stable 3D hexagonal-pyramidal configuration of tropylium trication, (C 7 H 7 ) 3+ , in which a heptacoordinate carbon atom is involved. We show that this tropylium trication is stable against deprotonation, dissociation, and structural deformation. In contrast, the pyramidal configurations of ionic C 8 H 8 compounds, which would contain an octacoordinate carbon atom, are unstable. These results provide insights for developing new molecular structures containing hypercarbon atoms, which may have potential applications in chemical synthesis and in hydrogen storage. Graphical abstract Possible structural transformations of stable configurations of (C 7 H 7 ) 3+ , which may result in the formation of the pyramidal structure that involves a heptacoordinate hypercarbon atom.

A novel Gaussian-Sinc mixed basis set for electronic structure calculations

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

Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.

2015-08-14

A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definablemore » and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H{sub 2}, O{sub 2}, and N{sub 2}, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.« less

The effect of local atomic structure on the optical properties of GeSi self-assembled islands buried in silicon matrix

NASA Astrophysics Data System (ADS)

Demchenko, I. N.; Lawniczak-Jablonska, K.; Kret, S.; Novikov, A. V.; Laval, J.-Y.; Zak, M.; Szczepanska, A.; Yablonskiy, A. N.; Krasilnik, Z. F.

2007-03-01

The local atomic structure of GeSi self-assembled islands buried in a silicon matrix strongly influences the optical properties of such systems. In the present paper this structure was determined by x-ray absorption fine-structure (XAFS) spectroscopy and high resolution transmission electron microscopy (HRTEM) and used to build a schematic description of the band structure model. Quantitative analysis of the extended XAFS (EXAFS) spectrum was performed for three coordination shells around the Ge absorbing atom with multiple scattering taken into account. It was proved that the coordination number of elements in an alloy resulting from EXAFS analysis for all three coordination spheres (i.e. 'mixing degree' parameters) cannot be taken as the concentration of alloy but can be used together with a proper model of the alloy unit cell to calculate a realistic concentration. The fraction of Ge calculated in this way is consistent with HRTEM results. The found model of the unit cell was used to generate a x-ray absorption near edge structure spectrum by ab initio calculations. This approach yielded a spectrum in good agreement with the experimental one. The information gained from XAFS and HRTEM was then used for calculation of the band structure diagram. Results of the calculation are discussed and compared with the experimental photoluminescence spectrum.

First-principles study on silicon atom doped monolayer graphene

NASA Astrophysics Data System (ADS)

Rafique, Muhammad; Shuai, Yong; Hussain, Nayyar

2018-01-01

This paper illustrates the structural, electronic and optical properties of individual silicon (Si) atom-doped single layer graphene using density functional theory method. Si atom forms tight bonding with graphene layer. The effect of doping has been investigated by varying the concentration of Si atoms from 3.125% to 9.37% (i.e. From one to three Si atoms in 4 × 4 pure graphene supercell containing 32 carbon atoms), respectively. Electronic structure, partial density of states (PDOS) and optical properties of pure and Si atom-doped graphene sheet were calculated using VASP (Vienna ab-initio Simulation Package). The calculated results for pure graphene sheet were then compared with Si atom doped graphene. It is revealed that upon Si doping in graphene, a finite band gap appears at the high symmetric K-point, thereby making graphene a direct band gap semiconductor. Moreover, the band gap value is directly proportional to the concentration of impurity Si atoms present in graphene lattice. Upon analyzing the optical properties of Si atom-doped graphene structures, it is found that, there is significant change in the refractive index of the graphene after Si atom substitution in graphene. In addition, the overall absorption spectrum of graphene is decreased after Si atom doping. Although a significant red shift in absorption is found to occur towards visible range of radiation when Si atom is substituted in its lattice. The reflectivity of graphene improves in low energy region after Si atom substitution in graphene. These results can be useful for tuning the electronic structure and to manipulate the optical properties of graphene layer in the visible region.

Spectrophores as one-dimensional descriptors calculated from three-dimensional atomic properties: applications ranging from scaffold hopping to multi-target virtual screening.

PubMed

Gladysz, Rafaela; Dos Santos, Fabio Mendes; Langenaeker, Wilfried; Thijs, Gert; Augustyns, Koen; De Winter, Hans

2018-03-07

Spectrophores are novel descriptors that are calculated from the three-dimensional atomic properties of molecules. In our current implementation, the atomic properties that were used to calculate spectrophores include atomic partial charges, atomic lipophilicity indices, atomic shape deviations and atomic softness properties. This approach can easily be widened to also include additional atomic properties. Our novel methodology finds its roots in the experimental affinity fingerprinting technology developed in the 1990's by Terrapin Technologies. Here we have translated it into a purely virtual approach using artificial affinity cages and a simplified metric to calculate the interaction between these cages and the atomic properties. A typical spectrophore consists of a vector of 48 real numbers. This makes it highly suitable for the calculation of a wide range of similarity measures for use in virtual screening and for the investigation of quantitative structure-activity relationships in combination with advanced statistical approaches such as self-organizing maps, support vector machines and neural networks. In our present report we demonstrate the applicability of our novel methodology for scaffold hopping as well as virtual screening.

Evolution in time of an N-atom system. II. Calculation of the eigenstates

NASA Astrophysics Data System (ADS)

Rudolph, Terry; Yavin, Itay; Freedhoff, Helen

2004-01-01

We calculate the energy eigenvalues and eigenstates corresponding to coherent single and multiple excitations of a number of different arrays of N identical two-level atoms (TLA’s) or qubits, including polygons, “diamond” structures, polygon multilayers, icosahedra, and dodecahedra. We assume only that the coupling occurs via an exchange interaction which depends on the separation between the atoms. We include the interactions between all pairs of atoms, and our results are valid for arbitrary separations relative to the radiation wavelength.

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

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

Electronic Structure of I-M8Ga16Sn30 (M = Ba, Sr, Yb) by First-Principles Calculation

NASA Astrophysics Data System (ADS)

Wang, Jin-song; Liu, Hong-xia; Deng, Shuping; Li, De-cong; Shen, Lan-xian; Cheng, Feng; Deng, Shu-kang

2017-05-01

Sn-based clathrates possess excellent thermoelectric properties ascribed to their higher Seebeck coefficient and lower thermal conductivity. Guest atoms significantly modulate the thermoelectric properties of Sn-based calculates because of their diverse atomic radius and interactions with framework atoms. Thus, we explored the electronic structure of I-M8Ga16Sn30 (M = Ba, Sr, Yb) by first-principles calculation. Results revealed significant differences between Yb8Ga16Sn30 and M8Ga16Sn30 (M = Ba, Sr,). In particular, the Yb-filled compound substitution possesses lowest formation energy and the off-center distance of the Yb atom is the largest compared with the other structures. I-M8Ga16Sn30 (M = Ba, Sr, Yb) is an indirect band gap semiconductor, and the enhanced hybridization effect between the guest and framework atoms' orbits exists because the Yb f orbit results in a decrease in band gap. Ba- and Sr-filled clathrates have similar valence bands but slightly different conduction bands; however, Yb8Ga16Sn30 possess the spiculate density of states near the Fermi level that reveals excellent thermoelectric properties.

Self-consistent average-atom scheme for electronic structure of hot and dense plasmas of mixture.

PubMed

Yuan, Jianmin

2002-10-01

An average-atom model is proposed to treat the electronic structures of hot and dense plasmas of mixture. It is assumed that the electron density consists of two parts. The first one is a uniform distribution with a constant value, which is equal to the electron density at the boundaries between the atoms. The second one is the total electron density minus the first constant distribution. The volume of each kind of atom is proportional to the sum of the charges of the second electron part and of the nucleus within each atomic sphere. By this way, one can make sure that electrical neutrality is satisfied within each atomic sphere. Because the integration of the electron charge within each atom needs the size of that atom in advance, the calculation is carried out in a usual self-consistent way. The occupation numbers of electron on the orbitals of each kind of atom are determined by the Fermi-Dirac distribution with the same chemical potential for all kinds of atoms. The wave functions and the orbital energies are calculated with the Dirac-Slater equations. As examples, the electronic structures of the mixture of Au and Cd, water (H2O), and CO2 at a few temperatures and densities are presented.

Deciphering chemical order/disorder and material properties at the single-atom level

DOE PAGES

Yang, Yongsoo; Chen, Chien-Chun; Scott, M. C.; ...

2017-02-01

Perfect crystals are rare in nature. Real materials often contain crystal defects and chemical order/disorder such as grain boundaries, dislocations, interfaces, surface reconstructions and point defects. Such disruption in periodicity strongly affects material properties and functionality. Despite rapid development of quantitative material characterization methods, correlating three-dimensional (3D) atomic arrangements of chemical order/disorder and crystal defects with material properties remains a challenge. On a parallel front, quantum mechanics calculations such as density functional theory (DFT) have progressed from the modelling of ideal bulk systems to modelling ‘real’ materials with dopants, dislocations, grain boundaries and interfaces; but these calculations rely heavily onmore » average atomic models extracted from crystallography. To improve the predictive power of first-principles calculations, there is a pressing need to use atomic coordinates of real systems beyond average crystallographic measurements. Here we determine the 3D coordinates of 6,569 iron and 16,627 platinum atoms in an iron-platinum nanoparticle, and correlate chemical order/disorder and crystal defects with material properties at the single-atom level. We identify rich structural variety with unprecedented 3D detail including atomic composition, grain boundaries, anti-phase boundaries, anti-site point defects and swap defects. We show that the experimentally measured coordinates and chemical species with 22 picometre precision can be used as direct input for DFT calculations of material properties such as atomic spin and orbital magnetic moments and local magnetocrystalline anisotropy. The work presented here combines 3D atomic structure determination of crystal defects with DFT calculations, which is expected to advance our understanding of structure–property relationships at the fundamental level.« less

Local atomic and electronic structures in ferromagnetic topological insulator Cr-doped (BixSb1-x) 2Te3 studied by XAFS and ab initio calculations

NASA Astrophysics Data System (ADS)

Liu, Zhen; Wei, Xinyuan; Wang, Jiajia; Pan, Hong; Ji, Fuhao; Ye, Mao; Yang, Zhongqin; Qiao, Shan

2015-09-01

The local atomic and electronic structures around the dopants in Cr-doped (BixSb1 -x )2Te3 are studied by x-ray absorption fine structure (XAFS) measurements and first-principles calculations. Both Cr and Bi are confirmed substituting Sb sites (CrSb and BiSb). The six nearest Te atoms around Cr move towards Cr and shorten the Cr-Te bond lengths to 2.76 Å and 2.77 Å for x =0.1 and x =0.2 , respectively. Importantly, we reveal the hybridization between the Sb/Te p states and Cr d states by the presence of a pre-edge peak at Cr K -absorption edge, which is also supported by our ab initio calculations. These findings provide important clues to understand the mechanism of ferromagnetic order in this system with quantum anomalous Hall effect.

Correlation of Hydrogen-Atom Abstraction Reaction Efficiencies for Aryl Radicals with their Vertical Electron Affinities and the Vertical Ionization Energies of the Hydrogen Atom Donors

PubMed Central

Jing, Linhong; Nash, John J.

2009-01-01

The factors that control the reactivities of aryl radicals toward hydrogen-atom donors were studied by using a dual-cell Fourier-transform ion cyclotron resonance mass spectrometer (FT – ICR). Hydrogen-atom abstraction reaction efficiencies for two substrates, cyclohexane and isopropanol, were measured for twenty-three structurally different, positively-charged aryl radicals, which included dehydrobenzenes, dehydronaphthalenes, dehydropyridines, and dehydro(iso)quinolines. A logarithmic correlation was found between the hydrogen-atom abstraction reaction efficiencies and the (calculated) vertical electron affinities (EA) of the aryl radicals. Transition state energies calculated for three of the aryl radicals with isopropanol were found to correlate linearly with their (calculated) EAs. No correlation was found between the hydrogen-atom abstraction reaction efficiencies and the (calculated) enthalpy changes for the reactions. Measurement of the reaction efficiencies for the reactions of several different hydrogen-atom donors with a few selected aryl radicals revealed a logarithmic correlation between the hydrogen-atom abstraction reaction efficiencies and the vertical ionization energies (IE) of the hydrogen-atom donors, but not the lowest homolytic X – H (X = heavy atom) bond dissociation energies of the hydrogen-atom donors. Examination of the hydrogen-atom abstraction reactions of twenty-nine different aryl radicals and eighteen different hydrogen-atom donors showed that the reaction efficiency increases (logarithmically) as the difference between the IE of the hydrogen-atom donor and the EA of the aryl radical decreases. This dependence is likely to result from the increasing polarization, and concomitant stabilization, of the transition state as the energy difference between the neutral and ionic reactants decreases. Thus, the hydrogen-atom abstraction reaction efficiency for an aryl radical can be “tuned” by structural changes that influence either the vertical EA of the aryl radical or the vertical IE of the hydrogen atom donor. PMID:19061320

Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design.

PubMed

Matta, Chérif F; Arabi, Alya A

2011-06-01

The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

Origin of the periodic structure in the conductance curve of gold nanojunctions in hydrogen environment

NASA Astrophysics Data System (ADS)

Jiang, Zhuoling; Wang, Hao; Sanvito, Stefano; Hou, Shimin

2016-03-01

The evolution of the atomic structure and the vibrational and electronic transport properties of gold atomic junctions incorporating molecular and atomic hydrogen upon elongation have been investigated with the nonequilibrium Green's function formalism combined with density functional theory. Our calculations show that for the case of gold junctions doped with a single H2 molecule the low-bias conductance drops rapidly with the electrodes' separation, while it remains almost constant if a single H atom replaces the molecule. In contrast, when one considers two H atoms adsorbed on a gold monatomic chain forming an Au-H-Au-H-Au double-bridge structure, the low-bias conductance increases first and then shows a plateau upon stretching the junction, in perfect agreement with experiments on gold nanocontacts in hydrogen environment. Furthermore, also the distribution of the calculated vibrational energies of the two H atoms is consistent with the experimental result in the low-conductance region, demonstrating clear evidence that hydrogen molecules can dissociate on stretched gold monatomic chains. These findings are helpful to improve our understanding of the structure-property relation of gold nanocontacts and also provide a new prospect for gold nanowires being used as chemical sensors and catalysts.

The heavy atom microwave structure of 2-methyltetrahydrofuran

NASA Astrophysics Data System (ADS)

Van, Vinh; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

2016-11-01

The rotational spectra of 2-methyltetrahydrofuran have been observed using a pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2-26.5 GHz. Conformational analysis using quantum chemical calculations yields two stable conformers; both of them possess an envelope structure. The conformational transformation can occur via two different transition states. The Cremer-Pople notation for five-membered rings is chosen for describing the conformations. Only one conformer with equatorial position of the methyl group is assigned in the experimental spectrum. The fits of its parent species, 13C- and 18O-isotopologues result in highly accurate molecular parameters, and enable the determination of a heavy atom rs structure using Kraitchman's equations. This experimentally determined structure is in excellent agreement with the structure calculated by anharmonic frequency calculations.

Crown oxygen-doping graphene with embedded main-group metal atoms

NASA Astrophysics Data System (ADS)

Wu, Liyuan; Wang, Qian; Yang, Chuanghua; Quhe, Ruge; Guan, Pengfei; Lu, Pengfei

2018-02-01

Different main-group metal atoms embedded in crown oxygen-doping graphene (metal@OG) systems are studied by the density functional theory. The binding energies and electronic structures are calculated by using first-principles calculations. The binding energy of metal@OG system mainly depends on the electronegativity of the metal atom. The lower the value of the electronegativity, the larger the binding energy, indicating the more stable the system. The electronic structure of metal@OG arouses the emergence of bandgap and shift of Dirac point. It is shown that interaction between metal atom and crown oxygen-doping graphene leads to the graphene's stable n-doping, and the metal@OG systems are stable semiconducting materials, which can be used in technological applications.

A Gaussian Approximation Potential for Silicon

NASA Astrophysics Data System (ADS)

Bernstein, Noam; Bartók, Albert; Kermode, James; Csányi, Gábor

We present an interatomic potential for silicon using the Gaussian Approximation Potential (GAP) approach, which uses the Gaussian process regression method to approximate the reference potential energy surface as a sum of atomic energies. Each atomic energy is approximated as a function of the local environment around the atom, which is described with the smooth overlap of atomic environments (SOAP) descriptor. The potential is fit to a database of energies, forces, and stresses calculated using density functional theory (DFT) on a wide range of configurations from zero and finite temperature simulations. These include crystalline phases, liquid, amorphous, and low coordination structures, and diamond-structure point defects, dislocations, surfaces, and cracks. We compare the results of the potential to DFT calculations, as well as to previously published models including Stillinger-Weber, Tersoff, modified embedded atom method (MEAM), and ReaxFF. We show that it is very accurate as compared to the DFT reference results for a wide range of properties, including low energy bulk phases, liquid structure, as well as point, line, and plane defects in the diamond structure.

Path integral Monte Carlo study on the structure and absorption spectra of alkali atoms (Li, Na, K) attached to superfluid helium clusters

NASA Astrophysics Data System (ADS)

Nakayama, Akira; Yamashita, Koichi

2001-01-01

Path integral Monte Carlo calculations have been performed to investigate the microscopic structure and thermodynamic properties of the AkṡHeN (Ak=Li, Na, K,N⩽300) clusters at T=0.5 K. Absorption spectra which correspond to the 2P←2S transitions of alkali atoms are also calculated within a pairwise additive model, which employs diatomic Ak-He potential energy curves. The size dependences of the cluster structure and absorption spectra that show the influence of the helium cluster environment are examined in detail. It is found that alkali atoms are trapped in a dimple on the helium cluster's surface and that, from the asymptotic behavior, the AkṡHe300 cluster, at least semiquantitatively, mimics the local structure of experimentally produced large helium clusters in the vicinity of alkali atoms. We have successfully reproduced the overall shapes of the spectra and explained their features from a static and structural point of view. The positions, relative intensities, and line widths of the absorption maxima are calculated to be in moderate agreement with experiments [F. Stienkemeier, J. Higgins, C. Callegari, S. I. Kanorsky, W. E. Ernst, and G. Scoles, Z. Phys. D 38, 253 (1996)].

Influence of tool shape on lattice rearrangement under loading conditions reproducing friction stir welding

NASA Astrophysics Data System (ADS)

Konovalenko, Ivan S.; Konovalenko, Igor S.

2015-10-01

Metal behavior under loading conditions that reproduce friction stir welding was studied on the atomic scale. Calculations were conducted based on molecular dynamics simulation with potentials calculated within the embedded atom method. The loading of the interface between two crystallites, whose structure corresponded to aluminum alloy 2024, was simulated by the motion of a cone-shaped tool along the interface with constant angular and translational velocities. The motion of the rotating tool causes fracture of the workpiece crystal structure with subsequent mixing of surface atoms of the interfacing crystallites. It is shown that the resistance force acting on the moving tool from the workpiece and the process of structural defect formation in the workpiece depend on the tool shape.

Probing the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters by density functional calculations

NASA Astrophysics Data System (ADS)

Lu, Sheng-Jie

2018-05-01

We present a theoretical investigation on the structural evolution and bonding properties of PtnC2-/0 (n = 1-7) clusters using density functional theoretical calculations. The results showed that both anionic and neutral PtnC2 (n = 1-7) clusters primarily adopt 2D planar chain-shaped or ring-based structures. The two C atoms directly interact with each other to form a Csbnd C bond for n = 1-3, while the two C atoms are separated by the Pt atoms for n = 4-7, except for neutral Pt5C2. Pt4C2- anion and Pt4C2 neutral both show σ plus π double delocalized bonding patterns.

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.

Numerical study of the defect adamantine compound CuGaGeSe4

NASA Astrophysics Data System (ADS)

Shen, Kesheng; Zhang, Xianzhou; Lu, Hai; Jiao, Zhaoyong

2018-06-01

The electronic structure, elastic and optical properties of the defect adamantine compound CuGaGeSe4 in ? structure are systematically investigated using first-principles calculations. Through detailed calculation and comparison, we obtain three independent atomic arrangements and predict the most stable atomic arrangement according to the lattice constants and enthalpy formation energies. The elastic constants are calculated, which can be used to predict the axial thermal expansion coefficients accurately. The optical properties of compound CuGaGeSe4, including the dielectric function, refractive index and absorption spectrum, are depicted for a more intuitive understanding. Our calculated zero-frequency limits ɛ1(0) and n(0) are very close to the other theoretical values, which proves that our calculations are reliable.

Atomic and Ionic Radii of Elements 1-96.

PubMed

Rahm, Martin; Hoffmann, Roald; Ashcroft, N W

2016-10-04

Atomic and cationic radii have been calculated for the first 96 elements, together with selected anionic radii. The metric adopted is the average distance from the nucleus where the electron density falls to 0.001 electrons per bohr(3) , following earlier work by Boyd. Our radii are derived using relativistic all-electron density functional theory calculations, close to the basis set limit. They offer a systematic quantitative measure of the sizes of non-interacting atoms, commonly invoked in the rationalization of chemical bonding, structure, and different properties. Remarkably, the atomic radii as defined in this way correlate well with van der Waals radii derived from crystal structures. A rationalization for trends and exceptions in those correlations is provided. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First principles pseudopotential calculation of electron energy loss near edge structures of lattice imperfections.

PubMed

Mizoguchi, Teruyasu; Matsunaga, Katsuyuki; Tochigi, Eita; Ikuhara, Yuichi

2012-01-01

Theoretical calculations of electron energy loss near edge structures (ELNES) of lattice imperfections, particularly a Ni(111)/ZrO₂(111) heterointerface and an Al₂O₃ stacking fault on the {1100} plane, are performed using a first principles pseudopotential method. The present calculation can qualitatively reproduce spectral features as well as chemical shifts in experiment by employing a special pseudopotential designed for the excited atom with a core-hole. From the calculation, spectral changes observed in O-K ELNES from a Ni/ZrO₂ interface can be attributable to interfacial oxygen-Ni interactions. In the O-K ELNES of Al₂O₃ stacking faults, theoretical calculation suggests that the spectral feature reflects coordination environment and chemical bonding. Powerful combinations of ELNES with a pseudopotential method used to investigate the atomic and electronic structures of lattice imperfections are demonstrated. Copyright © 2011 Elsevier Ltd. All rights reserved.

GPU implementation of the linear scaling three dimensional fragment method for large scale electronic structure calculations

NASA Astrophysics Data System (ADS)

Jia, Weile; Wang, Jue; Chi, Xuebin; Wang, Lin-Wang

2017-02-01

LS3DF, namely linear scaling three-dimensional fragment method, is an efficient linear scaling ab initio total energy electronic structure calculation code based on a divide-and-conquer strategy. In this paper, we present our GPU implementation of the LS3DF code. Our test results show that the GPU code can calculate systems with about ten thousand atoms fully self-consistently in the order of 10 min using thousands of computing nodes. This makes the electronic structure calculations of 10,000-atom nanosystems routine work. This speed is 4.5-6 times faster than the CPU calculations using the same number of nodes on the Titan machine in the Oak Ridge leadership computing facility (OLCF). Such speedup is achieved by (a) carefully re-designing of the computationally heavy kernels; (b) redesign of the communication pattern for heterogeneous supercomputers.

Density Functional Theory Study of Leaching Performance of Different Acids on Pyrochlore (100) Surface

NASA Astrophysics Data System (ADS)

Yang, Xiuli; Fang, Qing; Ouyang, Hui

2018-04-01

Pyrochlore leaching using hydrofluoric, sulfuric, and hydrochloric acids has been studied via experimental methods for years, but the interactions between niobium atoms on the pyrochlore surface and different acids have not been investigated. In this work, first-principles calculations based on density functional theory were used to elucidate the leaching performance of these three acids from the viewpoint of geometrical and electronic structures. The calculation results indicate that sulfate, chloride, and fluoride anions influence the geometric structure of pyrochlore (100) to different extents, decreasing in the order: sulfate, fluoride, chloride. Orbitals of O1 and O2 atoms of sulfate hybridized with those of surface niobium atom. Fluorine orbitals hybridized with those of surface niobium atoms. However, no obvious overlap exists between any orbitals of chlorine and surface niobium, revealing that chlorine does not interact chemically with surface niobium atoms.

Density Functional Theory Study of Leaching Performance of Different Acids on Pyrochlore (100) Surface

NASA Astrophysics Data System (ADS)

Yang, Xiuli; Fang, Qing; Ouyang, Hui

2018-06-01

Pyrochlore leaching using hydrofluoric, sulfuric, and hydrochloric acids has been studied via experimental methods for years, but the interactions between niobium atoms on the pyrochlore surface and different acids have not been investigated. In this work, first-principles calculations based on density functional theory were used to elucidate the leaching performance of these three acids from the viewpoint of geometrical and electronic structures. The calculation results indicate that sulfate, chloride, and fluoride anions influence the geometric structure of pyrochlore (100) to different extents, decreasing in the order: sulfate, fluoride, chloride. Orbitals of O1 and O2 atoms of sulfate hybridized with those of surface niobium atom. Fluorine orbitals hybridized with those of surface niobium atoms. However, no obvious overlap exists between any orbitals of chlorine and surface niobium, revealing that chlorine does not interact chemically with surface niobium atoms.

Faculty Member for Research in an Undergraduate Institution Prize Talk: Research and Teaching through high-precision spectroscopy of heavy atoms

NASA Astrophysics Data System (ADS)

Majumder, Tiku

2017-04-01

In recent decades, substantial experimental effort has centered on heavy (high-Z) atomic and molecular systems for atomic-physics-based tests of standard model physics, through (for example) measurements of atomic parity nonconservation and searches for permanent electric dipole moments. In all of this work, a crucial role is played by atomic theorists, whose accurate wave function calculations are essential in connecting experimental observables to tests of relevant fundamental physics parameters. At Williams College, with essential contributions from dozens of undergraduate students, we have pursued a series of precise atomic structure measurements in heavy metal atoms such as thallium, indium, and lead. These include measurements of hyperfine structure, transition amplitudes, and atomic polarizability. This work, involving diode lasers, heated vapor cells, and an atomic beam apparatus, has both tested the accuracy and helped guide the refinement of new atomic theory calculations. I will discuss a number of our recent experimental results, emphasizing the role played by students and the opportunities that have been afforded for research-training in this undergraduate environment. Work supported by Research Corporation, the NIST Precision Measurement Grants program, and the National Science Foundation.

Direct Determination of Atomic Structure and Magnetic Coupling of Magnetite Twin Boundaries.

PubMed

Chen, Chunlin; Li, Hongping; Seki, Takehito; Yin, Deqiang; Sanchez-Santolino, Gabriel; Inoue, Kazutoshi; Shibata, Naoya; Ikuhara, Yuichi

2018-03-27

Clarifying how the atomic structure of interfaces/boundaries in materials affects the magnetic coupling nature across them is of significant academic value and will facilitate the development of state-of-the-art magnetic devices. Here, by combining atomic-resolution transmission electron microscopy, atomistic spin-polarized first-principles calculations, and differential phase contrast imaging, we conduct a systematic investigation of the atomic and electronic structures of individual Fe 3 O 4 twin boundaries (TBs) and determine their concomitant magnetic couplings. We demonstrate that the magnetic coupling across the Fe 3 O 4 TBs can be either antiferromagnetic or ferromagnetic, which directly depends on the TB atomic core structures and resultant electronic structures within a few atomic layers. Revealing the one-to-one correspondence between local atomic structures and magnetic properties of individual grain boundaries will shed light on in-depth understanding of many interesting magnetic behaviors of widely used polycrystalline magnetic materials, which will surely promote the development of advanced magnetic materials and devices.

Atomic Structure

NASA Astrophysics Data System (ADS)

Whelan, Colm T.

2018-04-01

A knowledge of atomic theory should be an essential part of every physicist's and chemist's toolkit. This book provides an introduction to the basic ideas that govern our understanding of microscopic matter, and the essential features of atomic structure and spectra are presented in a direct and easily accessible manner. Semi-classical ideas are reviewed and an introduction to the quantum mechanics of one and two electron systems and their interaction with external electromagnetic fields is featured. Multielectron atoms are also introduced, and the key methods for calculating their properties reviewed.

A discrete search algorithm for finding the structure of protein backbones and side chains.

PubMed

Sallaume, Silas; Martins, Simone de Lima; Ochi, Luiz Satoru; Da Silva, Warley Gramacho; Lavor, Carlile; Liberti, Leo

2013-01-01

Some information about protein structure can be obtained by using Nuclear Magnetic Resonance (NMR) techniques, but they provide only a sparse set of distances between atoms in a protein. The Molecular Distance Geometry Problem (MDGP) consists in determining the three-dimensional structure of a molecule using a set of known distances between some atoms. Recently, a Branch and Prune (BP) algorithm was proposed to calculate the backbone of a protein, based on a discrete formulation for the MDGP. We present an extension of the BP algorithm that can calculate not only the protein backbone, but the whole three-dimensional structure of proteins.

Relativistic atomic structure calculations and electron impact excitations of Fe23+

NASA Astrophysics Data System (ADS)

El-Maaref, A. A.

2016-02-01

Relativistic calculations using the multiconfiguration Dirac-Fock method for energy levels, oscillator strengths, and electronic dipole transition probabilities of Li-like iron (Fe23+) are presented. A configuration state list with the quantum numbers nl, where n = 2 - 7 and l = s , p , d , f , g , h , i has been considered. Excitations up to three electrons and correlation contributions from higher orbitals up to 7 l have been included. Contributions from core levels have been taken into account, EOL (extended optimal level) type calculations have been applied, and doubly excited levels are considered. The calculations have been executed by using the fully relativistic atomic structure package GRASP2K. The present calculations have been compared with the available experimental and theoretical sources, the comparisons show a good agreement between the present results of energy levels and oscillator strengths with the literature. In the second part of the present study, the atomic data (energy levels, and radiative parameters) have been used to calculate the excitation and deexcitation rates of allowed transitions by electron impact, as well as the population densities of some excited levels at different electron temperatures.

Combination of large and small basis sets in electronic structure calculations on large systems

NASA Astrophysics Data System (ADS)

Røeggen, Inge; Gao, Bin

2018-04-01

Two basis sets—a large and a small one—are associated with each nucleus of the system. Each atom has its own separate one-electron basis comprising the large basis set of the atom in question and the small basis sets for the partner atoms in the complex. The perturbed atoms in molecules and solids model is at core of the approach since it allows for the definition of perturbed atoms in a system. It is argued that this basis set approach should be particularly useful for periodic systems. Test calculations are performed on one-dimensional arrays of H and Li atoms. The ground-state energy per atom in the linear H array is determined versus bond length.

First-principles study on the electronic structure and elastic properties of Mo2NiB2 doped with V

NASA Astrophysics Data System (ADS)

Li, Jinming; Li, Xiaobo; Gao, Haiyun; Peng, Dian

2018-04-01

The content of this study is to analyze the electronic structure and elastic properties that the different structures of Mo2NiB2 and doping with V of the tetragonal M3B2 (Mo2Ni1‑xVxB2 and Mo2‑yNi1‑yV2yB2) (x = 0.25, 0.5, 0.75 and y = 0.125, 0.25, 0.375) by first-principles calculations based on density functional theory (DFT) combined with the projection-plus-wave method. But the calculated formation energy shows that V atoms prefer to substitute the Mo and Ni atoms of the tetragonal Mo2NiB2. Moreover, with the increase of V content, the formation enthalpy of tetragonal Mo2NiB2 is reduced, and the formation enthalpy of Mo1.625Ni0.625V0.75B2 is the least as ‑53.23 kJ/mol. The calculated elastic constant suffices the condition of mechanical stability, indicate that they are stable. The calculated elastic modulus illustrates that Mo2NiB2 having better mechanical properties when V elements are at Mo and Ni sites instead of Ni sites. The calculated and analyzed density of states of Mo1.625Ni0.625V0.75B2 has the smallest the density of states at the Fermi level indicating that it has the more stable structure. For the theoretical analysis of the first-principles calculations, the addition of 15 atom% of the V and V doping modes of Mo and Ni are preferentially replaced by V atoms of Mo2NiB2 ternary boride has the best performance.

Unexpected Ground-State Structure and Mechanical Properties of Ir₂Zr Intermetallic Compound.

PubMed

Zhang, Meiguang; Cao, Rui; Zhao, Meijie; Du, Juan; Cheng, Ke

2018-01-10

Using an unbiased structure searching method, a new orthorhombic Cmmm structure consisting of ZrIr 12 polyhedron building blocks is predicted to be the thermodynamic ground-state of stoichiometric intermetallic Ir₂Zr in Ir-Zr systems. The formation enthalpy of the Cmmm structure is considerably lower than that of the previously synthesized Cu₂Mg-type phase, by ~107 meV/atom, as demonstrated by the calculation of formation enthalpy. Meanwhile, the phonon dispersion calculations further confirmed the dynamical stability of Cmmm phase under ambient conditions. The mechanical properties, including elastic stability, rigidity, and incompressibility, as well as the elastic anisotropy of Cmmm -Ir₂Zr intermetallic, have thus been fully determined. It is found that the predicted Cmmm phase exhibits nearly elastic isotropic and great resistance to shear deformations within the (100) crystal plane. Evidence of atomic bonding related to the structural stability for Ir₂Zr were manifested by calculations of the electronic structures.

DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes

PubMed Central

Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil

2011-01-01

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver. PMID:24683424

Polarized atomic orbitals for self-consistent field electronic structure calculations

NASA Astrophysics Data System (ADS)

Lee, Michael S.; Head-Gordon, Martin

1997-12-01

We present a new self-consistent field approach which, given a large "secondary" basis set of atomic orbitals, variationally optimizes molecular orbitals in terms of a small "primary" basis set of distorted atomic orbitals, which are simultaneously optimized. If the primary basis is taken as a minimal basis, the resulting functions are termed polarized atomic orbitals (PAO's) because they are valence (or core) atomic orbitals which have distorted or polarized in an optimal way for their molecular environment. The PAO's derive their flexibility from the fact that they are formed from atom-centered linear-combinations of the larger set of secondary atomic orbitals. The variational conditions satisfied by PAO's are defined, and an iterative method for performing a PAO-SCF calculation is introduced. We compare the PAO-SCF approach against full SCF calculations for the energies, dipoles, and molecular geometries of various molecules. The PAO's are potentially useful for studying large systems that are currently intractable with larger than minimal basis sets, as well as offering potential interpretative benefits relative to calculations in extended basis sets.

Influence of tool shape on lattice rearrangement under loading conditions reproducing friction stir welding

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

Konovalenko, Ivan S., E-mail: ivkon@ispms.tsc.ru; Konovalenko, Igor S., E-mail: igkon@ispms.tsc.ru; National Research Tomsk Polytechnic University, Tomsk, 634050

2015-10-27

Metal behavior under loading conditions that reproduce friction stir welding was studied on the atomic scale. Calculations were conducted based on molecular dynamics simulation with potentials calculated within the embedded atom method. The loading of the interface between two crystallites, whose structure corresponded to aluminum alloy 2024, was simulated by the motion of a cone-shaped tool along the interface with constant angular and translational velocities. The motion of the rotating tool causes fracture of the workpiece crystal structure with subsequent mixing of surface atoms of the interfacing crystallites. It is shown that the resistance force acting on the moving toolmore » from the workpiece and the process of structural defect formation in the workpiece depend on the tool shape.« less

Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

DOE PAGES

Holby, Edward F.; Taylor, Christopher D.

2015-03-19

We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH boundmore » structures have the highest calculated activity to date.« less

NNDC Tools and Publications

Science.gov Websites

Site Index NNDC Tools and Publications Nuclear Structure and Decay Tools Nuclear Reaction Tools Nuclear Structure and Decay Tools 2016 Atomic Mass Evaluation Atomic mass evaluation, by Wang, Audi values as a function of gamma energy and multipolarity. Calculations based on I.M. Band and S. Raman

Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

PubMed

Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

2013-04-01

When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.

Structures and stability of metal-doped Ge nM (n = 9, 10) clusters

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

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua

The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge 9 and Ge 10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge n clusters. However, the neutral and cationic FeGe 9,10,MnGe 9,10 and Ge 10Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge n clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge 9,10Fe and Ge 9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Structures and stability of metal-doped Ge nM (n = 9, 10) clusters

DOE PAGES

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; ...

2015-06-26

The lowest-energy structures of neutral and cationic Ge nM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge 9 and Ge 10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge n clusters. However, the neutral and cationic FeGe 9,10,MnGe 9,10 and Ge 10Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge n clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge 9,10Fe and Ge 9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

First-principles calculations of K-shell X-ray absorption spectra for warm dense nitrogen

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

Li, Zi; Zhang, Shen; Kang, Wei

2016-05-15

X-ray absorption spectrum is a powerful tool for atomic structure detection on warm dense matter. Here, we perform first-principles molecular dynamics and X-ray absorption spectrum calculations on warm dense nitrogen along a Hugoniot curve. From the molecular dynamics trajectory, the detailed atomic structures are examined for each thermodynamical condition. The K-shell X-ray absorption spectrum is calculated, and its changes with temperature and pressure along the Hugoniot curve are discussed. The warm dense nitrogen systems may contain isolated nitrogen atoms, N{sub 2} molecules, and nitrogen clusters, which show quite different contributions to the total X-ray spectrum due to their different electronmore » density of states. The changes of X-ray spectrum along the Hugoniot curve are caused by the different nitrogen structures induced by the temperature and the pressure. Some clear signatures on X-ray spectrum for different thermodynamical conditions are pointed out, which may provide useful data for future X-ray experiments.« less

Structures and stability of metal-doped GenM (n = 9, 10) clusters

NASA Astrophysics Data System (ADS)

Qin, Wei; Lu, Wen-Cai; Xia, Lin-Hua; Zhao, Li-Zhen; Zang, Qing-Jun; Wang, C. Z.; Ho, K. M.

2015-06-01

The lowest-energy structures of neutral and cationic GenM (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge9 and Ge10 clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Gen clusters. However, the neutral and cationic FeGe9,10,MnGe9,10 and Ge10Al are cage-like with the metal atom encapsulated inside. Such cage-like transition metal doped Gen clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge9,10Fe and Ge9Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.

Structure and functionality of bromine doped graphite.

PubMed

Hamdan, Rashid; Kemper, A F; Cao, Chao; Cheng, H P

2013-04-28

First-principles calculations are used to study the enhanced in-plane conductivity observed experimentally in Br-doped graphite, and to study the effect of external stress on the structure and functionality of such systems. The model used in the numerical calculations is that of stage two doped graphite. The band structure near the Fermi surface of the doped systems with different bromine concentrations is compared to that of pure graphite, and the charge transfer between carbon and bromine atoms is analyzed to understand the conductivity change along different high symmetry directions. Our calculations show that, for large interlayer separation between doped graphite layers, bromine is stable in the molecular form (Br2). However, with increased compression (decreased layer-layer separation) Br2 molecules tend to dissociate. While in both forms, bromine is an electron acceptor. The charge exchange between the graphite layers and Br atoms is higher than that with Br2 molecules. Electron transfer to the Br atoms increases the number of hole carriers in the graphite sheets, resulting in an increase of conductivity.

Nuclear magnetic and nuclear quadrupole resonance parameters of β-carboline derivatives calculated using density functional theory

NASA Astrophysics Data System (ADS)

Ahmadinejad, Neda; Tari, Mostafa Talebi

2017-04-01

A density functional theory (DFT) calculations using B3LYP/6-311++G( d,p) method were carried out to investigate the relative stability of the molecules of β-carboline derivatives such as harmaline, harmine, harmalol, harmane and norharmane. Calculated nuclear quadrupole resonance (NQR) parameters were used to determine the 14N nuclear quadrupole coupling constant χ, asymmetry parameter η and EFG tensor ( q zz ). For better understanding of the electronic structure of β-carboline derivatives, natural bond orbital (NBO) analysis, isotropic and anisotropic NMR chemical shieldings were calculated for 14N nuclei using GIAO method for the optimized structures. The NBO analysis shows that pyrrole ring nitrogen (N9) atom has greater tendency than pyridine ring nitrogen (N2) atom to participate in resonance interactions and aromaticity development in the all of these structures. The NMR and NQR parameters were studied in order to find the correlations between electronic structure and the structural stability of the studied molecules.

First-principles investigation of graphitic carbon nitride monolayer with embedded Fe atom

NASA Astrophysics Data System (ADS)

Abdullahi, Yusuf Zuntu; Yoon, Tiem Leong; Halim, Mohd Mahadi; Hashim, Md. Roslan; Lim, Thong Leng

2018-01-01

Density-functional theory (DFT) calculations with spin-polarized generalized gradient approximation and Hubbard U correction are carried out to investigate the mechanical, structural, electronic and magnetic properties of graphitic heptazine with embedded Fe atom under bi-axial tensile strain and applied perpendicular electric field. It was found that the binding energy of heptazine with embedded Fe atom system decreases as larger tensile strain is applied, while it increases as larger electric field strength is applied. Our calculations also predict a band gap at a peak value of 5% tensile strain but at expense of the structural stability of the system. The band gap open up at 5% tensile strain is due to distortion in the structure caused by the repulsive effect in the cavity between the lone pairs of the edge nitrogen atoms and dxy /dx2 -y2 orbital of Fe atom, forcing the unoccupied pz- orbital is forced to shift toward higher energy. The electronic and magnetic properties of the heptazine with embedded Fe system under perpendicular electric field up to a peak value of 8 V/nm is also well preserved despite an obvious buckled structure. Such properties are desirable for diluted magnetic semiconductors, spintronics, and sensing devices.

Structural, electronic and magnetic properties of chevron-type graphene, BN and BC{sub 2}N nanoribbons

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

Guerra, T.; Azevedo, S.; Kaschny, J.R.

2017-04-15

Graphene nanoribbons are predicted to be essential components in future nanoelectronics. The size, edge type, arrangement of atoms and width of nanoribbons drastically change their properties. Boronnitrogencarbon nanoribbons properties are not fully understood so far. In the present contribution it was investigated the structural, electronic and magnetic properties of chevron-type carbon, boron nitride and BC{sub 2}N nanoribbons, using first-principles calculations. The results indicate that the structural stability is closely related to the discrepancies in the bond lengths, which can induce structural deformations and stress. Such nanoribbons present a wide range of electronic behaviors, depending on their composition and particularities ofmore » the atomic arrangement. A net magnetic moment is found for structures that present carbon atoms at the nanoribbon borders. Nevertheless, the calculated magnetic moment depends on the peculiarities of the symmetric arrangement of atoms and imbalance of carbon atoms between different sublattices. It was found that all structures which have a significant energy gap do not present magnetic moment, and vice-versa. Such result indicates the strong correlation between the electronic and magnetic properties of the chevron-type nanoribbons. - Highlights: • Small discrepancies between distinct bond lengths can influence the formation energy of the BC{sub 2}N nanoribbons. • The electronic behavior of the BC{sub 2}N chevron-type nanoribbons depends on the atomic arrangement and structural symmetries. • There is a strong correlation between the electronic and magnetic properties for the BC{sub 2}N structures.« less

Lattice structures and electronic properties of MO/MoSe2 interface from first-principles calculations

NASA Astrophysics Data System (ADS)

Zhang, Yu; Tang, Fu-Ling; Xue, Hong-Tao; Lu, Wen-Jiang; Liu, Jiang-Fei; Huang, Min

2015-02-01

Using first-principles plane-wave calculations within density functional theory, we theoretically studied the atomic structure, bonding energy and electronic properties of the perfect Mo (110)/MoSe2 (100) interface with a lattice mismatch less than 4.2%. Compared with the perfect structure, the interface is somewhat relaxed, and its atomic positions and bond lengths change slightly. The calculated interface bonding energy is about -1.2 J/m2, indicating that this interface is very stable. The MoSe2 layer on the interface has some interface states near the Fermi level, the interface states are mainly caused by Mo 4d orbitals, while the Se atom almost have no contribution. On the interface, Mo-5s and Se-4p orbitals hybridize at about -6.5 to -5.0 eV, and Mo-4d and Se-4p orbitals hybridize at about -5.0 to -1.0 eV. These hybridizations greatly improve the bonding ability of Mo and Se atom in the interface. By Bader charge analysis, we find electron redistribution near the interface which promotes the bonding of the Mo and MoSe2 layer.

Transition metal atoms absorbed on MoS2/h-BN heterostructure: stable geometries, band structures and magnetic properties.

PubMed

Wu, Yanbing; Huang, Zongyu; Liu, Huating; He, Chaoyu; Xue, Lin; Qi, Xiang; Zhong, Jianxin

2018-06-15

We have studied the stable geometries, band structures and magnetic properties of transition-metal (V, Cr, Mn, Fe, Co and Ni) atoms absorbed on MoS2/h-BN heterostructure systems by first-principles calculations. By comparing the adsorption energies, we find that the adsorbed transition metal (TM) atoms prefer to stay on the top of Mo atoms. The results of the band structure without spin-orbit coupling (SOC) interaction indicate that the Cr-absorbed systems behave in a similar manner to metals, and the Co-absorbed system exhibits a half-metallic state. We also deduce that the V-, Mn-, Fe-absorbed systems are semiconductors with 100% spin polarization at the HOMO level. The Ni-absorbed system is a nonmagnetic semiconductor. In contrast, the Co-absorbed system exhibits metallic state, and the bandgap of V-absorbed system decreases slightly according to the SOC calculations. In addition, the magnetic moments of all the six TM atoms absorbed on the MoS2/h-BN heterostructure systems decrease when compared with those of their free-standing states.

Structure and property of metal melt I: The number of residual bonds after solid-liquid phase changes

NASA Astrophysics Data System (ADS)

Mi, Guangbao; Li, Peijie; He, Liangju

2010-09-01

Based on the mechanism of metal solid-liquid phase change and the theory of liquid metal’s micro-inhomogeneity, a physical model is established between latent heats of fusion and vaporization and the numbers of residual bonds and short-range ordered atoms at the melting point inside a metal melt. Meanwhile, the mathematical derivation and proof are also offered. This model produces the numbers of residual bonds and short-range ordered atoms after the solid-liquid phase change only by using basic parameters and thermophysical properties of the crystal structure. Therefore, it presents a more effective way to analyze the melt’s structural information. By using this model, this study calculates the numbers of residual bonds and short-range ordered atoms in Al and Ni melts. The calculated results are consistent with the experimental results. Simultaneously, this study discusses the atomic number’s influence on the numbers of residual bonds and short-range ordered atoms in the melts within the first (IA) and second main group (IIA) elements.

Structure and stability of molybdenum sulfide fullerenes.

PubMed

Bar-Sadan, M; Enyashin, A N; Gemming, S; Popovitz-Biro, R; Hong, S Y; Prior, Yehiam; Tenne, R; Seifert, G

2006-12-21

MoS2 nanooctahedra are believed to be the smallest stable closed-cage structures of MoS2, i.e., the genuine inorganic fullerenes. Here a combination of experiments and density functional tight binding calculations with molecular dynamics annealing are used to elucidate the structures and electronic properties of octahedral MoS2 fullerenes. Through the use of these calculations MoS2 octahedra were found to be stable beyond nMo > 100 but with the loss of 12 sulfur atoms in the six corners. In contrast to bulk and nanotubular MoS2, which are semiconductors, the Fermi level of the nanooctahedra is situated within the band, thus making them metallic-like. A model is used for extending the calculations to much larger sizes. These model calculations show that, in agreement with experiment, the multiwall nanooctahedra are stable over a limited size range of 104-105 atoms, whereupon they are converted into multiwall MoS2 nanoparticles with a quasi-spherical shape. On the experimental side, targets of MoS2 and MoSe2 were laser-ablated and analyzed mostly through transmission electron microscopy. This analysis shows that, in qualitative agreement with the theoretical analysis, multilayer nanooctahedra of MoS2 with 1000-25 000 atoms (Mo + S) are stable. Furthermore, this and previous work show that beyond approximately 105 atoms fullerene-like structures with quasi-spherical forms and 30-100 layers become stable. Laser-ablated WS2 samples yielded much less faceted and sometimes spherically symmetric nanocages.

The Electronic Structure and Optical Properties of Anatase TiO₂ with Rare Earth Metal Dopants from First-Principles Calculations.

PubMed

Xie, Kefeng; Jia, Qiangqiang; Wang, Yizhe; Zhang, Wenxue; Xu, Jingcheng

2018-01-24

The electronic and optical properties of the rare earth metal atom-doped anatase TiO₂ have been investigated systematically via density functional theory calculations. The results show that TiO₂ doped by Ce or Pr is the optimal choice because of its small band gap and strong optical absorption. Rare earth metal atom doping induces several impurity states that tune the location of valence and conduction bands and an obvious lattice distortion that should reduce the probability of electron-hole recombination. This effect of band change originates from the 4 f electrons of the rare earth metal atoms, which leads to an improved visible light absorption. This finding indicates that the electronic structure of anatase TiO₂ is tuned by the introduction of impurity atoms.

The Electronic Structure and Optical Properties of Anatase TiO2 with Rare Earth Metal Dopants from First-Principles Calculations

PubMed Central

Xie, Kefeng; Jia, Qiangqiang; Wang, Yizhe; Zhang, Wenxue; Xu, Jingcheng

2018-01-01

The electronic and optical properties of the rare earth metal atom-doped anatase TiO2 have been investigated systematically via density functional theory calculations. The results show that TiO2 doped by Ce or Pr is the optimal choice because of its small band gap and strong optical absorption. Rare earth metal atom doping induces several impurity states that tune the location of valence and conduction bands and an obvious lattice distortion that should reduce the probability of electron–hole recombination. This effect of band change originates from the 4f electrons of the rare earth metal atoms, which leads to an improved visible light absorption. This finding indicates that the electronic structure of anatase TiO2 is tuned by the introduction of impurity atoms. PMID:29364161

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

NASA Astrophysics Data System (ADS)

Brela, Mateusz Z.; Boczar, Marek; Malec, Leszek M.; Wójcik, Marek J.; Nakajima, Takahito

2018-05-01

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

The calculation of molecular Eigen-frequencies

NASA Technical Reports Server (NTRS)

Lindemann, F. A.

1984-01-01

A method of determining molecular eigen-frequencies based on the function of Einstein expressing the variation of the atomic heat of various elements is proposed. It is shown that the same equation can be utilized to calculate both atomic heat and optically identifiably eigen-frequencies - at least to an order of magnitude - suggesting that in both cases the same oscillating structure is responsible.

Virtual interface substructure synthesis method for normal mode analysis of super-large molecular complexes at atomic resolution.

PubMed

Chen, Xuehui; Sun, Yunxiang; An, Xiongbo; Ming, Dengming

2011-10-14

Normal mode analysis of large biomolecular complexes at atomic resolution remains challenging in computational structure biology due to the requirement of large amount of memory space and central processing unit time. In this paper, we present a method called virtual interface substructure synthesis method or VISSM to calculate approximate normal modes of large biomolecular complexes at atomic resolution. VISSM introduces the subunit interfaces as independent substructures that join contacting molecules so as to keep the integrity of the system. Compared with other approximate methods, VISSM delivers atomic modes with no need of a coarse-graining-then-projection procedure. The method was examined for 54 protein-complexes with the conventional all-atom normal mode analysis using CHARMM simulation program and the overlap of the first 100 low-frequency modes is greater than 0.7 for 49 complexes, indicating its accuracy and reliability. We then applied VISSM to the satellite panicum mosaic virus (SPMV, 78,300 atoms) and to F-actin filament structures of up to 39-mer, 228,813 atoms and found that VISSM calculations capture functionally important conformational changes accessible to these structures at atomic resolution. Our results support the idea that the dynamics of a large biomolecular complex might be understood based on the motions of its component subunits and the way in which subunits bind one another. © 2011 American Institute of Physics

Ab initio effective core potentials including relativistic effects and their application to the electronic structure calculations of heavy atoms and molecules

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

Lee, Y.S.

1977-11-01

The effects of the 4f shell of electrons and the relativity of valence electrons are compared. The effect of 4f shell (lanthanide contraction) is estimated from the numerical Hartree-Fock (HF) calculations of pseudo-atoms corresponding to Hf, Re, Au, Hg, Tl, Pb and Bi without 4f electrons and with atomic numbers reduced by 14. The relativistic effect estimated from the numerical Dirac-Hartree-Fock (DHF) calculations of those atoms is comparable in the magnitude with that of the 4f shell of electrons. Both are larger for 6s than for 5d or 6p electrons. The various relativistic effects on valence electrons are discussed inmore » detail to determine the proper level of the approximation for the valence electron calculations of systems with heavy elements. An effective core potential system has been developed for heavy atoms in which relativistic effects are included in the effective potentials.« less

Structure of a zinc oxide ultra-thin film on Rh(100)

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

Yuhara, J.; Kato, D.; Matsui, T.

The structural parameters of ultra-thin zinc oxide films on Rh(100) are investigated using low-energy electron diffraction intensity (LEED I–V) curves, scanning tunneling microscopy (STM), and first-principles density functional theory (DFT) calculations. From the analysis of LEED I–V curves and DFT calculations, two optimized models A and B are determined. Their structures are basically similar to the planer h-BN ZnO(0001) structure, although some oxygen atoms protrude from the surface, associated with an in-plane shift of Zn atoms. From a comparison of experimental STM images and simulated STM images, majority and minority structures observed in the STM images represent the two optimizedmore » models A and B, respectively.« less

A New Generation of Los Alamos Opacity Tables

DOE PAGES

Colgan, James Patrick; Kilcrease, David Parker; Magee, Jr., Norman H.; ...

2016-01-26

We present a new, publicly available, set of Los Alamos OPLIB opacity tables for the elements hydrogen through zinc. Our tables are computed using the Los Alamos ATOMIC opacity and plasma modeling code, and make use of atomic structure calculations that use fine-structure detail for all the elements considered. Our equation-of-state (EOS) model, known as ChemEOS, is based on the minimization of free energy in a chemical picture and appears to be a reasonable and robust approach to determining atomic state populations over a wide range of temperatures and densities. In this paper we discuss in detail the calculations thatmore » we have performed for the 30 elements considered, and present some comparisons of our monochromatic opacities with measurements and other opacity codes. We also use our new opacity tables in solar modeling calculations and compare and contrast such modeling with previous work.« less

Atomic structure data based on average-atom model for opacity calculations in astrophysical plasmas

NASA Astrophysics Data System (ADS)

Trzhaskovskaya, M. B.; Nikulin, V. K.

2018-03-01

Influence of the plasmas parameters on the electron structure of ions in astrophysical plasmas is studied on the basis of the average-atom model in the local thermodynamic equilibrium approximation. The relativistic Dirac-Slater method is used for the electron density estimation. The emphasis is on the investigation of an impact of the plasmas temperature and density on the ionization stages required for calculations of the plasmas opacities. The level population distributions and level energy spectra are calculated and analyzed for all ions with 6 ≤ Z ≤ 32 occurring in astrophysical plasmas. The plasma temperature range 2 - 200 eV and the density range 2 - 100 mg/cm3 are considered. The validity of the method used is supported by good agreement between our values of ionization stages for a number of ions, from oxygen up to uranium, and results obtained earlier by various methods among which are more complicated procedures.

Si(111) strained layers on Ge(111): Evidence for c (2 ×4 ) domains

NASA Astrophysics Data System (ADS)

Zhachuk, R.; Coutinho, J.; Dolbak, A.; Cherepanov, V.; Voigtländer, B.

2017-08-01

The tensile-strained Si (111 ) layers grown on top of Ge (111 ) substrates are studied by combining scanning tunneling microscopy, low-energy electron diffraction, and first-principles calculations. It is shown that the layers exhibit c (2 ×4 ) domains, which are separated by domain walls along <1 ¯10 > directions. A model structure for the c (2 ×4 ) domains is proposed, which shows low formation energy and good agreement with the experimental data. The results of our calculations suggest that Ge atoms are likely to replace Si atoms with dangling bonds on the surface (rest-atoms and adatoms), thus significantly lowering the surface energy and inducing the formation of domain walls. The experiments and calculations demonstrate that when surface strain changes from compressive to tensile, the (111) reconstruction converts from dimer-adatom-stacking fault-based to adatom-based structures.

Dirac R -matrix calculations for the electron-impact excitation of neutral tungsten providing noninvasive diagnostics for magnetic confinement fusion

NASA Astrophysics Data System (ADS)

Smyth, R. T.; Ballance, C. P.; Ramsbottom, C. A.; Johnson, C. A.; Ennis, D. A.; Loch, S. D.

2018-05-01

Neutral tungsten is the primary candidate as a wall material in the divertor region of the International Thermonuclear Experimental Reactor (ITER). The efficient operation of ITER depends heavily on precise atomic physics calculations for the determination of reliable erosion diagnostics, helping to characterize the influx of tungsten impurities into the core plasma. The following paper presents detailed calculations of the atomic structure of neutral tungsten using the multiconfigurational Dirac-Fock method, drawing comparisons with experimental measurements where available, and includes a critical assessment of existing atomic structure data. We investigate the electron-impact excitation of neutral tungsten using the Dirac R -matrix method, and by employing collisional-radiative models, we benchmark our results with recent Compact Toroidal Hybrid measurements. The resulting comparisons highlight alternative diagnostic lines to the widely used 400.88-nm line.

Influences of S, Se, Te and Po substitutions on structural, electronic and optical properties of hexagonal CuAlO2 using GGA and B3LYP functionals.

PubMed

Liu, Qi-Jun; Jiao, Zhen; Liu, Fu-Sheng; Liu, Zheng-Tang

2016-06-07

The effects of X-doping (X = S, Se, Te and Po) on the structural, electronic and optical properties of hexagonal CuAlO2 were studied using first-principles density functional theory. The calculated results showed the obtained lattice constants to increase with increasing atomic number, and the X-doping to be energetically more favorable under Al-rich conditions. The calculated electronic properties showed decreased bandgaps with increasing atomic number, which was due to the better covalent hybridizations after sulfuration doping. The enhanced covalency was further confirmed by calculating the Mulliken atomic populations and bond populations. The density of states indicated the increase of the contribution to antibonding from the X-p states to be a benefit for p-type conductivity. Moreover, the X-doping induced a red shift of the absorption edge.

Interactions of atomic hydrogen with amorphous SiO2

NASA Astrophysics Data System (ADS)

Yue, Yunliang; Wang, Jianwei; Zhang, Yuqi; Song, Yu; Zuo, Xu

2018-03-01

Dozens of models are investigated by the first-principles calculations to simulate the interactions of an atomic hydrogen with a defect-free random network of amorphous SiO2 (a-SiO2) and oxygen vacancies. A wide variety of stable configurations are discovered due to the disorder of a-SiO2, and their structures, charges, magnetic moments, spin densities, and density of states are calculated. The atomic hydrogen interacts with the defect-free a-SiO2 in positively or negatively charged state, and produces the structures absent in crystalline SiO2. It passivates the neutral oxygen vacancies and generates two neutral hydrogenated E‧ centers with different Si dangling bond projections. Electron spin resonance parameters, including Fermi contacts, and g-tensors, are calculated for these centers. The atomic hydrogen interacts with the positive oxygen vacancies in dimer configuration, and generate four different positive hydrogenated defects, two of which are puckered like the Eγ‧ centers. This research helps to understand the interactions between an atomic hydrogen, and defect-free a-SiO2 and oxygen vacancies, which may generate the hydrogen-complexed defects that play a key role in the degeneration of silicon/silica-based microelectronic devices.

Atomic approximation to the projection on electronic states in the Douglas-Kroll-Hess approach to the relativistic Kohn-Sham method.

PubMed

Matveev, Alexei V; Rösch, Notker

2008-06-28

We suggest an approximate relativistic model for economical all-electron calculations on molecular systems that exploits an atomic ansatz for the relativistic projection transformation. With such a choice, the projection transformation matrix is by definition both transferable and independent of the geometry. The formulation is flexible with regard to the level at which the projection transformation is approximated; we employ the free-particle Foldy-Wouthuysen and the second-order Douglas-Kroll-Hess variants. The (atomic) infinite-order decoupling scheme shows little effect on structural parameters in scalar-relativistic calculations; also, the use of a screened nuclear potential in the definition of the projection transformation shows hardly any effect in the context of the present work. Applications to structural and energetic parameters of various systems (diatomics AuH, AuCl, and Au(2), two structural isomers of Ir(4), and uranyl dication UO(2) (2+) solvated by 3-6 water ligands) show that the atomic approximation to the conventional second-order Douglas-Kroll-Hess projection (ADKH) transformation yields highly accurate results at substantial computational savings, in particular, when calculating energy derivatives of larger systems. The size-dependence of the intrinsic error of the ADKH method in extended systems of heavy elements is analyzed for the atomization energies of Pd(n) clusters (n

Exploring unimolecular dissociation kinetics of ethyl dibromide through electronic structure calculations

NASA Astrophysics Data System (ADS)

Gulvi, Nitin R.; Patel, Priyanka; Badani, Purav M.

2018-04-01

Pathway for dissociation of multihalogenated alkyls is observed to be competitive between molecular and atomic elimination products. Factors such as molecular structure, temperature and pressure are known to influence the same. Hence present work is focussed to explore mechanism and kinetics of atomic (Br) and molecular (HBr and Br2) elimination upon pyrolysis of 1,1- and 1,2-ethyl dibromide (EDB). For this purpose, electronic structure calculations were performed at DFT and CCSD(T) level of theory. In addition to concerted mechanism, an alternate energetically efficient isomerisation pathway has been exploited for molecular elimination. Energy calculations are further complimented by detailed kinetic investigation, over wide range of temperature and pressure, using suitable models like Canonical Transition State Theory, Statistical Adiabatic Channel Model and Troe's formalism. Our calculations suggest high branching ratio for dehydrohalogentation reaction, from both isomers of EDB. Fall off curve depicts good agreement between theoretically estimated and experimentally reported values.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

NASA Astrophysics Data System (ADS)

Kim, Jeongnim; Baczewski, Andrew D.; Beaudet, Todd D.; Benali, Anouar; Chandler Bennett, M.; Berrill, Mark A.; Blunt, Nick S.; Josué Landinez Borda, Edgar; Casula, Michele; Ceperley, David M.; Chiesa, Simone; Clark, Bryan K.; Clay, Raymond C., III; Delaney, Kris T.; Dewing, Mark; Esler, Kenneth P.; Hao, Hongxia; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M. Graham; Luo, Ye; Malone, Fionn D.; Martin, Richard M.; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Parker, William D.; Pineda Flores, Sergio D.; Romero, Nichols A.; Rubenstein, Brenda M.; Shea, Jacqueline A. R.; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F.; Townsend, Joshua P.; Tubman, Norm M.; Van Der Goetz, Brett; Vincent, Jordan E.; ChangMo Yang, D.; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-01

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

PubMed

Kim, Jeongnim; Baczewski, Andrew T; Beaudet, Todd D; Benali, Anouar; Bennett, M Chandler; Berrill, Mark A; Blunt, Nick S; Borda, Edgar Josué Landinez; Casula, Michele; Ceperley, David M; Chiesa, Simone; Clark, Bryan K; Clay, Raymond C; Delaney, Kris T; Dewing, Mark; Esler, Kenneth P; Hao, Hongxia; Heinonen, Olle; Kent, Paul R C; Krogel, Jaron T; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M Graham; Luo, Ye; Malone, Fionn D; Martin, Richard M; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A; Mitas, Lubos; Morales, Miguel A; Neuscamman, Eric; Parker, William D; Pineda Flores, Sergio D; Romero, Nichols A; Rubenstein, Brenda M; Shea, Jacqueline A R; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F; Townsend, Joshua P; Tubman, Norm M; Van Der Goetz, Brett; Vincent, Jordan E; Yang, D ChangMo; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-16

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

QEDMOD: Fortran program for calculating the model Lamb-shift operator

NASA Astrophysics Data System (ADS)

Shabaev, V. M.; Tupitsyn, I. I.; Yerokhin, V. A.

2018-02-01

We present Fortran package QEDMOD for computing the model QED operator hQED that can be used to account for the Lamb shift in accurate atomic-structure calculations. The package routines calculate the matrix elements of hQED with the user-specified one-electron wave functions. The operator can be used to calculate Lamb shift in many-electron atomic systems with a typical accuracy of few percent, either by evaluating the matrix element of hQED with the many-electron wave function, or by adding hQED to the Dirac-Coulomb-Breit Hamiltonian.

First principles calculations for interaction of tyrosine with (ZnO)3 cluster

NASA Astrophysics Data System (ADS)

Singh, Satvinder; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

2018-04-01

First Principles Calculations have been performed to study interactions of Phenol ring of Tyrosine (C6H5OH) with (ZnO)3 atomic cluster. All the calculations have been performed under the Density Functional Theory (DFT) framework. Structural and electronic properties of (ZnO)3/C6H5OH have been studied. Gaussian basis set approach has been adopted for the calculations. A ring type most stable (ZnO)3 atomic cluster has been modeled, analyzed and used for the calculations. The compatibility of the results with previous studies has been presented here.

In and Si adatoms on Si(111)5×2-Au : Scanning tunneling microscopy and first-principles density functional calculations

NASA Astrophysics Data System (ADS)

Stępniak, A.; Nita, P.; Krawiec, M.; Jałochowski, M.

2009-09-01

Structural properties of monatomic indium chains on Si(111)5×2-Au surface are investigated by scanning tunneling microscopy (STM) and first-principles density functional calculations (DFT). The STM topography data show that submonolayer coverage of indium leads to a well-ordered chain structure with the same periodicity as the Si adatoms form on Si(111)5×2-Au surface. Bias-dependent STM topography and spectroscopy reveal two different mechanisms of In-atoms adsorption on the surface: bonding to Si adatoms and substitution for Si atoms in the adatom positions. Those mechanisms are further corroborated by DFT calculations. The obtained structural model of In-modified Si(111)5×2-Au surface remains in good agreement with the experimental data.

Study of Structure and Deformation Pathways in Ti-7Al Using Atomistic Simulations, Experiments, and Characterization

NASA Astrophysics Data System (ADS)

Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.

2017-05-01

Ti-7Al is a good model material for mimicking the α phase response of near- α and α+ β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.

Electronic and magnetic properties of small rhodium clusters

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

Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

We report a theoretical study of the electronic and magnetic properties of rhodium-atomic clusters. The lowest energy structures at the semi-empirical level of rhodium clusters are first obtained from a novel global-minimum search algorithm, known as PTMBHGA, where Gupta potential is used to describe the atomic interaction among the rhodium atoms. The structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof generalized gradient approximation. For the purpose of calculating the magnetic moment of a given cluster, we calculate the optimized structure as a function of the spin multiplicity within the DFT framework.more » The resultant magnetic moments with the lowest energies so obtained allow us to work out the magnetic moment as a function of cluster size. Rhodium atomic clusters are found to display a unique variation in the magnetic moment as the cluster size varies. However, Rh{sub 4} and Rh{sub 6} are found to be nonmagnetic. Electronic structures of the magnetic ground-state structures are also investigated within the DFT framework. The results are compared against those based on different theoretical approaches available in the literature.« less

Spatial structure and electronic spectrum of TiSi{/n -} clusters ( n = 6-18)

NASA Astrophysics Data System (ADS)

Borshch, N. A.; Pereslavtseva, N. S.; Kurganskii, S. I.

2014-10-01

Results from optimizing the spatial structure and calculated electronic spectra of anion clusters TiSi{/n -} ( n = 6-18) are presented. Calculations are performed within the density functional theory. Spatial structures of clusters detected experimentally are established by comparing the calculated and experimental data. It is shown that prismatic and fullerene-like structures are the ones most energetically favorable for clusters TiSi{/n -}. It is concluded that these structures are basic when building clusters with close numbers of silicon atoms.

Proximity-induced magnetism in transition-metal substituted graphene

PubMed Central

Crook, Charles B.; Constantin, Costel; Ahmed, Towfiq; Zhu, Jian-Xin; Balatsky, Alexander V.; Haraldsen, Jason T.

2015-01-01

We investigate the interactions between two identical magnetic impurities substituted into a graphene superlattice. Using a first-principles approach, we calculate the electronic and magnetic properties for transition-metal substituted graphene systems with varying spatial separation. These calculations are compared for three different magnetic impurities, manganese, chromium, and vanadium. We determine the electronic band structure, density of states, and Millikan populations (magnetic moment) for each atom, as well as calculate the exchange parameter between the two magnetic atoms as a function of spatial separation. We find that the presence of magnetic impurities establishes a distinct magnetic moment in the graphene lattice, where the interactions are highly dependent on the spatial and magnetic characteristic between the magnetic and carbon atoms, which leads to either ferromagnetic or antiferromagnetic behavior. Furthermore, through an analysis of the calculated exchange energies and partial density of states, it is determined that interactions between the magnetic atoms can be classified as an RKKY interaction. PMID:26235646

QM/MM hybrid calculation of biological macromolecules using a new interface program connecting QM and MM engines

NASA Astrophysics Data System (ADS)

Hagiwara, Yohsuke; Ohta, Takehiro; Tateno, Masaru

2009-02-01

An interface program connecting a quantum mechanics (QM) calculation engine, GAMESS, and a molecular mechanics (MM) calculation engine, AMBER, has been developed for QM/MM hybrid calculations. A protein-DNA complex is used as a test system to investigate the following two types of QM/MM schemes. In a 'subtractive' scheme, electrostatic interactions between QM/MM regions are truncated in QM calculations; in an 'additive' scheme, long-range electrostatic interactions within a cut-off distance from QM regions are introduced into one-electron integration terms of a QM Hamiltonian. In these calculations, 338 atoms are assigned as QM atoms using Hartree-Fock (HF)/density functional theory (DFT) hybrid all-electron calculations. By comparing the results of the additive and subtractive schemes, it is found that electronic structures are perturbed significantly by the introduction of MM partial charges surrounding QM regions, suggesting that biological processes occurring in functional sites are modulated by the surrounding structures. This also indicates that the effects of long-range electrostatic interactions involved in the QM Hamiltonian are crucial for accurate descriptions of electronic structures of biological macromolecules.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

NASA Astrophysics Data System (ADS)

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-01

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

PubMed

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-07

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Low Resolution Refinement of Atomic Models Against Crystallographic Data.

PubMed

Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N

2017-01-01

This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, ProSMART and LORESTR, which are available as part of the CCP4 software suite.

Minima in generalized oscillator strengths for initially excited hydrogen-like atoms

NASA Technical Reports Server (NTRS)

Matsuzawa, M.; Omidvar, K.; Inokuti, M.

1976-01-01

Generalized oscillator strengths for transitions from an initially excited state of a hydrogenic atom to final states (either discrete or continuum) have complicated structures, including minima and shoulders, as functions of the momentum transfer. Extensive calculations carried out in the present work have revealed certain systematics of these structures. Some implications of the minima to the energy dependence of the inner-shell ionization cross section of heavy atoms by proton impact are discussed.

Electronic theoretical study of the influences of O adsorption on the electronic structure and optical properties of graphene

NASA Astrophysics Data System (ADS)

Shuang, Zhou; Guili, Liu; Dazhi, Fan

2017-02-01

The electronic structure and optical properties of adsorbing O atoms on graphene with different O coverage are researched using the density functional theory based upon the first-principle study to obtain further insight into properties of graphene. The adsorption energies, band structures, the density of states, light absorption coefficient and reflectivity of each system are calculated theoretically after optimizing structures of each system with different O coverage. Our calculations show that adsorption of O atoms on graphene increases the bond length of C-C which adjacent to the O atoms. When the O coverage is 9.4%, the adsorption energy (3.91 eV) is the maximum, which only increases about 1.6% higher than that of 3.1% O coverage. We find that adsorbed O atoms on pristine graphene opens up indirect gap of about 0.493-0.952 eV. Adsorbing O atoms make pristine graphene from metal into a semiconductor. When the O coverage is 9.4%, the band gap (0.952 eV) is the maximum. Comparing with pristine graphene, we find the density of states at Fermi level of O atoms adsorbing on graphene with different coverage are significantly increased. We also find that light absorption coefficient and reflectivity peaks are significantly reduced, and the larger the coverage, the smaller the absorption coefficient and reflectivity peaks are. And the blue shift phenomenon appears.

Bonding in Heavier Group 14 Zero-Valent Complexes-A Combined Maximum Probability Domain and Valence Bond Theory Approach.

PubMed

Turek, Jan; Braïda, Benoît; De Proft, Frank

2017-10-17

The bonding in heavier Group 14 zero-valent complexes of a general formula L 2 E (E=Si-Pb; L=phosphine, N-heterocyclic and acyclic carbene, cyclic tetrylene and carbon monoxide) is probed by combining valence bond (VB) theory and maximum probability domain (MPD) approaches. All studied complexes are initially evaluated on the basis of the structural parameters and the shape of frontier orbitals revealing a bent structural motif and the presence of two lone pairs at the central E atom. For the VB calculations three resonance structures are suggested, representing the "ylidone", "ylidene" and "bent allene" structures, respectively. The influence of both ligands and central atoms on the bonding situation is clearly expressed in different weights of the resonance structures for the particular complexes. In general, the bonding in the studied E 0 compounds, the tetrylones, is best described as a resonating combination of "ylidone" and "ylidene" structures with a minor contribution of the "bent allene" structure. Moreover, the VB calculations allow for a straightforward assessment of the π-backbonding (E→L) stabilization energy. The validity of the suggested resonance model is further confirmed by the complementary MPD calculations focusing on the E lone pair region as well as the E-L bonding region. Likewise, the MPD method reveals a strong influence of the σ-donating and π-accepting properties of the ligand. In particular, either one single domain or two symmetrical domains are found in the lone pair region of the central atom, supporting the predominance of either the "ylidene" or "ylidone" structures having one or two lone pairs at the central atom, respectively. Furthermore, the calculated average populations in the lone pair MPDs correlate very well with the natural bond orbital (NBO) populations, and can be related to the average number of electrons that is backdonated to the ligands. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Zinc-blende MnN bilayer formation on the GaN(111) surface

NASA Astrophysics Data System (ADS)

Gutierrez-Ojeda, S. J.; Guerrero-Sánchez, J.; Garcia-Diaz, R.; Ramirez-Torres, A.; Takeuchi, Noboru; H. Cocoletzi, Gregorio

2017-07-01

Atomic layers of manganese nitride, deposited on the cubic gallium nitride (111) surface, are investigated using spin polarized periodic density functional theory calculations. The adsorption of a manganese atom has been evaluated at different high symmetry sites. Incorporation into the GaN substrate by replacing gallium atoms drives the formation of a site in which the displaced Ga atom forms bonds with Ga atoms at the surface. This energetically favorable configuration shows a ferromagnetic alignment. Surface formation energy calculations demonstrate that when a full Mn ML is incorporated into the GaN structure, a Ga ML on top of a MnN bilayer may be formed for very Ga-rich conditions. On the other hand, when a full Mn ML is deposited on top of the nitrogen terminated surface, an epitaxial MnN bilayer is formed with antiferromagnetic characteristics. Density of states and partial density of states are reported to show the antiferromagnetic alignment in both structures. This behavior is mainly induced by the Mn-d orbitals.

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

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.

SU-C-204-03: DFT Calculations of the Stability of DOTA-Based-Radiopharmaceuticals

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

Khabibullin, A.R.; Woods, L.M.; Karolak, A.

2016-06-15

Purpose: Application of the density function theory (DFT) to investigate the structural stability of complexes applied in cancer therapy consisting of the 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated to Ac225, Fr221, At217, Bi213, and Gd68 radio-nuclei. Methods: The possibility to deliver a toxic payload directly to tumor cells is a highly desirable aim in targeted alpha particle therapy. The estimation of bond stability between radioactive atoms and the DOTA chelating agent is the key element in understanding the foundations of this delivery process. Thus, we adapted the Vienna Ab-initio Simulation Package (VASP) with the projector-augmented wave method and a plane-wave basis setmore » in order to study the stability and electronic properties of DOTA ligand chelated to radioactive isotopes. In order to count for the relativistic effect of radioactive isotopes we included Spin-Orbit Coupling (SOC) in the DFT calculations. Five DOTA complex structures were represented as unit cells, each containing 58 atoms. The energy optimization was performed for all structures prior to calculations of electronic properties. Binding energies, electron localization functions as well as bond lengths between atoms were estimated. Results: Calculated binding energies for DOTA-radioactive atom systems were −17.792, −5.784, −8.872, −13.305, −18.467 eV for Ac, Fr, At, Bi and Gd complexes respectively. The displacements of isotopes in DOTA cages were estimated from the variations in bond lengths, which were within 2.32–3.75 angstroms. The detailed representation of chemical bonding in all complexes was obtained with the Electron Localization Function (ELF). Conclusion: DOTA-Gd, DOTA-Ac and DOTA-Bi were the most stable structures in the group. Inclusion of SOC had a significant role in the improvement of DFT calculation accuracy for heavy radioactive atoms. Our approach is found to be proper for the investigation of structures with DOTA-based-radiopharmaceuticals and will enhance our understanding of processes occurring at subatomic levels.« less

Atomic and electronic structure of oxygen vacancies and Nb-impurity in SrTiO3

NASA Astrophysics Data System (ADS)

Hamid, A. S.

2009-12-01

We present the results of a first-principle full-potential linearized augmented plane wave (FLAPW) method to study the effect of defects on the electronic structure of SrTiO3. In addition, the relaxation of nearest neighbor atoms around those defects were calculated self-consistently. The calculations were performed using the local (spin) density approximations (L(S)DA), for the exchange-correlation potential. SrTiO3 was found to experience an insulator-to-metal transition upon the formation of oxygen vacancies or the substitution of Nb at the Ti site. The formation of oxygen divacancy disclosed additional states below the conduction band edge. The crystalline lattice relaxation showed displacements of atoms in rather large defective region. The magnitudes of atomic movements, however, were not large, normally not exceeding 0.15 Å. Our results were compared to the available experimental observations.

Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics.

PubMed

Brela, Mateusz Z; Boczar, Marek; Malec, Leszek M; Wójcik, Marek J; Nakajima, Takahito

2018-05-15

Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers. Copyright © 2018 Elsevier B.V. All rights reserved.

Quantum conductance oscillation in linear monatomic silicon chains

NASA Astrophysics Data System (ADS)

Liu, Fu-Ti; Cheng, Yan; Yang, Fu-Bin; Chen, Xiang-Rong

2014-02-01

The conductance of linear silicon atomic chains with n=1-8 atoms sandwiched between Au electrodes is investigated by using the density functional theory combined with non-equilibrium Green's function. The results show that the conductance oscillates with a period of two atoms as the number of atoms in the chain is varied. We optimize the geometric structure of nanoscale junctions in different distances, and obtain that the average bond-length of silicon atoms in each chain at equilibrium positions is 2.15±0.03 Å. The oscillation of average Si-Si bond-length can explain the conductance oscillation from the geometric structure of atomic chains. We calculate the transmission spectrum of the chains in the equilibrium positions, and explain the conductance oscillation from the electronic structure. The transport channel is mainly contributed by px and py orbital electrons of silicon atoms. The even-odd oscillation is robust under external voltage up to 1.2 V.

Molecules Without Atoms

NASA Astrophysics Data System (ADS)

Ruth, Anthony; Collins, Laura; Gomes, Kenjiro; Janko, Boldizsar

We present a real-space representation of molecules which results in the normal bonding rules and electronic structure of chemistry without atom-centered coulomb potentials. Using a simple mapping, we can generate atomless molecules from the structure of real molecules. Additionally, molecules without atoms show similar covalent bonding energies and transfer of charge in ionic bonds as real molecules. The atomless molecules contain only the valence and conduction electronic structure of the real molecule. Using the framework of the Atoms in Molecules (AIM) theory of Bader, we prove that the topological features of the valence charge distribution of molecules without atoms are identical to that of real molecules. In particular, the charge basins of atomless molecules show identical location and quantities of representative charge. We compare the accuracy, computational cost, and intuition gained from electronic structure calculations of molecules without atoms with the use of pseudopotentials to represent atomic cores in density functional theory. A. R. acknowledges support from a NASA Space Technology Research Fellowship.

First principles calculations of the magnetic and hyperfine properties of Fe/N/Fe and Fe/O/Fe multilayers in the ground state of cohesive energy

NASA Astrophysics Data System (ADS)

dos Santos, A. V.; Samudio Pérez, C. A.; Muenchen, D.; Anibele, T. P.

2015-01-01

The ground state properties of Fe/N/Fe and Fe/O/Fe multilayers were investigated using the first principles calculations. The calculations were performed using the Linearized Augmented Plane Wave (LAPW) method implemented in the Wien2k code. A supercell consisting of one layer of nitride (or oxide) between two layers of Fe in the bcc structure was used to model the structure of the multilayer. The research in new materials also stimulated theoretical and experimental studies of iron-based nitrides due to their variety of structural and magnetic properties for the potential applications as in high strength steels and for high corrosion resistance. It is obvious from many reports that magnetic iron nitrides such as γ-Fe4N and α-Fe16N2 have interesting magnetic properties, among these a high magnetisation saturation and a high density crimp. However, although Fe-N films and multilayers have many potential applications, they can be produced in many ways and are being extensively studied from the theoretical point of view there is no detailed knowledge of their electronic structure. Clearly, efforts to understand the influence of the nitrogen atoms on the entire electronic structure are needed as to correctly interpret the observed changes in the magnetic properties when going from Fe-N bulk compounds to multilayer structures. Nevertheless, the N atoms are not solely responsible for electronics alterations in solid compounds. Theoretical results showed that Fe4X bulk compounds, where X is a variable atom with increasing atomic number (Z), the nature of bonding between X and adjacent Fe atoms changes from more covalent to more ionic and the magnetic moments of Fe also increase for Z=7, i.e. N. This is an indicative that atoms with a Z number higher than 7, i.e., O, can produce several new alterations in the entire magnetic properties of Fe multilayers. This paper presents the first results of an ab-initio electronic structure calculations, performed for Fe-N and Fe-O multilayers. Firstly, the formation energy and the cohesive energy of the multilayers are discussed. For optimised values, the cohesive energy of the multilayers to obtain the lattice parameters at the equilibrium ground state was used, i.e. a new methodology for this calculus was applied. Secondly, the magnetic properties and hyperfine interactions (magnetic field, electric field gradient and the isomer shift) of the iron atoms of the multilayers are discussed.

Influence of the plasma environment on atomic structure using an ion-sphere model

NASA Astrophysics Data System (ADS)

Belkhiri, Madeny; Fontes, Christopher J.; Poirier, Michel

2015-09-01

Plasma environment effects on atomic structure are analyzed using various atomic structure codes. To monitor the effect of high free-electron density or low temperatures, Fermi-Dirac and Maxwell-Boltzmann statistics are compared. After a discussion of the implementation of the Fermi-Dirac approach within the ion-sphere model, several applications are considered. In order to check the consistency of the modifications brought here to extant codes, calculations have been performed using the Los Alamos Cowan Atomic Structure (cats) code in its Hartree-Fock or Hartree-Fock-Slater form and the parametric potential Flexible Atomic Code (fac). The ground-state energy shifts due to the plasma effects for the six most ionized aluminum ions have been calculated using the fac and cats codes and fairly agree. For the intercombination resonance line in Fe22 +, the plasma effect within the uniform electron gas model results in a positive shift that agrees with the multiconfiguration Dirac-Fock value of B. Saha and S. Fritzsche [J. Phys. B 40, 259 (2007), 10.1088/0953-4075/40/2/002]. Last, the present model is compared to experimental data in titanium measured on the terawatt Astra facility and provides values for electron temperature and density in agreement with the maria code.

Electronic structure, magnetism, and optical properties of Fe2SiO4 fayalite at ambient and high pressures: A GGA+U study

NASA Astrophysics Data System (ADS)

Jiang, Xuefan; Guo, G. Y.

2004-04-01

The electronic structure, magnetism, and optical properties of Fe2SiO4 fayalite, the iron-rich end member of the olivine-type silicate, one of the most abundant minerals in Earth’s upper mantle, have been studied by density-functional theory within the generalized gradient approximation (GGA) with the on-site Coulomb energy U=4.5 eV taken into account (GGA+U). The stable insulating antiferromagnetic solution with an energy gap ˜1.49 eV and a spin magnetic moment of 3.65μB and an orbital magnetic moment of 0.044μB per iron atom is obtained. It is found that the gap opening in this fayalite results mainly from the strong on-site Coulomb interaction on the iron atoms. In this band structure, the top of valence bands consists mainly of the 3d orbitals of Fe2 atoms, and the bottom of the conduction bands is mainly composed of the 3d orbitals of Fe1 atoms. Therefore, since the electronic transition from the Fe2 3d to Fe1 3d states is weak, significant electronic transitions would appear only about 1 eV above the absorption edge when Fe-O orbitals are involved in the final states. In addition, our band-structure calculations can explain the observed phenomena including redshift near the absorption edge and the decrease of the electrical resistivity of Fe2SiO4 upon compression. The calculated Fe p partial density of states agree well with Fe K-edge x-ray absorption spectrum. The calculated lattice constants and atomic coordinates for Fe2SiO4 fayalite in orthorhombic structure are in good agreement with experiments.

Atomic spectral-product representations of molecular electronic structure: metric matrices and atomic-product composition of molecular eigenfunctions.

PubMed

Ben-Nun, M; Mills, J D; Hinde, R J; Winstead, C L; Boatz, J A; Gallup, G A; Langhoff, P W

2009-07-02

Recent progress is reported in development of ab initio computational methods for the electronic structures of molecules employing the many-electron eigenstates of constituent atoms in spectral-product forms. The approach provides a universal atomic-product description of the electronic structure of matter as an alternative to more commonly employed valence-bond- or molecular-orbital-based representations. The Hamiltonian matrix in this representation is seen to comprise a sum over atomic energies and a pairwise sum over Coulombic interaction terms that depend only on the separations of the individual atomic pairs. Overall electron antisymmetry can be enforced by unitary transformation when appropriate, rather than as a possibly encumbering or unnecessary global constraint. The matrix representative of the antisymmetrizer in the spectral-product basis, which is equivalent to the metric matrix of the corresponding explicitly antisymmetric basis, provides the required transformation to antisymmetric or linearly independent states after Hamiltonian evaluation. Particular attention is focused in the present report on properties of the metric matrix and on the atomic-product compositions of molecular eigenstates as described in the spectral-product representations. Illustrative calculations are reported for simple but prototypically important diatomic (H(2), CH) and triatomic (H(3), CH(2)) molecules employing algorithms and computer codes devised recently for this purpose. This particular implementation of the approach combines Slater-orbital-based one- and two-electron integral evaluations, valence-bond constructions of standard tableau functions and matrices, and transformations to atomic eigenstate-product representations. The calculated metric matrices and corresponding potential energy surfaces obtained in this way elucidate a number of aspects of the spectral-product development, including the nature of closure in the representation, the general redundancy or linear dependence of its explicitly antisymmetrized form, the convergence of the apparently disparate atomic-product and explicitly antisymmetrized atomic-product forms to a common invariant subspace, and the nature of a chemical bonding descriptor provided by the atomic-product compositions of molecular eigenstates. Concluding remarks indicate additional studies in progress and the prognosis for performing atomic spectral-product calculations more generally and efficiently.

Tuning of electronic band gaps and optoelectronic properties of binary strontium chalcogenides by means of doping of magnesium atom(s)- a first principles based theoretical initiative with mBJ, B3LYP and WC-GGA functionals

NASA Astrophysics Data System (ADS)

Debnath, Bimal; Sarkar, Utpal; Debbarma, Manish; Bhattacharjee, Rahul; Chattopadhyaya, Surya

2018-02-01

First principle based theoretical initiative is taken to tune the optoelectronic properties of binary strontium chalcogenide semiconductors by doping magnesium atom(s) into their rock-salt unit cells at specific concentrations x = 0.0, 0.25, 0.50, 0.75 and 1.0 and such tuning is established by studying structural, electronic and optical properties of designed binary compounds and ternary alloys employing WC-GGA, B3LYP and mBJ exchange-correlation functionals. Band structure of each compound is constructed and respective band gaps under all the potential schemes are measured. The band gap bowing and its microscopic origin are calculated using quadratic fit and Zunger's approach, respectively. The atomic and orbital origins of electronic states in the band structure of any compound are explored from its density of states. The nature of chemical bonds between the constituent atoms in each compound is explored from the valence electron density contour plots. Optical properties of any specimen are explored from the computed spectra of its dielectric function, refractive index, extinction coefficient, normal incidence reflectivity, optical conductivity optical absorption and energy loss function. Several calculated results are compared with available experimental and earlier theoretical data.

Rich interfacial chemistry and properties of carbon-doped hexagonal boron nitride nanosheets revealed by electronic structure calculations

NASA Astrophysics Data System (ADS)

Xie, Wei; Tamura, Takahiro; Yanase, Takashi; Nagahama, Taro; Shimada, Toshihiro

2018-04-01

The effect of C doping to hexagonal boron nitride (h-BN) to its electronic structure is examined by first principles calculations using the association from π-electron systems of organic molecules embedded in a two-dimensional insulator. In a monolayered carbon-doped structure, odd-number doping with carbon atoms confers metallic properties with different work functions. Various electronic interactions occur between two layers with odd-number carbon substitution. A direct sp3 covalent chemical bond is formed when C replaces adjacent B and N in different layers. A charge transfer complex between layers is found when C replaces B and N in the next-neighboring region, which results in narrower band gaps (e.g., 0.37 eV). Direct bonding between C and B atoms is found when two C atoms in different layers are at a certain distance.

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

Thimmaiah, Srinivasa; Taufour, Valentin; Iowa State Univ., Ames, IA

Bi 21.2(1)(Mn 1–xCo x ) 20 is a new metastable phase which is synthesized via Bi self-flux, adopts a highly fibrous morpholo-gy, and decomposes endothermically near 168 °C. It crystallizes in the orthorhombic space group Imma with unit cell parameters α = 19.067(4) Å, $b$ = 4.6071(10) Å and c = 11.583(4) Å, adopting a low-temperature modification of BiNi-type structure by forming columns along the b-axis. Wave-length-dispersive X-ray spectroscopy (WDS) confirms the presence of Co in the structure, which is found to be 7 at.%. In each column, the transition metal (T) and Bi atoms construct a double-walled nanotubular arrangementmore » of atoms around the disordered central Bi atoms. Electronic structure calculations (LMTO-ASA, LSDA) show that the calculated Fermi level falls into a pseudogap and also indicate a possible low-temperature magnetic ordering in the phase.« less

Ab initio investigation of the structural and electronic properties of amorphous HgTe.

PubMed

Zhao, Huxian; Chen, Xiaoshuang; Lu, Jianping; Shu, Haibo; Lu, Wei

2014-01-29

We present the structure and electronic properties of amorphous mercury telluride obtained from first-principle calculations. The initial configuration of amorphous mercury telluride is created by computation alchemy. According to different exchange–correlation functions in our calculations, we establish two 256-atom models. The topology of both models is analyzed in terms of radial and bond angle distributions. It is found that both the Te and the Hg atoms tend to be fourfold, but with a wrong bond rate of about 10%. The fraction of threefold and fivefold atoms also shows that there are a significant number of dangling and floating bonds in our models. The electronic properties are also obtained. It is indicated that there is a bandgap in amorphous HgTe, in contrast to the zero bandgap for crystalline HgTe. The structures of the band tail and defect states are also discussed.

Copper(II) and zinc(II) as metal-carboxylate coordination complexes based on (1-methyl-1H-benzo[d]imidazol-2-yl) methanol derivative: Synthesis, crystal structure, spectroscopy, DFT calculations and antioxidant activity

NASA Astrophysics Data System (ADS)

Benhassine, Anfel; Boulebd, Houssem; Anak, Barkahem; Bouraiou, Abdelmalek; Bouacida, Sofiane; Bencharif, Mustapha; Belfaitah, Ali

2018-05-01

This work presents a combined experimental and theoretical study of two new metal-carboxylate coordination compounds. These complexes were prepared from (1-methyl-1H-benzimidazol-2-yl)methanol under mild conditions. The structures of the prepared compounds were characterized by single-crystal X-ray analysis, FTIR and UV-Vis spectroscopy. In the Cupper complex, the Cu(II) ion is coordinated by two ligands, which act as bidentate chelator through the non-substituted N and O atoms, and two carboxylicg oxygen atoms, displaying a hexa-coordinated compound in a distorted octahedral geometry, while in the Zinc complex the ligand is ligated to the Zn(II) ion in monodentate fashion through the N atom, and the metal ion is also bonded to carboxylic oxygen atoms. The tetra-coordinated compound displays a distorted tetrahedral shape. The density functional theory calculations are carried out for the determination of the optimized structures. The electronic transitions and fundamental vibrational wave numbers are calculated and are in good agreement with experimental. In addition, the ligand and its Cu(II) and Zn(II) complexes were screened and evaluated for their potential as DPPH radical scavenger.

Structures and stability of metal-doped Ge{sub n}M (n = 9, 10) clusters

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

Qin, Wei, E-mail: qinw@qdu.edu.cn; Xia, Lin-Hua; Zhao, Li-Zhen

The lowest-energy structures of neutral and cationic Ge{sub n}M (n = 9, 10; M = Si, Li, Mg, Al, Fe, Mn, Pb, Au, Ag, Yb, Pm and Dy) clusters were studied by genetic algorithm (GA) and first-principles calculations. The calculation results show that doping of the metal atoms and Si into Ge{sub 9} and Ge{sub 10} clusters is energetically favorable. Most of the metal-doped Ge cluster structures can be viewed as adding or substituting metal atom on the surface of the corresponding ground-state Ge{sub n} clusters. However, the neutral and cationic FeGe{sub 9,10},MnGe{sub 9,10} and Ge{sub 10}Al are cage-like withmore » the metal atom encapsulated inside. Such cage-like transition metal doped Ge{sub n} clusters are shown to have higher adsorption energy and thermal stability. Our calculation results suggest that Ge{sub 9,10}Fe and Ge{sub 9}Si would be used as building blocks in cluster-assembled nanomaterials because of their high stabilities.« less

Hirshfeld atom refinement.

PubMed

Capelli, Silvia C; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

2014-09-01

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree-Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints - even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å(2) as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements - an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.

Hirshfeld atom refinement

PubMed Central

Capelli, Silvia C.; Bürgi, Hans-Beat; Dittrich, Birger; Grabowsky, Simon; Jayatilaka, Dylan

2014-01-01

Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu’s), all other structural parameters agree within less than 2 csu’s. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å. PMID:25295177

Atomic and electronic structure of Pd40Ni40P20 bulk metallic glass from ab initio simulations

NASA Astrophysics Data System (ADS)

Kumar, Vijay; Fujita, T.; Konno, K.; Matsuura, M.; Chen, M. W.; Inoue, A.; Kawazoe, Y.

2011-10-01

The atomic structure of Pd40Ni40P20 bulk metallic glass has been simulated using an ab initio molecular dynamics method with projector-augmented wave pseudopotentials for electron-ion interaction and generalized gradient approximation for exchange-correlation energy. The calculated extended x-ray absorption fine structure (EXAFS) spectra of Pd-K and Ni-K edges, the mass density, and the electronic structure agree remarkably well with the available experimental data and the EXAFS spectra measured at the SPring-8 synchrotron radiation facility. Our results show that the atomic structure can be described in terms of P-centered polyhedra. There are no two P atoms that are nearest neighbors at this composition, and this could be a reason for the observed optimal P concentration of about 20 at.%. The neighboring polyhedra share metal (M) atoms and form a polar covalently bonded random network of P-M-P favoring certain angles. The remaining M atoms act as metallic glue with a tendency of nanoscale clustering of Pd-Pd and Ni-Ni atoms.

Impurity-doped Si10 cluster: Understanding the structural and electronic properties from first-principles calculations

NASA Astrophysics Data System (ADS)

Majumder, Chiranjib; Kulshreshtha, S. K.

2004-12-01

Structural and electronic properties of metal-doped silicon clusters ( MSi10 , M=Li , Be, B, C, Na, Mg, Al, and Si) have been investigated via ab initio molecular dynamics simulation under the formalism of the density functional theory. The exchange-correlation energy has been calculated using the generalized gradient approximation method. Several stable isomers of MSi10 clusters have been identified based on different initial configurations and their relative stabilities have been analyzed. From the results it is revealed that the location of the impurity atom depends on the nature of interaction between the impurity atom and the host cluster and the size of the impurty atom. Whereas Be and B atoms form stable isomers, the impurity atom being placed at the center of the bicapped tetragonal antiprism structure of the Si10 cluster, all other elements diffuse outside the cage of Si10 cluster. Further, to understand the stability and the chemical bonding, the LCAO-MO based all electron calculations have been carried out for the lowest energy isomers using the hybrid B3LYP energy functional. Based on the interaction energy of the M atoms with Si10 clusters it is found that p-p interaction dominates over the s-p interaction and smaller size atoms interact more strongly. Based on the binding energy, the relative stability of MSi10 clusters is found to follow the order of CSi10>BSi10>BeSi10>Si11>AlSi10>LiSi10>NaSi10>MgSi10 , leading one to infer that while the substitution of C, B and Be enhances the stability of the Si11 cluster, others have an opposite effect. The extra stability of the BeSi10 clusters is due to its encapsulated close packed structure and large energy gap between the HOMO and LUMO energy levels.

Atomically resolved structure of ligand-protected Au{sub 9} clusters on TiO{sub 2} nanosheets using aberration-corrected STEM

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

Al Qahtani, Hassan S.; Andersson, Gunther G., E-mail: gunther.andersson@flinders.edu.au, E-mail: nakayama.tomonobu@nims.go.jp; Kimoto, Koji

2016-03-21

Triphenylphosphine ligand-protected Au{sub 9} clusters deposited onto titania nanosheets show three different atomic configurations as observed by scanning transmission electron microscopy. The configurations observed are a 3-dimensional structure, corresponding to the previously proposed Au{sub 9} core of the clusters, and two pseudo-2-dimensional (pseudo-2D) structures, newly found by this work. With the help of density functional theory (DFT) calculations, the observed pseudo-2D structures are attributed to the low energy, de-ligated structures formed through interaction with the substrate. The combination of scanning transmission electron microscopy with DFT calculations thus allows identifying whether or not the deposited Au{sub 9} clusters have been de-ligatedmore » in the deposition process.« less

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.

Mechanical and thermodynamic properties of AlX (X = N, P, As) compounds

NASA Astrophysics Data System (ADS)

Xu, Lifang; Bu, Wei

2017-09-01

The Vickers hardness of various AlX (X = N, P, As) compound polymorphs were calculated with the bond resistance model. Thermodynamic properties, such as vibrational entropy, constant volume specific heat and Debye temperatures, were calculated using phonon dispersion relations and phonon density of states (DOS). The calculated values are in good agreement with the previous experimental and theoretical data. For the same structure of AlX (X = N, P, As) compounds, their hardness and Debye temperatures both decrease with the X atomic number. The wurtzite (wz) and zincblende (zb) structures of the same compounds AlX share an almost identical hardness, but have different Debye temperatures. The difference between wz and zb structures increases as the atomic number of X increases. The thermodynamic properties reveal that the constant volume specific heat approaches the Dulong-Petit rule at high temperatures.

Study of MoNbO(y) (y = 2-5) anion and neutral clusters using photoelectron spectroscopy and density functional theory calculations: impact of spin contamination on single point calculations.

PubMed

Waller, Sarah E; Mann, Jennifer E; Rothgeb, David W; Jarrold, Caroline C

2012-10-04

Results of a study combining anion photoelectron spectroscopy and density functional theory calculations on the heteronuclear MoNbO(y)(-) (y = 2-5) transition metal suboxide cluster series are reported and analyzed. The photoelectron spectra, which exhibit broad electronic bands with partially resolved vibrational structure, were compared to spectral simulations generated from calculated spectroscopic parameters for all computationally determined energetically competitive structures. Although computational results on the less oxidized clusters could not be satisfactorily reconciled with experimental spectra, possibly because of heavy spin contamination found in a large portion of the computational results, the results suggest that (1) neutral cluster electron affinity is a strong indicator of whether O-atoms are bound in M-O-M bridge positions or M═O terminal positions, (2) MoNbO(y) anions and neutrals have structures that can be described as intermediate with respect to the unary (homonuclear) Mo(2)O(y) and Nb(2)O(y) clusters, and (3) structures in which O-atoms preferentially bind to the Nb center are slightly more stable than alternative structures. Several challenges associated with the calculations are considered, including spin contamination, which appears to cause spurious single point calculations used to determine vertical detachment energies.

Progress in Visualizing Atomic Size Effects with DFT-Chemical Pressure Analysis: From Isolated Atoms to Trends in AB5 Intermetallics.

PubMed

Berns, Veronica M; Engelkemier, Joshua; Guo, Yiming; Kilduff, Brandon J; Fredrickson, Daniel C

2014-08-12

The notion of atomic size poses an important challenge to chemical theory: empirical evidence has long established that atoms have spatial requirements, which are summarized in tables of covalent, ionic, metallic, and van der Waals radii. Considerations based on these radii play a central role in the design and interpretation of experiments, but few methods are available to directly support arguments based on atomic size using electronic structure methods. Recently, we described an approach to elucidating atomic size effects using theoretical calculations: the DFT-Chemical Pressure analysis, which visualizes the local pressures arising in crystal structures from the interactions of atomic size and electronic effects. Using this approach, a variety of structural phenomena in intermetallic phases have already been understood in terms that provide guidance to new synthetic experiments. However, the applicability of the DFT-CP method to the broad range of the structures encountered in the solid state is limited by two issues: (1) the difficulty of interpreting the intense pressure features that appear in atomic core regions and (2) the need to divide space among pairs of interacting atoms in a meaningful way. In this article, we describe general solutions to these issues. In addressing the first issue, we explore the CP analysis of a test case in which no core pressures would be expected to arise: isolated atoms in large boxes. Our calculations reveal that intense core pressures do indeed arise in these virtually pressure-less model systems and allow us to trace the issue to the shifts in the voxel positions relative to atomic centers upon expanding and contracting the unit cell. A compensatory grid unwarping procedure is introduced to remedy this artifact. The second issue revolves around the difficulty of interpreting the pressure map in terms of interatomic interactions in a way that respects the size differences of the atoms and avoids artificial geometrical constraints. In approaching this challenge, we have developed a scheme for allocating the grid pressures to contacts inspired by the Hirshfeld charge analysis. Here, each voxel is allocated to the contact between the two atoms whose free atom electron densities show the largest values at that position. In this way, the differing sizes of atoms are naturally included in the division of space without resorting to empirical radii. The use of the improved DFT-CP method is illustrated through analyses of the applicability of radius ratio arguments to Laves phase structures and the structural preferences of AB5 intermetallics between the CaCu5 and AuBe5 structure types.

Site specific interaction between ZnO nanoparticles and tyrosine: A density functional theory study

NASA Astrophysics Data System (ADS)

Singh, Satvinder; Singh, Janpreet; Singh, Baljinder; Singh, Gurinder; Kaura, Aman; Tripathi, S. K.

2018-05-01

First Principles Calculations have been performed on ZnO/Tyrosine atomic complex to study site specific interaction of Tyrosine and ZnO nanoparticles. Calculated results shows that -COOH group present in Tyrosine is energetically more favorable than -NH2 group. Interactions show ionic bonding between ZnO and Tyrosine. All the calculations have been performed under the Density Functional Theory (DFT) framework. Structural and electronic properties of (ZnO)3/Tyrosine complex have been studied. Gaussian basis set approach has been adopted for the calculations. A ring type most stable (ZnO)3 atomic cluster has been modeled, analyzed and used for the calculations.

The structural and electronic properties of amorphous HgCdTe from first-principles calculations

NASA Astrophysics Data System (ADS)

Zhao, Huxian; Chen, Xiaoshuang; Lu, Jianping; Shu, Haibo; Lu, Wei

2014-01-01

Amorphous mercury cadmium telluride (a-MCT) model structures, with x being 0.125 and 0.25, are obtained from first-principles calculations. We generate initial structures by computation alchemy method. It is found that most atoms in the network of amorphous structures tend to be fourfold and form tetrahedral structures, implying that the chemical ordered continuous random network with some coordination defects is the ideal structure for a-MCT. The electronic structure is also concerned. The gap is found to be 0.30 and 0.26 eV for a-Hg0.875Cd0.125Te and a-Hg0.75Cd0.25Te model structures, independent of the composition. By comparing with the properties of crystalline MCT with the same composition, we observe a blue-shift of energy band gap. The localization of tail states and its atomic origin are also discussed.

Local Energies and Energy Fluctuations — Applied to the High Entropy Alloy CrFeCoNi

NASA Astrophysics Data System (ADS)

Fukushima, Tetsuya; Katayama-Yoshida, Hiroshi; Sato, Kazunori; Ogura, Masako; Zeller, Rudolf; Dederichs, Peter H.

2017-11-01

High entropy alloys show a variety of fascinating properties like high hardness, wear resistance, corrosion resistance, etc. They are random solid solutions of many components with rather high concentrations. We perform ab-initio calculations for the high entropy alloy CrFeCoNi, which equal concentration of 25% for each element. By the KKRnano program package, which is based on an order-N screened Korringa-Kohn-Rostoker Green's function method, we consider a face-centered cubic (FCC) supercell with 1372 randomly distributed elements, and in addition also smaller supercells with 500 and 256 atoms. It is found from our calculations that the local moments of the Cr atoms show a large environmental variation, ranging from -1.70 μB to +1.01 μB with an average of about -0.51 μB. We present a new method to calculate "local energies" of all atoms. This is based on the partitioning of the whole space into Voronoi cells and allows to calculate the energetic contribution of each atomic cell to the total energy of the supercell. The supercell calculations show very large variations of the local energies, analogous to the variations of the local moments. This shows that the random solid solution is not stable and has a tendency to form an L12-structure with the Cr-atoms ordered at the corner of the cube and the elements Fe, Co, and Ni randomly distributed on the three other FCC sublattices. For this structure the variation of the local moments are much smaller.

Hydrogen incorporation into BN fullerene-like nanostructures: A first-principles study

NASA Astrophysics Data System (ADS)

Ganji, M. D.; Abbaszadeh, B.; Ahaz, B.

2011-10-01

We performed density functional theory calculations to investigate the possibility of formation of endohedrally H@(BN) n-fullerene ( n: 24, 36, 60) and H@C 60 complexes for potential applications in solid-state quantum-computers. Spin-polarized approach within the generalized gradient approximation with the Perdew-Burke-Ernzerhof functional was used for the total energies and structural relaxation calculations. The calculated binding energies show that H atom being incorporated into B 60N 60 nanocage can form most stable complexes while the B 24N 24 and C 60 nanocages might form unstable complex with positive binding energy. We have also examined the penetration of an H atom into the respective nanocages and the calculated barrier energies indicate that the H atom prefers to penetrate into the B 24N 24 and B 60N 60 nanocages with barrier energy of about 0.47 eV (10.84 kcal/mol). Furthermore the binding characteristic is rationalized by analyzing the electronic structures. Our findings reveal that the B 60N 60 nanocage has fascinating potential application in future solid-state quantum-computers.

Fluorescence detection of white-beam X-ray absorption anisotropy: towards element-sensitive projections of local atomic structure

PubMed Central

Korecki, P.; Tolkiehn, M.; Dąbrowski, K. M.; Novikov, D. V.

2011-01-01

Projections of the atomic structure around Nb atoms in a LiNbO3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples. PMID:21997909

The structural, electronic, magnetic, and mechanical properties of perovskite oxides PbM1/2Nb1/2O3 (M = Fe, Co and Ni)

NASA Astrophysics Data System (ADS)

Erkisi, A.; Surucu, G.; Deligoz, E.

2018-03-01

In this study, the structural, electronic, magnetic, and mechanical properties of perovskite oxides PbM1/2Nb1/2O3 (M = Fe, Co and Ni) are investigated. The systems are treated in ferromagnetic order. The calculations are carried out in the framework of density functional theory (DFT) within the plane-wave pseudopotential method. The exchange-correlation potential is approximated by generalized-gradient spin approach (GGA). The intra-atomic Coulomb repulsion is also taken into account in calculations (GGA + U). We have considered two generalized-gradient spin approximation functionals, which are Perdew-Burke-Ernzerhof (PBE) and PBE for solids (PBEsol) for structural parameter calculations when it included Hubbard potential. Although the spin-polarized electronic band structures of PbCo1/2Nb1/2O3 and PbNi1/2Nb1/2O3 systems exhibit metallic property in ferromagnetic phase, a bandgap is observed in spin-down states of PbFe1/2Nb1/2O3 resulting in half-metallic behavior. The main reason for this behavior is attributed to the hybridization between d-states of transition metal atoms and p-states of oxygen atoms. The stability mechanically and the calculated mechanical properties by using elastic constants show that these compounds are mechanically stable in tetragonal phase and have anisotropic character mechanically.

Al6H18: A baby crystal of γ-AlH3

NASA Astrophysics Data System (ADS)

Kiran, B.; Kandalam, Anil K.; Xu, Jing; Ding, Y. H.; Sierka, M.; Bowen, K. H.; Schnöckel, H.

2012-10-01

Using global-minima search methods based on the density functional theory calculations of (AlH3)n (n = 1-8) clusters, we show that the growth pattern of alanes for n ≥ 4 is dominated by structures containing hexa-coordinated Al atoms. This is in contrast to the earlier studies where either linear or ring structures of AlH3 were predicted to be the preferred structures in which the Al atoms can have a maximum of five-fold coordination. Our calculations also reveal that the Al6H18 cluster, with its hexa-coordination of the Al atoms, resembles the unit-cell of γ-AlH3, thus Al6H18 is designated as the "baby crystal." The fragmentation energies of the (AlH3)n (n = 2-8) along with the dimerization energies for even n clusters indicate an enhanced stability of the Al6H18 cluster. Both covalent (hybridization) and ionic (charge) contribution to the bonding are the driving factors in stabilizing the isomers containing hexa-coordinated Al atoms.

Structural and elastoplastic properties of β -Ga2O3 films grown on hybrid SiC/Si substrates

NASA Astrophysics Data System (ADS)

Osipov, A. V.; Grashchenko, A. S.; Kukushkin, S. A.; Nikolaev, V. I.; Osipova, E. V.; Pechnikov, A. I.; Soshnikov, I. P.

2018-04-01

Structural and mechanical properties of gallium oxide films grown on (001), (011) and (111) silicon substrates with a buffer layer of silicon carbide are studied. The buffer layer was fabricated by the atom substitution method, i.e., one silicon atom per unit cell in the substrate was substituted by a carbon atom by chemical reaction with carbon monoxide. The surface and bulk structure properties of gallium oxide films have been studied by atomic-force microscopy and scanning electron microscopy. The nanoindentation method was used to investigate the elastoplastic characteristics of gallium oxide, and also to determine the elastic recovery parameter of the films under study. The ultimate tensile strength, hardness, elastic stiffness constants, elastic compliance constants, Young's modulus, linear compressibility, shear modulus, Poisson's ratio and other characteristics of gallium oxide have been calculated by quantum chemistry methods based on the PBESOL functional. It is shown that all these properties of gallium oxide are essentially anisotropic. The calculated values are compared with experimental data. We conclude that a change in the silicon orientation leads to a significant reorientation of gallium oxide.

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

NASA Astrophysics Data System (ADS)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

Electronic structure studies of Ni( 1 0 0 ) surface reconstructions resulting from carbon, nitrogen, or oxygen atom adsorption

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2003-01-01

Solid-state Fenske-Hall band structure calculations have been used to study the different surface structures which result from adsorption of a half monolayer of C, N, or O atoms on the Ni(1 0 0) surface. C or N atoms sit nearly coplanar with the surface Ni atoms and induce the "clock" reconstruction of the surface. In contrast, adsorbed O atoms sit slightly above the Ni(1 0 0) surface plane and have little effect on the overall surface structure. The local environments of the C, N, and O atoms on these surfaces are similar to their environments in a series of late transition metal carbonyl clusters, suggesting that some of the same electronic factors may play a role in favoring the different structures. Results of the calculations indicate that when adsorbates occupy coplanar sites on Ni(1 0 0), much of the Ni-Ni bonding within the surface layer and between the surface- and second-layers is disrupted. On the C- and N-covered surfaces the disruption is more than compensated for by the formation of strong adsorbate-Ni bonds and by new Ni-Ni surface bonds resulting from the clock reconstruction. When O is forced into a coplanar site, however, both the higher electron count and increased electronegativity of the O atoms lead to severe disruption of the surface bonding and weak Ni-O bonds. When O atoms sit above the surface, they form more polar Ni-O bonds, contribute less electron density to the Ni surface bands, and cause less disruption to Ni-Ni surface bonds. These results suggest that, similar to the organometallic clusters, the site preferences of C, N, and O atoms are directly related to their electron count, and in turn to the relative occupation of both Ni-Ni and X-Ni (X=C, N, O) antibonding bands.

Structural and electronic properties of monolayer group III monochalcogenides

NASA Astrophysics Data System (ADS)

Demirci, S.; Avazlı, N.; Durgun, E.; Cahangirov, S.

2017-03-01

We investigate the structural, mechanical, and electronic properties of the two-dimensional hexagonal structure of group III-VI binary monolayers, M X (M =B , Al, Ga, In and X =O , S, Se, Te) using first-principles calculations based on the density functional theory. The structural optimization calculations and phonon spectrum analysis indicate that all of the 16 possible binary compounds are thermally stable. In-plane stiffness values cover a range depending on the element types and can be as high as that of graphene, while the calculated bending rigidity is found to be an order of magnitude higher than that of graphene. The obtained electronic band structures show that M X monolayers are indirect band-gap semiconductors. The calculated band gaps span a wide optical spectrum from deep ultraviolet to near infrared. The electronic structure of oxides (M O ) is different from the rest because of the high electronegativity of oxygen atoms. The dispersions of the electronic band edges and the nature of bonding between atoms can also be correlated with electronegativities of constituent elements. The unique characteristics of group III-VI binary monolayers can be suitable for high-performance device applications in nanoelectronics and optics.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

Silicene on Ag(1 1 1): Geometric and electronic structures of a new honeycomb material of Si

NASA Astrophysics Data System (ADS)

Takagi, Noriaki; Lin, Chun-Liang; Kawahara, Kazuaki; Minamitani, Emi; Tsukahara, Noriyuki; Kawai, Maki; Arafune, Ryuichi

2015-02-01

Silicene, a two-dimensional honeycomb sheet consisting of Si atoms, has attracted much attention as a new low-dimensional material because it gains various fascinating characteristics originating from the combination of Dirac fermion features with spin-orbit coupling. The novel properties such as the quantum spin Hall effect and the compatibility with the current Si device technologies have fueled competition to realize the silicene. This review article focuses on the geometric and electronic structures of silicene grown on Ag(1 1 1) investigated by scanning tunneling microcopy (STM), low energy electron diffraction (LEED) and density functional theory (DFT) calculations. The silicene on Ag(1 1 1) takes locally-buckled structure in which the Si atoms are displaced perpendicularly to the basal plane. As a result, several superstructures such as 4 × 4,√{ 13 } ×√{ 13 } R 13.9 °, 4 /√{ 3 } × 4 /√{ 3 } , and etc. emerge. The atomic arrangement of the 4 × 4 silicene has been determined by STM, DFT calculations and LEED dynamical analysis, while the other superstructures remain to be fully-resolved. In the 4 × 4 silicene, Si atoms are arranged to form a buckled honeycomb structure where six Si atoms of 18 Si atoms in the unit cell are displaced vertically. The displacements lead to the vertical shift of the substrate Ag atoms, indicating the non-negligible coupling at the interface between the silicene layer and the substrate. The interface coupling significantly modifies the electronic structure of the 4 × 4 silicene. No Landau level sequences were observed by scanning tunneling spectroscopy (STS) with magnetic fields applied perpendicularly to the sample surface. The DFT calculations showed that the π and π∗ bands derived from the Si 3pz are hybridized with the Ag electronic states, leading to the drastic modification in the band structure and then the absence of Dirac fermion features together with the two-dimensionality in the electronic states. These findings demonstrate that the strong coupling at the interface causes the symmetry breaking for the 4 × 4 silicene and as a result the disappearance of Dirac fermion features. The geometric and electronic structures of other superstructures are also discussed.

Theoretical discovery of stable structures of group III-V monolayers: The materials for semiconductor devices

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

Suzuki, Tatsuo, E-mail: dr.tatsuosuzuki@gmail.com

Group III-V compounds are very important as the materials of semiconductor devices. Stable structures of the monolayers of group III-V binary compounds have been discovered by using first-principles calculations. The primitive unit cell of the discovered structures is a rectangle, which includes four group-III atoms and four group-V atoms. A group-III atom and its three nearest-neighbor group-V atoms are placed on the same plane; however, these connections are not the sp{sup 2} hybridization. The bond angles around the group-V atoms are less than the bond angle of sp{sup 3} hybridization. The discovered structure of GaP is an indirect transition semiconductor,more » while the discovered structures of GaAs, InP, and InAs are direct transition semiconductors. Therefore, the discovered structures of these compounds have the potential of the materials for semiconductor devices, for example, water splitting photocatalysts. The discovered structures may become the most stable structures of monolayers which consist of other materials.« less

Electron impact excitation of N IV: calculations with the DARC code and a comparison with ICFT results

NASA Astrophysics Data System (ADS)

Aggarwal, K. M.; Keenan, F. P.; Lawson, K. D.

2016-10-01

There have been discussions in the recent literature regarding the accuracy of the available electron impact excitation rates (equivalently effective collision strengths Υ) for transitions in Be-like ions. In the present paper we demonstrate, once again, that earlier results for Υ are indeed overestimated (by up to four orders of magnitude), for over 40 per cent of transitions and over a wide range of temperatures. To do this we have performed two sets of calculations for N IV, with two different model sizes consisting of 166 and 238 fine-structure energy levels. As in our previous work, for the determination of atomic structure the GRASP (General-purpose Relativistic Atomic Structure Package) is adopted and for the scattering calculations (the standard and parallelised versions of) the Dirac Atomic R-matrix Code (DARC) are employed. Calculations for collision strengths and effective collision strengths have been performed over a wide range of energy (up to 45 Ryd) and temperature (up to 2.0 × 106 K), useful for applications in a variety of plasmas. Corresponding results for energy levels, lifetimes and A-values for all E1, E2, M1 and M2 transitions among 238 levels of N IV are also reported.

Dirac R-matrix calculations of photoionization cross sections of Ni XII and atomic structure data of Ni XIII

NASA Astrophysics Data System (ADS)

Nazir, R. T.; Bari, M. A.; Bilal, M.; Sardar, S.; Nasim, M. H.; Salahuddin, M.

2017-02-01

We performed R-matrix calculations for photoionization cross sections of the two ground state configuration 3s23p5 (^2P^o3/2,1/2) levels and 12 excited states of Ni XII using relativistic Dirac Atomic R-matrix Codes (DARC) across the photon energy range between the ionizations thresholds of the corresponding states and well above the thresholds of the last level of the Ni XIII target ion. Generally, a good agreement is obtained between our results and the earlier theoretical photoionization cross sections. Moreover, we have used two independent fully relativistic GRASP and FAC codes to calculate fine-structure energy levels, wavelengths, oscillator strengths, transitions rates among the lowest 48 levels belonging to the configuration (3s23p4, 3s3p5, 3p6, 3s23p33d) in Ni XIII. Additionally, radiative lifetimes of all the excited states of Ni XIII are presented. Our results of the atomic structure of Ni XIII show good agreement with other theoretical and experimental results available in the literature. A good agreement is found between our calculated lifetimes and the experimental ones. Our present results are useful for plasma diagnostic of fusion and astrophysical plasmas.

Generalization of soft phonon modes

NASA Astrophysics Data System (ADS)

Rudin, Sven P.

2018-04-01

Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. Here, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system with N atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, PVM0, represents the 3 N -dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, PVM0 serves as a generalization of soft phonon modes. At low temperatures, PVM0 reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case PVM0 culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, PVM0 can be equally well calculated on either side of the structural phase transition. Two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the β phase of uranium, the higher-symmetry structure of which stabilizes with temperature.

Structural, electronic and magnetic properties of carbon doped boron nitride nanowire: Ab initio study

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

Jalilian, Jaafar, E-mail: JaafarJalilian@gmail.com; Kanjouri, Faramarz, E-mail: kanjouri@khu.ac.ir

2016-11-15

Using spin-polarized density functional theory calculations, we demonstrated that carbon doped boron nitride nanowire (C-doped BNNW) has diverse electronic and magnetic properties depending on position of carbon atoms and their percentages. Our results show that only when one carbon atom is situated on the edge of the nanowire, C-doped BNNW is transformed into half-metal. The calculated electronic structure of the C-doped BNNW suggests that doping carbon can induce localized edge states around the Fermi level, and the interaction among localized edge states leads to semiconductor to half-metal transition. Overall, the bond reconstruction causes of appearance of different electronic behavior suchmore » as semiconducting, half-metallicity, nonmagnetic metallic, and ferromagnetic metallic characters. The formation energy of the system shows that when a C atom is doped on surface boron site, system is more stable than the other positions of carbon impurity. Our calculations show that C-doped BNNW may offer unique opportunities for developing nanoscale spintronic materials.« less

Calculation of the electron structure of vacancies and their compensated states in III-VI semiconductors

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

Mehrabova, M. A., E-mail: Mehrabova@mail.ru; Madatov, R. S.

2011-08-15

The Green's functions theory and the bond-orbital model are used as a basis for calculations of the electron structure of local defects-specifically, vacancies and their compensated states in III-VI semiconductors. The energy levels in the band gap are established, and the changes induced in the electron densities in the GaS, GaSe, and InSe semiconductors by anion and cation vacancies and their compensated states are calculated. It is established that, if a vacancy is compensated by an atom of an element from the same subgroup with the same tetrahedral coordination and if the ionic radius of the compensating atom is smallermore » than that of the substituted atom, the local levels formed by the vacancy completely disappear. It is shown that this mechanism of compensation of vacancies provides a means not only for recovering the parameters of the crystal, but for improving the characteristics of the crystal as well.« less

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

DOE PAGES

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.; ...

2018-04-19

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

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

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

Proximity-induced magnetism in transition-metal substituted graphene

DOE PAGES

Crook, Charles B.; Constantin, Costel; Ahmed, Towfiq; ...

2015-08-03

We investigate the interactions between two identical magnetic impurities substituted into a graphene superlattice. Using a first-principles approach, we calculate the electronic and magnetic properties for transition-metal substituted graphene systems with varying spatial separation. These calculations are compared for three different magnetic impurities, manganese, chromium, and vanadium. We determine the electronic band structure, density of states, and Millikan populations (magnetic moment) for each atom, as well as calculate the exchange parameter between the two magnetic atoms as a function of spatial separation. We find that the presence of magnetic impurities establishes a distinct magnetic moment in the graphene lattice, wheremore » the interactions are highly dependent on the spatial and magnetic characteristic between the magnetic and carbon atoms, which leads to either ferromagnetic or antiferromagnetic behavior. Furthermore, through an analysis of the calculated exchange energies and partial density of states, it is determined that interactions between the magnetic atoms can be classified as an RKKY interaction.« less

Thermodynamic Stability of Molybdenum Oxycarbides Formed from Orthorhombic Mo 2 C in Oxygen-Rich Environments

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

Likith, S. R. J.; Farberow, C. A.; Manna, S.

Molybdenum carbide (Mo 2C) nanoparticles and thin films are particularly suitable catalysts for catalytic fast pyrolysis (CFP) as they are effective for deoxygenation and can catalyze certain reactions that typically occur on noble metals. Oxygen deposited during deoxygenation reactions may alter the carbide structure, leading to the formation of oxycarbides, which can determine changes in catalytic activity or selectivity. Despite emerging spectroscopic evidence of bulk oxycarbides, so far there have been no reports of their precise atomic structure or their relative stability with respect to orthorhombic Mo 2C. This knowledge is essential for assessing the catalytic properties of molybdenum (oxy)carbidesmore » for CFP. In this article, we use density functional theory (DFT) calculations to (a) describe the thermodynamic stability of surface and subsurface configurations of oxygen and carbon atoms for a commonly studied Mo-terminated surface of orthorhombic Mo 2C and (b) determine atomic structures for oxycarbides with a Mo:C ratio of 2:1. The surface calculations suggest that oxygen atoms are not stable under the top Mo layer of the Mo 2C(100) surface. Coupling DFT calculations with a polymorph sampling method, we determine (Mo 2C) xO y oxycarbide structures for a wide range of oxygen compositions. Oxycarbides with lower oxygen content (y/x = 2) adopt layered structures reminiscent of the parent carbide phase, with flat Mo layers separated by layers of oxygen and carbon; for higher oxygen content, our results suggest the formation of amorphous phases, as the atomic layers lose their planarity with increasing oxygen content. We characterize the oxidation states of Mo in the oxycarbide structures determined computationally, and simulate their X-ray diffraction (XRD) patterns in order to facilitate comparisons with experiments. Our study may provide a platform for large-scale investigations of the catalytic properties of oxycarbides and their surfaces and for tailoring the catalytic properties for different desired reactions.« less

Thermodynamic Stability of Molybdenum Oxycarbides Formed from Orthorhombic Mo 2 C in Oxygen-Rich Environments

DOE PAGES

Likith, S. R. J.; Farberow, C. A.; Manna, S.; ...

2017-12-20

Molybdenum carbide (Mo 2C) nanoparticles and thin films are particularly suitable catalysts for catalytic fast pyrolysis (CFP) as they are effective for deoxygenation and can catalyze certain reactions that typically occur on noble metals. Oxygen deposited during deoxygenation reactions may alter the carbide structure, leading to the formation of oxycarbides, which can determine changes in catalytic activity or selectivity. Despite emerging spectroscopic evidence of bulk oxycarbides, so far there have been no reports of their precise atomic structure or their relative stability with respect to orthorhombic Mo 2C. This knowledge is essential for assessing the catalytic properties of molybdenum (oxy)carbidesmore » for CFP. In this article, we use density functional theory (DFT) calculations to (a) describe the thermodynamic stability of surface and subsurface configurations of oxygen and carbon atoms for a commonly studied Mo-terminated surface of orthorhombic Mo 2C and (b) determine atomic structures for oxycarbides with a Mo:C ratio of 2:1. The surface calculations suggest that oxygen atoms are not stable under the top Mo layer of the Mo 2C(100) surface. Coupling DFT calculations with a polymorph sampling method, we determine (Mo 2C) xO y oxycarbide structures for a wide range of oxygen compositions. Oxycarbides with lower oxygen content (y/x = 2) adopt layered structures reminiscent of the parent carbide phase, with flat Mo layers separated by layers of oxygen and carbon; for higher oxygen content, our results suggest the formation of amorphous phases, as the atomic layers lose their planarity with increasing oxygen content. We characterize the oxidation states of Mo in the oxycarbide structures determined computationally, and simulate their X-ray diffraction (XRD) patterns in order to facilitate comparisons with experiments. Our study may provide a platform for large-scale investigations of the catalytic properties of oxycarbides and their surfaces and for tailoring the catalytic properties for different desired reactions.« less

Structures and magnetic properties of Co-Zr-B magnets studied by first-principles calculations

DOE PAGES

Zhao, Xin; Ke, Liqin; Nguyen, Manh Cuong; ...

2015-06-23

The structures and magnetic properties of Co-Zr-B alloys near the composition of Co 5Zr with B at. % ≤6% were studied using adaptive genetic algorithm and first-principles calculations. The energy and magnetic moment contour maps as a function of chemical composition were constructed for the Co-Zr-B magnet alloys through extensive structure searches and calculations. We found that Co-Zr-B system exhibits the same structure motif as the “Co 11Zr 2” polymorphs, and such motif plays a key role in achieving strong magnetic anisotropy. Boron atoms were found to be able to substitute cobalt atoms or occupy the “interruption” sites. First-principles calculationsmore » showed that the magnetocrystalline anisotropy energies of the boron-doped alloys are close to that of the high-temperature rhombohedral Co 5Zr phase and larger than that of the low-temperature Co 5.25Zr phase. As a result, our calculations provide useful guidelines for further experimental optimization of the magnetic performances of these alloys.« less

Electronic Structure Calculation of Permanent Magnets using the KKR Green's Function Method

NASA Astrophysics Data System (ADS)

Doi, Shotaro; Akai, Hisazumi

2014-03-01

Electronic structure and magnetic properties of permanent magnetic materials, especially Nd2Fe14B, are investigated theoretically using the KKR Green's function method. Important physical quantities in magnetism, such as magnetic moment, Curie temperature, and anisotropy constant, which are obtained from electronics structure calculations in both cases of atomic-sphere-approximation and full-potential treatment, are compared with past band structure calculations and experiments. The site preference of heavy rare-earth impurities are also evaluated through the calculation of formation energy with the use of coherent potential approximations. Further, the development of electronic structure calculation code using the screened KKR for large super-cells, which is aimed at studying the electronic structure of realistic microstructures (e.g. grain boundary phase), is introduced with some test calculations.

STM study on the surface structures and defects of SnSe

NASA Astrophysics Data System (ADS)

Kim, Jungdae; Duvjir, Ganbat; Ly, Trinh Thi; Min, Taewon; Kim, Taehoon; Kim, Sang Hwa; Duong, Anh-Tuan; Rhim, S. H.; Cho, Sunglae; Lee, Jaekwang

Tin selenide (SnSe) is a IV-VI semiconductor with a band gap of 1.0 eV, and also one of layered chalcogenide materials (LCMs) where each layer is coupled by weak van der Waals interactions. SnSe has been widely studied due to its many potential applications that take advantage of its excellent thermoelectric, photovoltaic, and optoelectronic properties. However, experimental investigations into the microscopic structure of SnSe remain largely unexplored. The atomic and electronic structures of SnSe surfaces are studied by a home-built low temperature scanning tunneling microscope (STM). The cleaved surface of SnSe is comprised of covalently bonded Se and Sn atoms in zigzag patterns. However, rectangular periodicity was observed in the atomic images of SnSe surfaces for filled and empty state probing. Detailed atomic structures are analyzed by density functional theory (DFT) calculations, indicating that the bright extrusions of both filled and empty state images are mostly located at the positions of Sn atoms. We also report the origin of p-type behavior in SnSe by investigating three dominant intrinsic defects (Sn, Se, and Se-Sn-Se vacancies) using STM and DFT calculations. This work was supported by the National Research Foundation of Korea (NRF-2015R1D1A1A01057271, NRF-2009-0093818, and NRF-2014R1A4A1071686).

PDBToSDF: Create ligand structure files from PDB file.

PubMed

Muppalaneni, Naresh Babu; Rao, Allam Appa

2011-01-01

Protein Data Bank (PDB) file contains atomic data for protein and ligand in protein-ligand complexes. Structure data file (SDF) contains data for atoms, bonds, connectivity and coordinates of molecule for ligands. We describe PDBToSDF as a tool to separate the ligand data from pdb file for the calculation of ligand properties like molecular weight, number of hydrogen bond acceptors, hydrogen bond receptors easily.

Atomic structure calculations and identification of EUV and SXR spectral lines in Sr XXX

NASA Astrophysics Data System (ADS)

Goyal, Arun; Khatri, Indu; Aggarwal, Sunny; Singh, A. K.; Mohan, Man

2015-08-01

We report an extensive theoretical study of atomic data for Sr XXX in a wide range with L-shell electron excitations to the M-shell. We have calculated energy levels, wave-function compositions and lifetimes for lowest 113 fine structure levels and wavelengths of an extreme Ultraviolet (EUV) and soft X-ray (SXR) transitions. We have employed multi-configuration Dirac Fock method (MCDF) approach within the framework of Dirac-Coulomb Hamiltonian including quantum electrodynamics (QED) and Breit corrections. We have also presented the radiative data for electric and magnetic dipole (E1, M1) and quadrupole (E2, M2) transitions from the ground state. We have made comparisons with available energy levels compiled by NIST and achieve good agreement. But due to inadequate data in the literature, analogous relativistic distorted wave calculations have also been performed using flexible atomic code (FAC) to assess the reliability and accuracy of our results. Additionally, we have provided new atomic data for Sr XXX which is not published elsewhere in the literature and we believe that our results may be beneficial in fusion plasma research and astrophysical investigations and applications.

DiffPy-CMI-Python libraries for Complex Modeling Initiative

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

Billinge, Simon; Juhas, Pavol; Farrow, Christopher

2014-02-01

Software to manipulate and describe crystal and molecular structures and set up structural refinements from multiple experimental inputs. Calculation and simulation of structure derived physical quantities. Library for creating customized refinements of atomic structures from available experimental and theoretical inputs.

Theoretical studies on the electronic structures and photoelectron spectra of tri-rhenium oxide clusters: Re3O(n)(-) and Re3O(n) (n=1-6).

PubMed

Zhou, Qi; Gong, Wei-Chao; Xie, Lu; Zheng, Cun-Gong; Zhang, Wei; Wang, Bin; Zhang, Yong-Fan; Huang, Xin

2014-01-03

Density functional theory (DFT) calculations are performed to study the structural and electronic properties of tri-rhenium oxide clusters Re3On(-/0) (n=1-6). Generalized Koopmans' theorem is applied to predict the vertical detachment energies (VDEs) and simulate the photoelectron spectra (PES). Theoretical calculations at the B3LYP level are carried out to search for the global minima for both the anions and the neutrals. For the anions, the first two O atoms prefer the same corner position of a Re3 triangle. Whereas, Re3O3(-) possesses a C2v symmetry with one bridging and two terminal O atoms. The next three O atoms (n=4-6) are adding sequentially on the basis of Re3O3(-) motif, i.e., adding one terminal O atom for Re3O4(-), one terminal and one bridging O atoms for Re3O5(-), and one terminal and two bridging O atoms for Re3O6(-), respectively. Their corresponding neutral species are similar to the anions in geometry except Re3O4 and Re3O5. Molecular orbital analyses are employed to investigate the chemical bonding and structural evolution in these tri-rhenium oxide clusters. Copyright © 2013 Elsevier B.V. All rights reserved.

Oxygen adsorption on the Al₉Co₂(001) surface: first-principles and STM study.

PubMed

Villaseca, S Alarcón; Loli, L N Serkovic; Ledieu, J; Fournée, V; Gille, P; Dubois, J-M; Gaudry, E

2013-09-04

Atomic oxygen adsorption on a pure aluminum terminated Al9Co2(001) surface is studied by first-principle calculations coupled with STM measurements. Relative adsorption energies of oxygen atoms have been calculated on different surface sites along with the associated STM images. The local electronic structure of the most favourable adsorption site is described. The preferential adsorption site is identified as a 'bridge' type site between the cluster entities exposed at the (001) surface termination. The Al-O bonding between the adsorbate and the substrate presents a covalent character, with s-p hybridization occurring between the states of the adsorbed oxygen atom and the aluminum atoms of the surface. The simulated STM image of the preferential adsorption site is in agreement with experimental observations. This work shows that oxygen adsorption generates important atomic relaxations of the topmost surface layer and that sub-surface cobalt atoms strongly influence the values of the adsorption energies. The calculated Al-O distances are in agreement with those reported in Al2O and Al2O3 oxides and for oxygen adsorption on Al(111).

Theoretical study of Ag doping-induced vacancies defects in armchair graphene

NASA Astrophysics Data System (ADS)

Benchallal, L.; Haffad, S.; Lamiri, L.; Boubenider, F.; Zitoune, H.; Kahouadji, B.; Samah, M.

2018-06-01

We have performed a density functional theory (DFT) study of the absorption of silver atoms (Ag,Ag2 and Ag3) in graphene using SIESTA code, in the generalized gradient approximation (GGA). The absorption energy, geometry, magnetic moments and charge transfer of Ag clusters-graphene system are calculated. The minimum energy configuration demonstrates that all structures remain planar and silver atoms fit into this plane. The charge transfer between the silver clusters and carbon atoms constituting the graphene surface is an indicative of a strong bond. The structure doped with a single silver atom has a magnetic moment and the two other are nonmagnetic.

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin, E-mail: linlin@math.berkeley.edu; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

DOE PAGES

Zhang, Gaigong; Lin, Lin; Hu, Wei; ...

2017-01-27

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

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

Zhang, Gaigong; Lin, Lin; Hu, Wei

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynmanmore » forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Sin ce the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H 2 and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.« less

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

NASA Astrophysics Data System (ADS)

Zhang, Gaigong; Lin, Lin; Hu, Wei; Yang, Chao; Pask, John E.

2017-04-01

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H2 and liquid Al-Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

Atom chips with free-standing two-dimensional electron gases: advantages and challenges

NASA Astrophysics Data System (ADS)

Sinuco-León, G. A.; Krüger, P.; Fromhold, T. M.

2018-03-01

In this work, we consider the advantages and challenges of using free-standing two-dimensional electron gases (2DEG) as active components in atom chips for manipulating ultracold ensembles of alkali atoms. We calculate trapping parameters achievable with typical high-mobility 2DEGs in an atom chip configuration and identify advantages of this system for trapping atoms at sub-micron distances from the atom chip. We show how the sensitivity of atomic gases to magnetic field inhomogeneity can be exploited for controlling the atoms with quantum electronic devices and, conversely, using the atoms to probe the structural and transport properties of semiconductor devices.

Surface structure. Subatomic resolution force microscopy reveals internal structure and adsorption sites of small iron clusters.

PubMed

Emmrich, Matthias; Huber, Ferdinand; Pielmeier, Florian; Welker, Joachim; Hofmann, Thomas; Schneiderbauer, Maximilian; Meuer, Daniel; Polesya, Svitlana; Mankovsky, Sergiy; Ködderitzsch, Diemo; Ebert, Hubert; Giessibl, Franz J

2015-04-17

Clusters built from individual iron atoms adsorbed on surfaces (adatoms) were investigated by atomic force microscopy (AFM) with subatomic resolution. Single copper and iron adatoms appeared as toroidal structures and multiatom clusters as connected structures, showing each individual atom as a torus. For single adatoms, the toroidal shape of the AFM image depends on the bonding symmetry of the adatom to the underlying structure [twofold for copper on copper(110) and threefold for iron on copper(111)]. Density functional theory calculations support the experimental data. The findings correct our previous work, in which multiple minima in the AFM signal were interpreted as a reflection of the orientation of a single front atom, and suggest that dual and triple minima in the force signal are caused by dimer and trimer tips, respectively. Copyright © 2015, American Association for the Advancement of Science.

Synthesis, crystal structure and electronic structure of the binary phase Rh2Cd5

NASA Astrophysics Data System (ADS)

Koley, Biplab; Chatterjee, S.; Jana, Partha P.

2017-02-01

A new phase in the Rh-Cd binary system - Rh2Cd5 has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh2Cd5 crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh2Cd5 can be described as a defect form of the In3Pd5 structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist of (35) (37)- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh2Cd5.

Conformation and structure of 3-methoxyphenyl-salicylaldimine

NASA Astrophysics Data System (ADS)

Elmali, A.; Kabak, M.; Elerman, Y.

1999-06-01

3-methoxyphenyl-salicylaldimine (C 14H 13NO 2) was studied by X-ray analysis and AM1 molecular orbital methods. It crystallises in the monoclinic space group P2 1/c with a=20.486(4) Å, b=4.7935(8) Å Å, c=12.310(5) Å, β=107.43(2)°, V=1153.3(6) Å 3, Z=4, D 0=1.309 g cm -3, Z=4, and μ(MoK α)=0.088 mm -1. The structure was solved by direct methods and refined to R=0.033 for 1635 reflections [ I<2(( I)]. The title molecule was nearly planar. There was a strong intramolecular hydrogen bond of distance 2.598(2) Å between the hydroxyl oxygen atom and imine nitrogen atom, the hydrogen atom essentially being bonded to the oxygen atom. Minimum energy conformations from AM1 were calculated as a function of the three torsion angles θ1(C8-N1-C7-C6), θ2(N1-C7-C6-C5), and θ3(C9-C8-N1-C7) varied every 10°. The theoretical calculations were carried out to compare with experimental results of the molecular conformations. The optimized geometry of the crystal structure corresponding to a non-planar conformation is the most stable conformation in all theoretical calculations.

Atomic Structure and Properties of Extended Defects in Silicon

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

Buczko, R.; Chisholm, M.F.; Kaplan, T.

1998-10-15

The Z-contrast technique represents a new approach to high-resolution electron microscopy allowing for the first time incoherent imaging of materials on the atomic scale. The key advantages of the technique, an intrinsically higher resolution limit and directly interpretable, compositionally sensitive imaging, allow a new level of insight into the atomic configurations of extended defects in silicon. This experimental technique has been combined with theoretical calculations (a combination of first principles, tight binding, and classical methods) to extend this level of insight by obtaining the energetic and electronic structure of the defects.

Structure and superconductivity in the ternary silicide CaAlSi

NASA Astrophysics Data System (ADS)

Ma, Rong; Huang, Gui-Qin; Liu, Mei

2007-06-01

Using the linear response-linearized Muffin-tin orbital (LR-LMTO) method, we study the electronic band structure, phonon spectra, electron-phonon coupling and superconductivity for c-axis ferromagnetic-like (F-like) and antiferromagnetic-like (AF-like) structures in ternary silicide CaAlSi. The following conclusions are drawn from our calculations. If Al and Si atoms are assumed to arrange along the c axis in an F-like long-range ordering (-Al-Al-Al-and-Si-Si-Si-), one could obtain the ultrasoft B1g phonon mode and thus very strong electron-phonon coupling in CaAlSi. However, the appearance of imaginary frequency phonon modes indicates the instability of such a structure. For Al and Si atoms arranging along the c axis in an AF-like long-range ordering (-Al-Si-Al-), the calculated electron-phonon coupling constant is equal to 0.8 and the logarithmically averaged frequency is 146.8 K. This calculated result can correctly yield the superconducting transition temperature of CaAlSi by the standard BCS theory in the moderate electron-phonon coupling strength. We propose that an AF-like superlattice model for Al (or Si) atoms along the c direction may mediate the inconsistency estimated from theory and experiment, and explain the anomalous superconductivity in CaAlSi.

Mono-Mercury Doping of Au25 and the HOMO/LUMO Energies Evaluation Employing Differential Pulse Voltammetry.

PubMed

Liao, Lingwen; Zhou, Shiming; Dai, Yafei; Liu, Liren; Yao, Chuanhao; Fu, Cenfeng; Yang, Jinlong; Wu, Zhikun

2015-08-05

Controlling the bimetal nanoparticle with atomic monodispersity is still challenging. Herein, a monodisperse bimetal nanoparticle is synthesized in 25% yield (on gold atom basis) by an unusual replacement method. The formula of the nanoparticle is determined to be Au24Hg1(PET)18 (PET: phenylethanethiolate) by high-resolution ESI-MS spectrometry in conjunction with multiple analyses including X-ray photoelectron spectroscopy (XPS) and thermogravimetric analysis (TGA). X-ray single-crystal diffraction reveals that the structure of Au24Hg1(PET)18 remains the structural framework of Au25(PET)18 with one of the outer-shell gold atoms replaced by one Hg atom, which is further supported by theoretical calculations and experimental results as well. Importantly, differential pulse voltammetry (DPV) is first employed to estimate the highest occupied molecular orbit (HOMO) and the lowest unoccupied molecular orbit (LUMO) energies of Au24Hg1(PET)18 based on previous calculations.

First-principles calculations of orientation dependence of Si thermal oxidation based on Si emission model

NASA Astrophysics Data System (ADS)

Nagura, Takuya; Kawachi, Shingo; Chokawa, Kenta; Shirakawa, Hiroki; Araidai, Masaaki; Kageshima, Hiroyuki; Endoh, Tetsuo; Shiraishi, Kenji

2018-04-01

It is expected that the off-state leakage current of MOSFETs can be reduced by employing vertical body channel MOSFETs (V-MOSFETs). However, in fabricating these devices, the structure of the Si pillars sometimes cannot be maintained during oxidation, since Si atoms sometimes disappear from the Si/oxide interface (Si missing). Thus, in this study, we used first-principles calculations based on the density functional theory, and investigated the Si emission behavior at the various interfaces on the basis of the Si emission model including its atomistic structure and dependence on Si crystal orientation. The results show that the order in which Si atoms are more likely to be emitted during thermal oxidation is (111) > (110) > (310) > (100). Moreover, the emission of Si atoms is enhanced as the compressive strain increases. Therefore, the emission of Si atoms occurs more easily in V-MOSFETs than in planar MOSFETs. To reduce Si missing in V-MOSFETs, oxidation processes that induce less strain, such as wet or pyrogenic oxidation, are necessary.

Realisation of magnetically and atomically abrupt half-metal/semiconductor interface: Co2FeSi0.5Al0.5/Ge(111)

PubMed Central

Nedelkoski, Zlatko; Kuerbanjiang, Balati; Glover, Stephanie E.; Sanchez, Ana M.; Kepaptsoglou, Demie; Ghasemi, Arsham; Burrows, Christopher W.; Yamada, Shinya; Hamaya, Kohei; Ramasse, Quentin M.; Hasnip, Philip J.; Hase, Thomas; Bell, Gavin R.; Hirohata, Atsufumi; Lazarov, Vlado K.

2016-01-01

Halfmetal-semiconductor interfaces are crucial for hybrid spintronic devices. Atomically sharp interfaces with high spin polarisation are required for efficient spin injection. In this work we show that thin film of half-metallic full Heusler alloy Co2FeSi0.5Al0.5 with uniform thickness and B2 ordering can form structurally abrupt interface with Ge(111). Atomic resolution energy dispersive X-ray spectroscopy reveals that there is a small outdiffusion of Ge into specific atomic planes of the Co2FeSi0.5Al0.5 film, limited to a very narrow 1 nm interface region. First-principles calculations show that this selective outdiffusion along the Fe-Si/Al atomic planes does not change the magnetic moment of the film up to the very interface. Polarized neutron reflectivity, x-ray reflectivity and aberration-corrected electron microscopy confirm that this interface is both magnetically and structurally abrupt. Finally, using first-principles calculations we show that this experimentally realised interface structure, terminated by Co-Ge bonds, preserves the high spin polarization at the Co2FeSi0.5Al0.5/Ge interface, hence can be used as a model to study spin injection from half-metals into semiconductors. PMID:27869132

Effects of doping Na and Cl atom on electronic structure of silicene: Density functional theory calculation

NASA Astrophysics Data System (ADS)

Pamungkas, Mauludi Ariesto; Sobirin, Kafi; Abdurrouf

2018-04-01

Silicene is a material in which silicon atoms are packed in two-dimensional hexagonal lattice, similar to that of graphene. Compared to graphene, silicene has promising potential to be applied in microelectronic technology because of its compatibility with silicon comonly used in semiconducting devices. Natrium and chlorine are easy to extract and can be used as dopants in FET (Field Effect Transistor). In this work, the effects of adsorption energy and electronic structure of silicene to both natrium and chlorine atoms are calculated with Density Functional Theory (DFT). The results show that dopings of Na transform silicene which is initially semimetal into a metal. Then dopings of Cl Top-site transform silicene into a semiconducting material and doping of Na and Cl simultaneously transfoms silicene into a conducting material.

Strong influence of off-site symmetry positions of hydrogen atoms in ScH3 hcp phases

NASA Astrophysics Data System (ADS)

Pakornchote, T.; Bovornratanaraks, T.; Vannarat, S.; Pinsook, U.

2016-01-01

We investigate the wave-like arrangements of H atoms around metal plane (Hm) in the ScH3 hcp phase by using the ab-initio method. We found that only P63 / mmc, P 3 bar c 1, P63cm and P63 phases are energetically favorable. The wave-like arrangement allows the off-site symmetry positions of the H atoms, and leads to substantial changes in the pair distribution between Sc and H atoms which are associating with the changes in the electronic structure in such a way that the total energy is lowering. The symmetry breaking from P63mmc is also responsible for the band gap opening. In the P63 structure, the calculated band gap is 0.823 eV and 1.223 eV using GGA and sX-LDA functionals, respectively. This band gap can be compared with 1.7 eV derived from the optical measurement and 1.55 eV from the HSE06 calculation. Thus, the broken symmetry structures can be viewed as Peierls distortion of the P63 / mmc structure. Furthermore, we found that only the P63 structure is dynamically stable, unlike YH3 where the P63cm structure is also stable. The stability of P63 comes from sufficiently strong interactions between two neighboring H atoms at their off-site symmetry positions, i.e. near the metal plane and near the tetragonal site. The P63 phonon density of states is in good agreement with the data from the neutron experiment.

Revision of the Li13Si4 structure.

PubMed

Zeilinger, Michael; Fässler, Thomas F

2013-11-06

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li-Si system is the phase Li13Si4 (trideca-lithium tetra-silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10-13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si-Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si-Si dumbbells at z = 0.5.

Communication: Finite size correction in periodic coupled cluster theory calculations of solids.

PubMed

Liao, Ke; Grüneis, Andreas

2016-10-14

We present a method to correct for finite size errors in coupled cluster theory calculations of solids. The outlined technique shares similarities with electronic structure factor interpolation methods used in quantum Monte Carlo calculations. However, our approach does not require the calculation of density matrices. Furthermore we show that the proposed finite size corrections achieve chemical accuracy in the convergence of second-order Møller-Plesset perturbation and coupled cluster singles and doubles correlation energies per atom for insulating solids with two atomic unit cells using 2 × 2 × 2 and 3 × 3 × 3 k-point meshes only.

Doping of the step-edge Si chain: Ag on a Si(557)-Au surface

NASA Astrophysics Data System (ADS)

Krawiec, M.; Jałochowski, M.

2010-11-01

Structural and electronic properties of monatomic Ag chains on the Au-induced, highly ordered Si(557) surface are investigated by scanning tunneling microscopy (STM)/spectroscopy and first-principles density functional theory (DFT) calculations. The STM topography data show that a small amount of Ag (0.25 ML) very weakly modifies the one-dimensional structure induced by Au atoms. However, the bias-dependent STM topography and spectroscopy point to the importance of the electronic effects in this system, which are further corroborated by the DFT calculations. The obtained results suggest that Ag atoms act as electron donors leaving the geometry of the surface almost unchanged.

Synthesis and first-principle calculations of the structural and electronic properties of Ge-substituted type-VIII Ba8Ga16Sn30 clathrate

NASA Astrophysics Data System (ADS)

Shen, Lanxian; Li, Decong; Liu, Hongxia; Liu, Zuming; Deng, Shukang

2016-12-01

In this study, the structural and electronic structural properties of Ba8Ga16Sn30-xGex (0≤x≤30) are determined by the first-principle method on the basis of density functional theory. Consistent with experimental findings, calculated results reveal that Ge atoms preferentially occupy the 2a and 24g sites in these compounds. As the content of Ge in Ge-substituted clathrate is increased, the lattice parameter is decreased, and the structural stability is enhanced. The bandgaps of the compound at 1≤x≤10 are smaller than those of Ba8Ga16Sn30. By contrast, the bandgaps of the compound at x>10 are larger than those of Ba8Ga16Sn30. The substitution of Ge for Sn affects p-type conductivity but not n-type conductivity. As Ge content increases, the whole conduction band moves to the direction of high energy, and the density of states of valence-band top decreases. The calculated potential energy versus displacement of Ba indicates that the vibration energy of this atom increases as cage size decreases. Because Ge substitution also affects clathrate structural symmetry, the distance of Ba atom deviation from the center of the cage initially increases and subsequently decreases as the Ge content increases.

Structures of Mo2Oy- and Mo2Oy (y=2, 3, and 4) studied by anion photoelectron spectroscopy and density functional theory calculations.

PubMed

Yoder, Bruce L; Maze, Joshua T; Raghavachari, Krishnan; Jarrold, Caroline Chick

2005-03-01

The competitive structural isomers of the Mo(2)O(y) (-)Mo(2)O(y) (y=2, 3, and 4) clusters are investigated using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. The PE spectrum and calculations for MoO(3) (-)MoO(3) are also presented to show the level of agreement to be expected between the spectra and calculations. For MoO(3) (-) and MoO(3), the calculations predict symmetric C(3v) structures, an adiabatic electron affinity of 3.34 eV, which is above the observed value 3.17(2) eV. However, there is good agreement between observed and calculated vibrational frequencies and band profiles. The PE spectra of Mo(2)O(2) (-) and Mo(2)O(3) (-) are broad and congested, with partially resolved vibrational structure on the lowest energy bands observed in the spectra. The electron affinities (EA(a)s) of the corresponding clusters are 2.24(2) and 2.33(7) eV, respectively. Based on the calculations, the most stable structure of Mo(2)O(2) (-) is Y shaped, with the two Mo atoms directly bonded. Assignment of the Mo(2)O(3) (-) spectrum is less definitive, but a O-Mo-O-Mo-O structure is more consistent with overall electronic structure observed in the spectrum. The PE spectrum of Mo(2)O(4) (-) shows cleanly resolved vibrational structure and electronic bands, and the EA of the corresponding Mo(2)O(4) is determined to be 2.13(4) eV. The structure most consistent with the observed spectrum has two oxygen bridge bonds between the Mo atoms.

Effects of Al-Impurity Type on Formation Energy, Crystal Structure, Electronic Structure, and Optical Properties of ZnO by Using Density Functional Theory and the Hubbard-U Method.

PubMed

Wu, Hsuan-Chung; Chen, Hsing-Hao; Zhu, Yu-Ren

2016-08-01

We systematically investigated the effects of Al-impurity type on the formation energy, crystal structure, charge density, electronic structure, and optical properties of ZnO by using density functional theory and the Hubbard-U method. Al-related defects, such as those caused by the substitution of Zn and O atoms by Al atoms (Al s(Zn) and Al s(O) , respectively) and the presence of an interstitial Al atom at the center of a tetrahedron (Al i(tet) ) or an octahedron (Al i(oct) ), and various Al concentrations were evaluated. The calculated formation energy follows the order E f (Al s(Zn) ) < E f (Al i(tet) ) < E f (Al i(oct) ) < E f (Al s(O) ). Electronic structure analysis showed that the Al s(Zn) , Al s(O) , Al i(tet) , and Al i(oct) models follow n -type conduction, and the optical band gaps are higher than that of pure ZnO. The calculated carrier concentrations of the Al s(O) and Al i(tet) /Al i(oct) models are higher than that of the Al s(Zn) model. However, according to the curvature of the band structure, the occurrence of interstitial Al atoms or the substitution of O atoms by Al atoms results in a high effective mass, possibly reducing the carrier mobility. The average transmittance levels in the visible light and ultraviolet (UV) regions of the Al s(Zn) model are higher than those of pure ZnO. However, the presence of an interstitial Al atom within the ZnO crystal reduces transmittance in the visible light region; Al s(O) substantially reduces the transmittance in the visible light and UV regions. In addition, the properties of ZnO doped with various Al s(Zn) concentrations were analyzed.

Theoretical Study of tip apex electronic structure in Scanning Tunneling Microscope

NASA Astrophysics Data System (ADS)

Choi, Heesung; Huang, Min; Randall, John; Cho, Kyeongjae

2011-03-01

Scanning Tunneling Microscope (STM) has been widely used to explore diverse surface properties with an atomic resolution, and STM tip has played a critical role in controlling surface structures. However, detailed information of atomic and electronic structure of STM tip and the fundamental understanding of STM images are still incomplete. Therefore, it is important to develop a comprehensive understanding of the electronic structure of STM tip. We have studied the atomic and electronic structures of STM tip with various transition metals (TMs) by DFT method. The d-electrons of TM tip apex atoms show different orbital states near the Fermi level. We will present comprehensive data of STM tips from our DFT calculation. Verified quantification of the tip electronic structures will lead to fundamental understanding of STM tip structure-property relationship. This work is supported by the DARPA TBN Program and the Texas ETF. DARPA Tip Based Nanofabrication Program and the Emerging Technology Fund of the State of Texas.

Quantum Monte Carlo study of the phase diagram of solid molecular hydrogen at extreme pressures

PubMed Central

Drummond, N. D.; Monserrat, Bartomeu; Lloyd-Williams, Jonathan H.; Ríos, P. López; Pickard, Chris J.; Needs, R. J.

2015-01-01

Establishing the phase diagram of hydrogen is a major challenge for experimental and theoretical physics. Experiment alone cannot establish the atomic structure of solid hydrogen at high pressure, because hydrogen scatters X-rays only weakly. Instead, our understanding of the atomic structure is largely based on density functional theory (DFT). By comparing Raman spectra for low-energy structures found in DFT searches with experimental spectra, candidate atomic structures have been identified for each experimentally observed phase. Unfortunately, DFT predicts a metallic structure to be energetically favoured at a broad range of pressures up to 400 GPa, where it is known experimentally that hydrogen is non-metallic. Here we show that more advanced theoretical methods (diffusion quantum Monte Carlo calculations) find the metallic structure to be uncompetitive, and predict a phase diagram in reasonable agreement with experiment. This greatly strengthens the claim that the candidate atomic structures accurately model the experimentally observed phases. PMID:26215251

Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

PubMed

Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

2017-03-07

The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

Atom by atom: HRTEM insights into inorganic nanotubes and fullerene-like structures

PubMed Central

Sadan, Maya Bar; Houben, Lothar; Enyashin, Andrey N.; Seifert, Gotthard; Tenne, Reshef

2008-01-01

The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS2 nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS2 nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism. PMID:18838681

Atom by atom: HRTEM insights into inorganic nanotubes and fullerene-like structures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Enyashin, Andrey N; Seifert, Gotthard; Tenne, Reshef

2008-10-14

The characterization of nanostructures down to the atomic scale is essential to understand some physical properties. Such a characterization is possible today using direct imaging methods such as aberration-corrected high-resolution transmission electron microscopy (HRTEM), when iteratively backed by advanced modeling produced by theoretical structure calculations and image calculations. Aberration-corrected HRTEM is therefore extremely useful for investigating low-dimensional structures, such as inorganic fullerene-like particles and inorganic nanotubes. The atomic arrangement in these nanostructures can lead to new insights into the growth mechanism or physical properties, where imminent commercial applications are unfolding. This article will focus on two structures that are symmetric and reproducible. The first structure that will be dealt with is the smallest stable symmetric closed-cage structure in the inorganic system, a MoS(2) nanooctahedron. It is investigated by means of aberration-corrected microscopy which allowed validating the suggested DFTB-MD model. It will be shown that structures diverging from the energetically most stable structures are present in the laser ablated soot and that the alignment of the different shells is parallel, unlike the bulk material where the alignment is antiparallel. These findings correspond well with the high-energy synthetic route and they provide more insight into the growth mechanism. The second structure studied is WS(2) nanotubes, which have already been shown to have a unique structure with very desirable mechanical properties. The joint HRTEM study combined with modeling reveals new information regarding the chirality of the different shells and provides a better understanding of their growth mechanism.

A 3D QSAR pharmacophore model and quantum chemical structure--activity analysis of chloroquine(CQ)-resistance reversal.

PubMed

Bhattacharjee, Apurba K; Kyle, Dennis E; Vennerstrom, Jonathan L; Milhous, Wilbur K

2002-01-01

Using CATALYST, a three-dimensional QSAR pharmacophore model for chloroquine(CQ)-resistance reversal was developed from a training set of 17 compounds. These included imipramine (1), desipramine (2), and 15 of their analogues (3-17), some of which fully reversed CQ-resistance, while others were without effect. The generated pharmacophore model indicates that two aromatic hydrophobic interaction sites on the tricyclic ring and a hydrogen bond acceptor (lipid) site at the side chain, preferably on a nitrogen atom, are necessary for potent activity. Stereoelectronic properties calculated by using AM1 semiempirical calculations were consistent with the model, particularly the electrostatic potential profiles characterized by a localized negative potential region by the side chain nitrogen atom and a large region covering the aromatic ring. The calculated data further revealed that aminoalkyl substitution at the N5-position of the heterocycle and a secondary or tertiary aliphatic aminoalkyl nitrogen atom with a two or three carbon bridge to the heteroaromatic nitrogen (N5) are required for potent "resistance reversal activity". Lowest energy conformers for 1-17 were determined and optimized to afford stereoelectronic properties such as molecular orbital energies, electrostatic potentials, atomic charges, proton affinities, octanol-water partition coefficients (log P), and structural parameters. For 1-17, fairly good correlation exists between resistance reversal activity and intrinsic basicity of the nitrogen atom at the tricyclic ring system, frontier orbital energies, and lipophilicity. Significantly, nine out of 11 of a group of structurally diverse CQ-resistance reversal agents mapped very well on the 3D QSAR pharmacophore model.

Structure of alkali tellurite glasses from neutron diffraction and molecular orbital calculations

NASA Astrophysics Data System (ADS)

Niida, Haruki; Uchino, Takashi; Jin, Jisun; Kim, Sae-Hoon; Fukunaga, Toshiharu; Yoko, Toshinobu

2001-01-01

The structure of pure TeO2 and alkali tellurite glasses has been examined by neutron diffraction and ab initio molecular orbital methods. The experimental radial distribution functions along with the calculated results have demonstrated that the basic structural units in tellurite glasses change from highly strained TeO4 trigonal bipyramids to more regular TeO3 trigonal pyramids with increasing alkali content. It has also been shown that the TeO3 trigonal pyramids do not exist in the form of isolated units in the glass network but interact with each other to form intertrigonal Te⋯O linkages. The present results suggest that nonbridging oxygen (NBO) atoms in tellurite glasses do not exist in their "pure" form; that is, all the NBO atoms in TeO3 trigonal bipyramids will interact with the first- and/or second-neighbor Te atoms, resulting in the three-dimensional continuous random network even in tellurite glasses with over 30 mol % of alkali oxides.

Diffusion and viscosity of liquid tin: Green-Kubo relationship-based calculations from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Mouas, Mohamed; Gasser, Jean-Georges; Hellal, Slimane; Grosdidier, Benoît; Makradi, Ahmed; Belouettar, Salim

2012-03-01

Molecular dynamics (MD) simulations of liquid tin between its melting point and 1600 °C have been performed in order to interpret and discuss the ionic structure. The interactions between ions are described by a new accurate pair potential built within the pseudopotential formalism and the linear response theory. The calculated structure factor that reflects the main information on the local atomic order in liquids is compared to diffraction measurements. Having some confidence in the ability of this pair potential to give a good representation of the atomic structure, we then focused our attention on the investigation of the atomic transport properties through the MD computations of the velocity autocorrelation function and stress autocorrelation function. Using the Green-Kubo formula (for the first time to our knowledge for liquid tin) we determine the macroscopic transport properties from the corresponding microscopic time autocorrelation functions. The selfdiffusion coefficient and the shear viscosity as functions of temperature are found to be in good agreement with the experimental data.

Simulation of atomic diffusion in the Fcc NiAl system: A kinetic Monte Carlo study

DOE PAGES

Alfonso, Dominic R.; Tafen, De Nyago

2015-04-28

The atomic diffusion in fcc NiAl binary alloys was studied by kinetic Monte Carlo simulation. The environment dependent hopping barriers were computed using a pair interaction model whose parameters were fitted to relevant data derived from electronic structure calculations. Long time diffusivities were calculated and the effect of composition change on the tracer diffusion coefficients was analyzed. These results indicate that this variation has noticeable impact on the atomic diffusivities. A reduction in the mobility of both Ni and Al is demonstrated with increasing Al content. As a result, examination of the pair interaction between atoms was carried out formore » the purpose of understanding the predicted trends.« less

Nanothermodynamics of iron clusters: Small clusters, icosahedral and fcc-cuboctahedral structures

NASA Astrophysics Data System (ADS)

Angelié, C.; Soudan, J.-M.

2017-05-01

The study of the thermodynamics and structures of iron clusters has been carried on, focusing on small clusters and initial icosahedral and fcc-cuboctahedral structures. Two combined tools are used. First, energy intervals are explored by the Monte Carlo algorithm, called σ-mapping, detailed in the work of Soudan et al. [J. Chem. Phys. 135, 144109 (2011), Paper I]. In its flat histogram version, it provides the classical density of states, gp(Ep), in terms of the potential energy of the system. Second, the iron system is described by a potential which is called "corrected EAM" (cEAM), explained in the work of Basire et al. [J. Chem. Phys. 141, 104304 (2014), Paper II]. Small clusters from 3 to 12 atoms in their ground state have been compared first with published Density Functional Theory (DFT) calculations, giving a complete agreement of geometries. The series of 13, 55, 147, and 309 atom icosahedrons is shown to be the most stable form for the cEAM potential. However, the 147 atom cluster has a special behaviour, since decreasing the energy from the liquid zone leads to the irreversible trapping of the cluster in a reproducible amorphous state, 7.38 eV higher in energy than the icosahedron. This behaviour is not observed at the higher size of 309 atoms. The heat capacity of the 55, 147, and 309 atom clusters revealed a pronounced peak in the solid zone, related to a solid-solid transition, prior to the melting peak. The corresponding series of 13, 55, and 147 atom cuboctahedrons has been compared, underscoring the unstability towards the icosahedral structure. This unstability occurs clearly in several steps for the 147 atom cluster, with a sudden transformation at a transition state. This illustrates the concerted icosahedron-cuboctahedron transformation of Buckminster Fuller-Mackay, which is calculated for the cEAM potential. Two other clusters of initial fcc structures with 24 and 38 atoms have been studied, as well as a 302 atom cluster. Each one relaxes towards a more stable structure without regularity. The 38 atom cluster exhibits a nearly glassy relaxation, through a cascade of six metastable states of long life. This behaviour, as that of the 147 atom cluster towards the amorphous state, shows that difficulties to reach ergodicity in the lower half of the solid zone are related to particular features of the potential energy landscape, and not necessarily to a too large size of the system. Comparisons of the cEAM iron system with published results about Lennard-Jones systems and DFT calculations are made. The results of the previous clusters have been combined with that of Paper II to plot the cohesive energy Ec and the melting temperature Tm in terms of the cluster atom number Nat. The Nat -1 /3 linear dependence of the melting temperature (Pawlow law) is observed again for Nat > 150. In contrast, for Nat < 150, the curve diverges strongly from the Pawlow law, giving it an overall V-shape, with a linear increase of Tm when Nat goes from 55 to 13 atoms. Surprisingly, the 38 atom cluster is anomalously below the overall curve.

Insight into the Dzyaloshinskii-Moriya interaction through first-principles study of chiral magnetic structures

NASA Astrophysics Data System (ADS)

Sandratskii, L. M.

2017-07-01

The purpose of the paper is to gain deeper insight into microscopic formation of the Dzyaloshinskii-Moriya interaction (DMI). The paper aims at the development of the physical picture able to address apparently contradicting conclusions of recent studies concerning the location of the DMI energy in the real and reciprocal spaces as well as the relation between values of the atomic moments and the DMI strength. The main tools of our study are the first-principles calculations of the energies of the spiral magnetic states with opposite chiralities. We suggest a method of the calculation of the spiral structures with account for the spin-orbit coupling (SOC). It is based on the application of the generalized Bloch theorem and generalized Bloch functions and allows to reduce the consideration of arbitrary incommensurate spiral to small chemical unit cell. The method neglects the anisotropy in the plane orthogonal to the rotation axis of the spirals that does not influence importantly the DMI energy. For comparison, the supercell calculation with full account for the SOC is performed. The concrete calculations are performed for the Co/Pt bilayer. We consider the distribution of the DMI energy in both real and reciprocal spaces and the dependence of the DMI on the number of electrons. The results of the calculations reveal a number of energy compensations in the formation of the DMI. Thus, the partial atomic contributions as functions of the spiral wave vector q are nonmonotonic and have strongly varying slopes. However, in the total DMI energy these atom-related features compensate each other, resulting in a smooth q dependence. The reason for the peculiar form of the partial DMI contributions is a q -dependent difference in the charge distribution between q and -q spirals. The strongly q -dependent relation between atomic contributions shows that the real-space distribution of the DMI energy obtained for a selected q value cannot be considered as a general characteristic of a given material. Our study shows that it is physically most consistent to consider the electronic hybridization as a primary effect reflecting the nature of the DMI whereas the q -dependent real-space distribution of the DMI energy is a consequence of the complex processes in the electronic structure including the charge transfer process. The physical process of the DMI formation is connected with the difference in the hybridization of the Co and Pt states for q and -q spirals under the influence of the SOC and broken spatial inversion. It depends sensitively on details of the electronic structure. The calculations with constraints on the values of the Co and Pt atomic moments show that there is no direct relation between these atomic quantities and the DMI strength since the details of the electronic structure crucial for the DMI are not reflected in these integral characteristics. The application of the method to the calculation of the magnon energies in systems with DMI is briefly addressed.

Atomic-scale properties of Ni-based FCC ternary, and quaternary alloys

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

Tamm, Artur; Aabloo, Alvo; Klintenberg, Mattias

2015-08-26

The aim of our study is to characterize some atomic-scale properties of Ni-based FCC multicomponent alloys. For this purpose, we use Monte Carlo method combined with density functional theory calculations to study short-range order (SRO), atomic displacements, electronic density of states, and magnetic moments in equimolar ternary NiCrCo, and quaternary NiCrCoFe alloys. The salient features for the ternary alloy are a negative SRO parameter between Ni Cr and a positive between Cr Cr pairs as well as a weakly magnetic state. For the quaternary alloy we predict negative SRO parameter for Ni Cr and Ni Fe pairs and positive formore » Cr Cr and Fe Fe pairs. Atomic displacements for both ternary and quaternary alloys are negligible. In contrast to the ternary, the quaternary alloy shows a complex magnetic structure. The electronic structure of the ternary and quaternary alloys shows differences near the Fermi energy between a random solid solution and the predicted structure with SRO. Despite that, the calculated EXAFS spectra does not show enough contrast to discriminate between random and ordered structures. Finally, the predicted SRO has an impact on point-defect energetics, electron phonon coupling and thermodynamic functions and thus, SRO should not be neglected when studying properties of these two alloys.« less

Peculiar bonding associated with atomic doping and hidden honeycombs in borophene

NASA Astrophysics Data System (ADS)

Lee, Chi-Cheng; Feng, Baojie; D'angelo, Marie; Yukawa, Ryu; Liu, Ro-Ya; Kondo, Takahiro; Kumigashira, Hiroshi; Matsuda, Iwao; Ozaki, Taisuke

2018-02-01

Engineering atomic-scale structures allows great manipulation of physical properties and chemical processes for advanced technology. We show that the B atoms deployed at the centers of honeycombs in boron sheets, borophene, behave as nearly perfect electron donors for filling the graphitic σ bonding states without forming additional in-plane bonds by first-principles calculations. The dilute electron density distribution owing to the weak bonding surrounding the center atoms provides easier atomic-scale engineering and is highly tunable via in-plane strain, promising for practical applications, such as modulating the extraordinarily high thermal conductance that exceeds the reported value in graphene. The hidden honeycomb bonding structure suggests an unusual energy sequence of core electrons that has been verified by our high-resolution core-level photoelectron spectroscopy measurements. With the experimental and theoretical evidence, we demonstrate that borophene exhibits a peculiar bonding structure and is distinctive among two-dimensional materials.

Molecular, crystal, and electronic structure of the cobalt(II) complex with 10-(2-benzothiazolylazo)-9-phenanthrol

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

Linko, R. V., E-mail: rlinko@mail.ru; Sokol, V. I.; Polyanskaya, N. A.

2013-05-15

The reaction of 10-(2-benzothiazolylazo)-9-phenanthrol (HL) with cobalt(II) acetate gives the coordination compound [CoL{sub 2}] {center_dot} CHCl{sub 3} (I). The molecular and crystal structure of I is determined by X-ray diffraction. The coordination polyhedron of the Co atom in complex I is an octahedron. The anion L acts as a tridentate chelating ligand and is coordinated to the Co atom through the phenanthrenequinone O1 atom and the benzothiazole N1 atom of the moieties L and the N3 atom of the azo group to form two five-membered metallocycles. The molecular and electronic structures of the compounds HL, L, and CoL{sub 2} aremore » studied at the density functional theory level. The results of the quantum-chemical calculations are in good agreement with the values determined by X-ray diffraction.« less

Widths of atomic 4s and 4p vacancy states, 46 less than or equal to Z less than or equal to 50

NASA Technical Reports Server (NTRS)

Hsiungchen, M.; Crasemann, B.; Yin, L. I.; Tsang, T.; Adler, I.

1975-01-01

Auger and X-ray photoelectron spectra involving N1, N2, and N3 vacancy states of Pd, Ag, Cd, In, and Sn were measured and compared with results of free atom calculations. As previously observed in Cu and Zn Auger spectra that involve 3d-band electrons, free-atom characteristics with regard to widths and structure were found in the Ag and Cd M4-N4,5N4,5 and M5-N4,5N4,5 Auger spectra that arise from transitions of 4d-band electrons. Theoretical N1 widths computed with calculated free-atom Auger energies agree well with measurements. Theory however predicts wider N2 than N3 vacancy states (as observed for Xe), while the measured N2 and N3 widths are nearly equal to each other and to the average of the calculated N2 and N3 widths. The calculations are made difficult by the exceedingly short lifetime of some 4p vacancies and by the extreme sensitivity of super-Coster-Kronig rates, which dominate the deexcitation, to the transition energy and to the fine details of the atomic potential.

Janus Monolayer Transition-Metal Dichalcogenides.

PubMed

Zhang, Jing; Jia, Shuai; Kholmanov, Iskandar; Dong, Liang; Er, Dequan; Chen, Weibing; Guo, Hua; Jin, Zehua; Shenoy, Vivek B; Shi, Li; Lou, Jun

2017-08-22

The crystal configuration of sandwiched S-Mo-Se structure (Janus SMoSe) at the monolayer limit has been synthesized and carefully characterized in this work. By controlled sulfurization of monolayer MoSe 2 , the top layer of selenium atoms is substituted by sulfur atoms, while the bottom selenium layer remains intact. The structure of this material is systematically investigated by Raman, photoluminescence, transmission electron microscopy, and X-ray photoelectron spectroscopy and confirmed by time-of-flight secondary ion mass spectrometry. Density functional theory (DFT) calculations are performed to better understand the Raman vibration modes and electronic structures of the Janus SMoSe monolayer, which are found to correlate well with corresponding experimental results. Finally, high basal plane hydrogen evolution reaction activity is discovered for the Janus monolayer, and DFT calculation implies that the activity originates from the synergistic effect of the intrinsic defects and structural strain inherent in the Janus structure.

Janus Monolayer Transition-Metal Dichalcogenides

DOE PAGES

Zhang, Jing; Jia, Shuai; Kholmanov, Iskandar; ...

2017-08-03

In this work, the crystal configuration of sandwiched S–Mo–Se structure (Janus SMoSe) at the monolayer limit has been synthesized and carefully characterized. By controlled sulfurization of monolayer MoSe 2, the top layer of selenium atoms is substituted by sulfur atoms, while the bottom selenium layer remains intact. Furthermore, the structure of this material is systematically investigated by Raman, photoluminescence, transmission electron microscopy, and X-ray photoelectron spectroscopy and confirmed by time-of-flight secondary ion mass spectrometry. Density functional theory (DFT) calculations are performed to better understand the Raman vibration modes and electronic structures of the Janus SMoSe monolayer, which are found tomore » correlate well with corresponding experimental results. Finally, high basal plane hydrogen evolution reaction activity is discovered for the Janus monolayer, and DFT calculation implies that the activity originates from the synergistic effect of the intrinsic defects and structural strain inherent in the Janus structure.« less

The structural and magnetic properties of Fe2-xNiGa1+x Heusler alloys

NASA Astrophysics Data System (ADS)

Zhang (张玉洁), Y. J.; Xi (郗学奎), X. K.; Meng (孟凡斌), F. B.; Wang (王文洪), W. H.; Liu (刘恩克), E. K.; Chen (陈京兰), J. L.; Wu (吴光恒), G. H.

2015-04-01

The structural and magnetic properties of Fe2-xNiGa1+x (x=0~1) Heusler alloys have been investigated by experimental observation and calculation. In this system, a structural transition is found as a function of composition. A higher Ga content leads to an atomic-order transformation from Hg2CuTi to B2. The magnetization decreases due to the dilution effect and the competition between the magnetic interactions and enhanced covalent bonding. The calculation of electronic structure indicates that adding Ga enhances the p-d orbital hybridization between the transition-metal and main-group-element atoms at nearest-neighbor distance. A magnetic and a structural phase diagram have been obtained in which the composition dependences of the lattice constant, the ordering temperature and the Curie temperature show cusps at a critical composition of x=0.32.

New structures of Fe3S for rare-earth-free permanent magnets

NASA Astrophysics Data System (ADS)

Yu, Shu; Zhao, Xin; Wu, Shunqing; Nguyen, Manh Cuong; Zhu, Zi-zhong; Wang, Cai-Zhuang; Ho, Kai-Ming

2018-02-01

We applied an adaptive genetic algorithm (AGA) to search for low-energy crystal structures of Fe3S. A number of structures with energies lower than that of the experimentally reported Pnma and I-4 structures have been obtained from our AGA searches. These low-energy structures can be classified as layer-motif and column-motif structures. In the column-motif structures, Fe atoms self-assemble into rods with a bcc type of underlying lattice, which are separated by the holes terminated by S atoms. In the layer-motif structures, the bulk Fe is broken into slabs of several layers passivated by S atoms. Magnetic property calculations showed that the column-motif structures exhibit reasonably high uniaxial magnetic anisotropy. In addition, we examined the effect of Co doping to Fe3S and found that magnetic anisotropy can be enhanced through Co doping.

New structures of Fe3S for rare-earth-free permanent magnets

DOE PAGES

Yu, Shu; Zhao, Xin; Wu, Shunqing; ...

2018-02-25

We applied adaptive genetic algorithm (AGA) to search for low-energy crystal structures of Fe 3S. A number of structures with energies lower than that of the experimentally reported Pnma and I-4 structures have been obtained from our AGA searches. These low-energy structures can be classified as layer-motif and column-motif structures. In the column-motif structures, Fe atoms self-assemble into rods with bcc type of underlying lattice, which are separated by the holes terminated by S atoms. In the layer-motif structures, the bulk Fe is broken into slabs of several layers passivated by S atoms. Magnetic properties calculations showed that the column-motifmore » structures exhibit reasonably high uniaxial magnetic anisotropy. In addition, we examined the effect of Co doping to Fe 3S and found magnetic anisotropy can be enhanced through Co doping.« less

Generalization of soft phonon modes

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

Rudin, Sven P.

Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. In this paper, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system withmore » $N$ atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, $${\\mathrm{PVM}}_{0}$$, represents the $3N$-dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, $${\\mathrm{PVM}}_{0}$$ serves as a generalization of soft phonon modes. At low temperatures, $${\\mathrm{PVM}}_{0}$$ reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case $${\\mathrm{PVM}}_{0}$$ culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, $${\\mathrm{PVM}}_{0}$$ can be equally well calculated on either side of the structural phase transition. Finally, two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the $${\\beta}$$ phase of uranium, the higher-symmetry structure of which stabilizes with temperature.« less

Generalization of soft phonon modes

DOE PAGES

Rudin, Sven P.

2018-04-27

Soft phonon modes describe a collective movement of atoms that transform a higher-symmetry crystal structure into a lower-symmetry crystal structure. Such structural transformations occur at finite temperatures, where the phonons (i.e., the low-temperature vibrational modes) and the static perfect crystal structures provide an incomplete picture of the dynamics. In this paper, principal vibrational modes (PVMs) are introduced as descriptors of the dynamics of a material system withmore » $N$ atoms. The PVMs represent the independent collective movements of the atoms at a given temperature. Molecular dynamics (MD) simulations, here in the form of quantum MD using density functional theory calculations, provide both the data describing the atomic motion and the data used to construct the PVMs. The leading mode, $${\\mathrm{PVM}}_{0}$$, represents the $3N$-dimensional direction in which the system moves with greatest amplitude. For structural phase transitions, $${\\mathrm{PVM}}_{0}$$ serves as a generalization of soft phonon modes. At low temperatures, $${\\mathrm{PVM}}_{0}$$ reproduces the soft phonon mode in systems where one phonon dominates the phase transformation. In general, multiple phonon modes combine to describe a transformation, in which case $${\\mathrm{PVM}}_{0}$$ culls these phonon modes. Moreover, while soft phonon modes arise in the higher-symmetry crystal structure, $${\\mathrm{PVM}}_{0}$$ can be equally well calculated on either side of the structural phase transition. Finally, two applications demonstrate these properties: first, transitions into and out of bcc titanium, and, second, the two crystal structures proposed for the $${\\beta}$$ phase of uranium, the higher-symmetry structure of which stabilizes with temperature.« less

Amp: A modular approach to machine learning in atomistic simulations

NASA Astrophysics Data System (ADS)

Khorshidi, Alireza; Peterson, Andrew A.

2016-10-01

Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which makes it compatible with a wide variety of commercial and open-source electronic structure codes. We finally demonstrate that the neural network model inside Amp can accurately interpolate electronic structure energies as well as forces of thousands of multi-species atomic systems.

Electronic structure of the heavy-fermion caged compound Ce 3 Pd 20 X 6 ( X = Si, Ge ) studied by density functional theory and photoelectron spectroscopy

DOE PAGES

Yamaoka, Hitoshi; Schwier, Eike F.; Arita, Masashi; ...

2015-03-30

The electronic structure of Ce₃Pd₂₀X₆ (X = Si, Ge) has been studied using detailed density functional theory (DFT) calculations and high-resolution photoelectron spectroscopy (PES) measurements. The orbital decomposition of the electronic structure by DFT calculations indicates that Ce atoms at the (8c) site surrounded by 16 Pd atoms have a more localized nature and a tendency to be magnetic. Ce atoms in the (4a) site surrounded by 12 Pd and 6 X atoms, on the other, show only a negligible magnetic moment. In the photoemission valence-band spectra we observe a strong f⁰ (Ce⁴⁺) component with a small fraction of f¹more » (Ce³⁺) component. The spectral weight of f¹ component near the Fermi level Ce₃Pd₂₀Si₆ is stronger than that for Ce₃Pd₂₀Ge₆ at the 4d-4f resonance, suggesting stronger c-f hybridization in the former. This may hint to the origin of the large electronic specific coefficient of Ce₃Pd₂₀Si₆ compared to Ce₃Pd₂₀Ge₆.« less

Calculations of rate constants for the three-body recombination of H2 in the presence of H2

NASA Technical Reports Server (NTRS)

Schwenke, David W.

1988-01-01

A new global potential energy hypersurface for H2 + H2 is constructed and quasiclassical trajectory calculations performed using the resonance complex theory and energy transfer mechanism to estimate the rate of three body recombination over the temperature range 100 to 5000 K. The new potential is a faithful representation of ab initio electron structure calculations, is unchanged under the operation of exchanging H atoms, and reproduces the accurate H3 potential as one H atom is pulled away. Included in the fitting procedure are geometries expected to be important when one H2 is near or above the dissociation limit. The dynamics calculations explicitly include the motion of all four atoms and are performed efficiently using a vectorized variable-stepsize integrator. The predicted rate constants are approximately a factor of two smaller than experimental estimates over a broad temperature range.

Self-consistent-field KKR-CPA calculations in the atomic-sphere approximations

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

Singh, P.P. Gonis, A.; de Fontaine, D.

1991-12-03

We present a formulation of the Korringa-Kohn-Rostoker coherent potential approximation (KKR-CPA) for the treatment of substitutionally disordered alloys within the KKR atomic-sphere approximations (ASA). This KKR-ASA-CPA represents the first step toward the implementation of a full cell potential CPA, and combines the accuracy of the KKR-CPA method with the flexibility of treating complex crystal structures. The accuracy of this approach has been tested by comparing the self-consistent-field (SCF) KKR-ASA-CPA calculations of Cu-Pd alloys with experimental results and previous SCF-KKR-CPA calculations.

New group-V elemental bilayers: A tunable structure model with four-, six-, and eight-atom rings

NASA Astrophysics Data System (ADS)

Kong, Xiangru; Li, Linyang; Leenaerts, Ortwin; Liu, Xiong-Jun; Peeters, François M.

2017-07-01

Two-dimensional group-V elemental materials have attracted widespread attention due to their nonzero band gap while displaying high electron mobility. Using first-principles calculations, we propose a series of new elemental bilayers with group-V elements (Bi, Sb, As). Our study reveals the dynamical stability of four-, six-, and eight-atom ring structures, demonstrating their possible coexistence in such bilayer systems. The proposed structures for Sb and As are large-gap semiconductors that are potentially interesting for applications in future nanodevices. The Bi structures have nontrivial topological properties with a direct nontrivial band gap. The nontrivial gap is shown to arise from a band inversion at the Brillouin zone center due to the strong intrinsic spin-orbit coupling in Bi atoms. Moreover, we demonstrate the possibility of tuning the properties of these materials by enhancing the ratio of six-atom rings to four- and eight-atom rings, which results in wider nontrivial band gaps and lower formation energies.

Electronic structure studies of a clock-reconstructed Al/Pd(1 0 0) surface alloy

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Tainter, Craig J.

We have employed solid-state Fenske-Hall band structure calculations to examine the electronic structure of Al/Pd(1 0 0), a surface alloy that undergoes a reconstruction, or rearrangement, of the atoms in the top few surface layers. Surface alloys are materials that consist primarily of a single elemental metal, but which have a bimetallic surface composition that is only a few atomic layers in thickness. The results of this study indicate that reconstruction into a clock configuration simultaneously optimizes the intralayer bonding within the surface plane and the bonding between the first and second atomic layers. These results also allow us to examine the fundamental relationship between the electronic and physical structures of this reconstructed surface alloy.

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

Zhu, Li; Fuhrer, Tobias; Schaefer, Bastian

Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe periodic systems, are quantities not directly suitable as fingerprints to distinguish structures. Based on a characterization of the local environment of all atoms in a cell, we introduce crystal fingerprints that can be calculated easily and define configurational distances between crystalline structures that satisfy the mathematical properties of a metric. This distance between two configurations is a measure of their similarity/dissimilarity and it allows in particular to distinguish structures.more » The new method can be a useful tool within various energy landscape exploration schemes, such as minima hopping, random search, swarm intelligence algorithms, and high-throughput screenings.« less

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.

Ab initio investigation of competing antiferromagnetic structures in low Si-content FeMn(PSi) alloy

NASA Astrophysics Data System (ADS)

Li, Guijiang; Eriksson, Olle; Johansson, Börje; Vitos, Levente

2016-06-01

The antiferromagnetic structures of a low Si-content FeMn(PSi) alloy were investigated by first principles calculations. One possible antiferromagnetic structure in supercell along the c-axis was revealed in FeMnP0.75Si0.25 alloy. It was found that atomic disorder occupation between Fe atom on 3f and Mn atoms on 3g sites is responsible for the formation of antiferromagnetic structures. Furthermore the magnetic competition and the coupling between possible AFM supercells along the c and a-axis can promote a non-collinear antiferromagnetic structure. These theoretical investigations help to deeply understand the magnetic order in FeMn(PSi) alloys and benefit to explore the potential magnetocaloric materials in Fe2P-type alloys.

Structure assignment, electronic properties, and magnetism quenching of endohedrally doped neutral silicon clusters, Si(n)Co (n = 10-12).

PubMed

Li, Yejun; Tam, Nguyen Minh; Claes, Pieterjan; Woodham, Alex P; Lyon, Jonathan T; Ngan, Vu Thi; Nguyen, Minh Tho; Lievens, Peter; Fielicke, André; Janssens, Ewald

2014-09-18

The structures of neutral cobalt-doped silicon clusters have been assigned by a combined experimental and theoretical study. Size-selective infrared spectra of neutral Si(n)Co (n = 10-12) clusters are measured using a tunable IR-UV two-color ionization scheme. The experimental infrared spectra are compared with calculated spectra of low-energy structures predicted at the B3P86 level of theory. It is shown that the Si(n)Co (n = 10-12) clusters have endohedral caged structures, where the silicon frameworks prefer double-layered structures encapsulating the Co atom. Electronic structure analysis indicates that the clusters are stabilized by an ionic interaction between the Co dopant atom and the silicon cage due to the charge transfer from the silicon valence sp orbitals to the cobalt 3d orbitals. Strong hybridization between the Co dopant atom and the silicon host quenches the local magnetic moment on the encapsulated Co atom.

Structure determination in 55-atom Li-Na and Na-K nanoalloys.

PubMed

Aguado, Andrés; López, José M

2010-09-07

The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions.

An ignition key for atomic-scale engines

NASA Astrophysics Data System (ADS)

Dundas, Daniel; Cunningham, Brian; Buchanan, Claire; Terasawa, Asako; Paxton, Anthony T.; Todorov, Tchavdar N.

2012-10-01

A current-carrying resonant nanoscale device, simulated by non-adiabatic molecular dynamics, exhibits sharp activation of non-conservative current-induced forces with bias. The result, above the critical bias, is generalized rotational atomic motion with a large gain in kinetic energy. The activation exploits sharp features in the electronic structure, and constitutes, in effect, an ignition key for atomic-scale motors. A controlling factor for the effect is the non-equilibrium dynamical response matrix for small-amplitude atomic motion under current. This matrix can be found from the steady-state electronic structure by a simpler static calculation, providing a way to detect the likely appearance, or otherwise, of non-conservative dynamics, in advance of real-time modelling.

Tuning the electronic and optical properties of hexagonal boron-nitride nanosheet by inserting graphene quantum dots

NASA Astrophysics Data System (ADS)

Ding, Yi-Min; Shi, Jun-Jie; Zhang, Min; Wu, Meng; Wang, Hui; Cen, Yu-Lang; Pan, Shu-Hang; Guo, Wen-Hui

2018-02-01

It is difficult to integrate two-dimensional (2D) graphene and hexagonal boron-nitride (h-BN) in optoelectronic nanodevices, due to the semi-metal and insulator characteristic of graphene and h-BN, respectively. Using the state-of-the-art first-principles calculations based on many-body perturbation theory, we investigate the electronic and optical properties of h-BN nanosheet embedded with graphene dots. We find that C atom impurities doped in h-BN nanosheet tend to phase-separate into graphene quantum dots (QD), and BNC hybrid structure, i.e. a graphene dot within a h-BN background, can be formed. The band gaps of BNC hybrid structures have an inverse relationship with the size of graphene dot. The calculated optical band gaps for BNC structures vary from 4.71 eV to 3.77 eV, which are much smaller than that of h-BN nanosheet. Furthermore, the valence band maximum is located in C atoms bonded to B atoms and conduction band minimum is located in C atoms bonded to N atoms, which means the electron and hole wave functions are closely distributed around the graphene dot. The bound excitons, localized around the graphene dot, determine the optical spectra of the BNC hybrid structures, in which the exciton binding energies decrease with increase in the size of graphene dots. Our results provide an important theoretical basis for the design and development of BNC-based optoelectronic nanodevices.

Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems.

PubMed

Suzuki, Kimichi; Morokuma, Keiji; Maeda, Satoshi

2017-10-05

We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. MSM is a simple extension of the geometrical microiteration technique. In conventional microiteration, the structure of the non-reaction-center (surrounding) part is optimized by fixing atoms in the reaction-center part before displacements of the reaction-center atoms. In this method, the surrounding part is described as the weighted sum of multiple surrounding structures that are independently optimized. Then, geometric displacements of the reaction-center atoms are performed in the mean field generated by the weighted sum of the surrounding parts. MSM was combined with the QM/MM-ONIOM method and applied to chemical reactions in aqueous solution or enzyme. In all three cases, MSM gave lower reaction energy profiles than the QM/MM-ONIOM-microiteration method over the entire reaction paths with comparable computational costs. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

INTERNATIONAL CONFERENCE ON SEMICONDUCTOR INJECTION LASERS SELCO-87: Method for calculation of electrical and optical properties of laser active media

NASA Astrophysics Data System (ADS)

Aleksandrov, D. G.; Filipov, F. I.

1988-11-01

A method is proposed for calculation of the electron band structure of multicomponent semiconductor solid solutions. Use is made of virtual atomic orbitals formed from real orbitals. The method represents essentially an approximation of a multicomponent solid solution by a binary one. The matrix elements of the Hamiltonian are obtained in the methods of linear combinations of atomic and bound orbitals. Some approximations used in these methods are described.

Symmetry and equivalence restrictions in electronic structure calculations

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Taylor, Peter R.

1988-01-01

A simple method for obtaining MCSCF orbitals and CI natural orbitals adapted to degenerate point groups, with full symmetry and equivalnece restrictions, is described. Among several advantages accruing from this method are the ability to perform atomic SCF calculations on states for which the SCF energy expression cannot be written in terms of Coulomb and exchange integrals over real orbitals, and the generation of symmetry-adapted atomic natural orbitals for use in a recently proposed method for basis set contraction.

Structural and electronic properties of double-walled boron nitride nanocones

NASA Astrophysics Data System (ADS)

Brito, E.; Silva, T. S.; Guerra, T.; Leite, L.; Azevedo, S.; Freitas, A.; Kaschny, J. R.

2018-01-01

First principles calculations were applied to study the structural and electronic properties of different configurations of double-walled boron nitride nanocones with a disclination angle of 60°. The analysis includes different rotation angles, distance between apexes, as well as distinct types of antiphase boundaries. The calculations indicate that the non-rotated configuration of double-walled nanocone with a defective line composed by C and N atoms, forming C-N bonds, is the most stable configuration. It was found that the yam angle, apexes distance and defective line composition present significant influence on the electronic properties of such structures. Moreover, analyzing the spin charge density, for the electronic states near the Fermi level, it was also found that the configuration with a defective line containing C atoms presents a net magnetic moment.

Electronic structure studies of adsorbate-induced surface reconstructions: oxygen on Rh(1 0 0)

NASA Astrophysics Data System (ADS)

Kirsch, Janet E.; Harris, Suzanne

2004-03-01

Solid-state Fenske-Hall band structure calculations have been used to study the electronic structure and bonding that occur on an "asymmetric" clock reconstructed Rh(1 0 0) surface with a half-monolayer of O atom adsorbates. The displacement of the top-layer Rh atoms on reconstructed O/Rh(1 0 0) is similar to that observed when a half-monolayer of C or N atoms adsorb onto clean Ni(1 0 0). Unlike the five-coordinate C or N adsorbates that adsorb into effectively coplanar sites on the Ni(1 0 0) surface, however, O atoms sit well above the Rh surface plane and occupy three-coordinate adsorption sites. The results of these calculations show that the asymmetric clock reconstruction of O/Rh(1 0 0) increases the negative charge localized on the highly electronegative O atoms and strengthens the O-Rh bonding relative to an unreconstructed surface. This suggests that, in contrast to the C(N)/Ni(1 0 0) clock, which appears to be driven primarily by the restoration of metal-metal bonding, the asymmetric O/Rh(1 0 0) clock reconstruction is driven by the optimization of the O atom bonding environment. Comparisons of the O/Rh(1 0 0) and C(N, O)/Ni(1 0 0) surfaces further indicate that the electronegativity and electron count of the adsorbed species, as well as the electron count and physical size of the metal, all play a role in determining the preferred atomic geometries of these adsorbate-covered transition metal surfaces.

Tight-Binding study of Boron structures

NASA Astrophysics Data System (ADS)

McGrady, Joseph W.; Papaconstantopoulos, Dimitrios A.; Mehl, Michael J.

2014-10-01

We have performed Linearized Augmented Plane Wave (LAPW) calculations for five crystal structures (alpha, dhcp, sc, fcc, bcc) of Boron which we then fitted to a non-orthogonal tight-binding model following the Naval Research Laboratory Tight-Binding (NRL-TB) method. The predictions of the NRL-TB approach for complicated Boron structures such as R105 (or β-rhombohedral) and T190 are in agreement with recent first-principles calculations. Fully utilizing the computational speed of the NRL-TB method we calculated the energy differences of various structures, including those containing vacancies using supercells with up to 5000 atoms.

The gas phase structure of α -pinene, a main biogenic volatile organic compound

NASA Astrophysics Data System (ADS)

Neeman, Elias M.; Avilés Moreno, Juan Ramón; Huet, Thérèse R.

2017-12-01

The gas phase structure of the bicyclic atmospheric aerosol precursor α-pinene was investigated employing a combination of quantum chemical calculation and Fourier transform microwave spectroscopy coupled to a supersonic jet expansion. The very weak rotational spectra of the parent species and all singly substituted 13C in natural abundance have been identified, from 2 to 20 GHz, and fitted to Watson's Hamiltonian model. The rotational constants were used together with geometrical parameters from density functional theory and ab initio calculations to determine the rs, r0, and rm(1 ) structures of the skeleton, without any structural assumption in the fit concerning the heavy atoms. The double C=C bond was found to belong to a quasiplanar skeleton structure containing 6 carbon atoms. Comparison with solid phase structure is reported. The significant differences of α-pinene in gas phase and other gas phase bicyclic monoterpene structures (β-pinene, nopinone, myrtenal, and bicyclo[3.1.1]heptane) are discussed.

Spin-orbit coupling effect on structural and magnetic properties of ConRh13-n (n = 0-13) clusters

NASA Astrophysics Data System (ADS)

Bai, Xi; Lv, Jin; Zhang, Fu-Qiang; Jia, Jian-Feng; Wu, Hai-Shun

2018-04-01

The effect of spin-orbit interaction on the structures and magnetism of ConRh13-n (n = 0-13) clusters have been systematically investigated by using the spin-orbit coupling (SOC) implementation of the density functional theory (DFT). The results calculated without SOC (NSOC) show that Rh13 prefers the double simple-cubic configuration, and icosahedron is the favorable structure for n = 1-9, while n ≥ 10, clusters favor the hexagonal bilayer structure. The inclusion of SOC in calculation does not change the geometries of clusters. Compared with that in NSOC calculation, although the binding energy per atom in clusters with same composition decreases in SOC calculation, the relative stability of clusters with different compositions does not change. An interesting result is that the spin moments of clusters for n = 1-9 are almost constant (21 μB). Spin-orbit interaction recovers orbital moment and its anisotropy by removing crystal-field effect in calculation. The destruction of bonding symmetry and relaxation of bonding account for high anisotropies of orbital moments in Co11Rh2 and CoRh12 clusters. With atomic composition (Co/Rh) around 4/9-5/8 and 9/4, the Co-Rh clusters exhibit high magnetic anisotropy energies.

Calculation of the Energy-Band Structure of the Kronig-Penney Model Using the Nearly-Free and Tightly-Bound-Electron Approximations

ERIC Educational Resources Information Center

Wetsel, Grover C., Jr.

1978-01-01

Calculates the energy-band structure of noninteracting electrons in a one-dimensional crystal using exact and approximate methods for a rectangular-well atomic potential. A comparison of the two solutions as a function of potential-well depth and ratio of lattice spacing to well width is presented. (Author/GA)

Revision of the Li13Si4 structure

PubMed Central

Zeilinger, Michael; Fässler, Thomas F.

2013-01-01

Besides Li17Si4, Li16.42Si4, and Li15Si4, another lithium-rich representative in the Li–Si system is the phase Li13Si4 (trideca­lithium tetra­silicide), the structure of which has been determined previously [Frank et al. (1975 ▶). Z. Naturforsch. Teil B, 30, 10–13]. A careful analysis of X-ray diffraction patterns of Li13Si4 revealed discrepancies between experimentally observed and calculated Bragg positions. Therefore, we redetermined the structure of Li13Si4 on the basis of single-crystal X-ray diffraction data. Compared to the previous structure report, decisive differences are (i) the introduction of a split position for one Li site [occupancy ratio 0.838 (7):0.162 (7)], (ii) the anisotropic refinement of atomic displacement parameters for all atoms, and (iii) a high accuracy of atom positions and unit-cell parameters. The asymmetric unit of Li13Si4 contains two Si and seven Li atoms. Except for one Li atom situated on a site with symmetry 2/m, all other atoms are on mirror planes. The structure consists of isolated Si atoms as well as Si–Si dumbbells surrounded by Li atoms. Each Si atom is either 12- or 13-coordinated. The isolated Si atoms are situated in the ab plane at z = 0 and are strictly separated from the Si–Si dumbbells at z = 0.5. PMID:24454148

ptchg: A FORTRAN program for point-charge calculations of electric field gradients (EFGs)

NASA Astrophysics Data System (ADS)

Spearing, Dane R.

1994-05-01

ptchg, a FORTRAN program, has been developed to calculate electric field gradients (EFG) around an atomic site in crystalline solids using the point-charge direct-lattice summation method. It uses output from the crystal structure generation program Atoms as its input. As an application of ptchg, a point-charge calculation of the EFG quadrupolar parameters around the oxygen site in SiO 2 cristobalite is demonstrated. Although point-charge calculations of electric field gradients generally are limited to ionic compounds, the computed quadrupolar parameters around the oxygen site in SiO 2 cristobalite, a highly covalent material, are in good agreement with the experimentally determined values from nuclear magnetic resonance (NMR) spectroscopy.

Density functional study for crystalline structures and electronic properties of Si1- x Sn x binary alloys

NASA Astrophysics Data System (ADS)

Nagae, Yuki; Kurosawa, Masashi; Shibayama, Shigehisa; Araidai, Masaaki; Sakashita, Mitsuo; Nakatsuka, Osamu; Shiraishi, Kenji; Zaima, Shigeaki

2016-08-01

We have carried out density functional theory (DFT) calculation for Si1- x Sn x alloy and investigated the effect of the displacement of Si and Sn atoms with strain relaxation on the lattice constant and E- k dispersion. We calculated the formation probabilities for all atomic configurations of Si1- x Sn x according to the Boltzmann distribution. The average lattice constant and E- k dispersion were weighted by the formation probability of each configuration of Si1- x Sn x . We estimated the displacement of Si and Sn atoms from the initial tetrahedral site in the Si1- x Sn x unit cell considering structural relaxation under hydrostatic pressure, and we found that the breaking of the degenerated electronic levels of the valence band edge could be caused by the breaking of the tetrahedral symmetry. We also calculated the E- k dispersion of the Si1- x Sn x alloy by the DFT+U method and found that a Sn content above 50% would be required for the indirect-direct transition.

Simulations of Metallic Nanoscale Structures

NASA Astrophysics Data System (ADS)

Jacobsen, Karsten W.

2003-03-01

Density-functional-theory calculations can be used to understand and predict materials properties based on their nanoscale composition and structure. In combination with efficient search algorithms DFT can furthermore be applied in the nanoscale design of optimized materials. The first part of the talk will focus on two different types of nanostructures with an interesting interplay between chemical activity and conducting states. MoS2 nanoclusters are known for their catalyzing effect in the hydrodesulfurization process which removes sulfur-containing molecules from oil products. MoS2 is a layered material which is insulating. However, DFT calculations indicates the exsistence of metallic states at some of the edges of MoS2 nanoclusters, and the calculations show that the conducting states are not passivated by for example the presence of hydrogen gas. The edge states may play an important role for the chemical activity of MoS_2. Metallic nanocontacts can be formed during the breaking of a piece of metal, and atomically thin structures with conductance of only a single quantum unit may be formed. Such open metallic structures are chemically very active and susceptible to restructuring through interactions with molecular gases. DFT calculations show for example that atomically thin gold wires may incorporate oxygen atoms forming a new type of metallic nanowire. Adsorbates like hydrogen may also affect the conductance. In the last part of the talk I shall discuss the possibilities for designing alloys with optimal mechanical properties based on a combination of DFT calculations with genetic search algorithms. Simulaneous optimization of several parameters (stability, price, compressibility) is addressed through the determination of Pareto optimal alloy compositions within a large database of more than 64000 alloys.

All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

PubMed Central

2017-01-01

Recent advances in understanding protein folding have benefitted from coarse-grained representations of protein structures. Empirical energy functions derived from these techniques occasionally succeed in distinguishing native structures from their corresponding ensembles of nonnative folds or decoys which display varying degrees of structural dissimilarity to the native proteins. Here we utilized atomic coordinates of single protein chains, comprising a large diverse training set, to develop and evaluate twelve all-atom four-body statistical potentials obtained by exploring alternative values for a pair of inherent parameters. Delaunay tessellation was performed on the atomic coordinates of each protein to objectively identify all quadruplets of interacting atoms, and atomic potentials were generated via statistical analysis of the data and implementation of the inverted Boltzmann principle. Our potentials were evaluated using benchmarking datasets from Decoys-‘R'-Us, and comparisons were made with twelve other physics- and knowledge-based potentials. Ranking 3rd, our best potential tied CHARMM19 and surpassed AMBER force field potentials. We illustrate how a generalized version of our potential can be used to empirically calculate binding energies for target-ligand complexes, using HIV-1 protease-inhibitor complexes for a practical application. The combined results suggest an accurate and efficient atomic four-body statistical potential for protein structure prediction and assessment. PMID:29119109

Geminal embedding scheme for optimal atomic basis set construction in correlated calculations

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

Sorella, S., E-mail: sorella@sissa.it; Devaux, N.; Dagrada, M., E-mail: mario.dagrada@impmc.upmc.fr

2015-12-28

We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wavemore » function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.« less

Structure-activity correlations for organophosphorus ester anticholinesterases. Part 2: CNDO/2 calculations applied to ester hydrolysis rates

NASA Technical Reports Server (NTRS)

Johnson, H.; Kenley, R. A.; Rynard, C.; Golub, M. A.

1984-01-01

Quantitative structure-activity relationships are presented for the hydrolysis of organophosphorus esters, RR'P(O)X, where R and R' are alkyl and/or alkoxy groups and X is fluorine, chlorine or a phenoxy group. CNDO/2 calculations provide values for molecular parameters that correlate with alkaline hydrolysis rates. For each subset of esters with the same leaving group, X, the CNDO-derived net atomic charge at the central phosphorus atom correlates well with the alkaline hydrolysis rate constants. For the whole set of esters with different leaving groups, equations are derived that relate charge, orbital energy and bond order to the hydrolysis rate constants.

Full multiple-scattering calculations on silicates and oxides at the Al K edge

NASA Astrophysics Data System (ADS)

Cabaret, Delphine; Sainctavit, Philippe; Ildefonse, Philippe; Flank, Anne-Marie

1996-05-01

We present full multiple-scattering calculations at the aluminium K edge that we compare with experiments for four crystalline silicates and oxide minerals. In the different minerals aluminium atoms are either fourfold or sixfold coordinated to oxygen atoms in Al sites that are poorly symmetric. The calculations are based on different choices of one-electron potentials according to aluminium coordinations and crystallographic structures of the compounds. Hence it is possible to determine how the near-edge spectral features are a sensitive probe of the effective potential seen by the photoelectron in the molecular environment. The purpose of this work is to determine on the one hand the relation between Al K-edge spectral features and the geometrical arrangements around the aluminium sites, and on the other hand the electronic structure of the compounds.

Atomic-scale structural and electronic properties of SrTiO3/GaAs interfaces: A combined STEM-EELS and first-principles study

NASA Astrophysics Data System (ADS)

Hong, Liang; Bhatnagar, Kunal; Droopad, Ravi; Klie, Robert F.; Öǧüt, Serdar

2017-07-01

The electronic properties of epitaxial oxide thin films grown on compound semiconductors are largely determined by the interfacial atomic structure, as well as the thermodynamic conditions during synthesis. Ferroelectric polarization and Fermi-level pinning in SrTiO3 films have been attributed to the presence of oxygen vacancies at the oxide/semiconductor interface. Here, we present scanning transmission electron microscopy (STEM) and electron energy-loss spectroscopy analyses of GaAs films grown on SrTiO3 combined with first-principles calculations to determine the atomic and electronic structures of the SrTiO3/GaAs interfaces. An atomically abrupt SrO/As interface is observed and the interfacial SrO layer is found to be O-deficient. First-principles density functional theory (DFT) calculations show SrO/Ga and Sr/As interfaces are favorable under O-rich and O-poor conditions, respectively. The SrO/Ga interface is reconstructed via the formation of Ga-Ga dimers while the Sr/As interface is abrupt and consistent with the experiment. DFT calculations further reveal that intrinsic two-dimensional electron gas (2DEG) forms in both SrO/Ga and Sr/As interfaces, and the Fermi level is pinned to the localized 2DEG states. Interfacial O vacancies can enhance the 2DEG density while it is possible for Ga/As vacancies to unpin the Fermi level from the 2DEG states.

First principles calculation of current-induced forces in atomic gold contacts

NASA Astrophysics Data System (ADS)

Brandbyge, Mads; Stokbro, Kurt; Taylor, Jeremy; Mozos, Jose-Luis; Ordejon, Pablo

2002-03-01

We have recently developed an first principles method [1] for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density functional theory (DFT) as implemented in the well tested SIESTA program [2]. We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including selfconsistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. In this talk we show results for the forces acting on the contact atoms due to the nonequilibrium situation in the electronic subsystem, i.e. in the presence of an electronic current. We concentrate on one atom wide gold contacts/wires connected to bulk gold electrodes. References [1] Our implementation is called TranSIESTA and is described in M. Brandbyge, J. Taylor, K. Stokbro, J-L. Mozos, and P. Ordejon, cond-mat/0110650 [2] D. Sanchez-Portal, P. Ordejon, E. Artacho and J. Soler, Int. J. Quantum Chem. 65, 453 (1997).

Double-atomic layer of Tl on Si(111): Atomic arrangement and electronic properties

NASA Astrophysics Data System (ADS)

Mihalyuk, Alexey N.; Bondarenko, Leonid V.; Tupchaya, Alexandra Y.; Gruznev, Dimitry V.; Chou, Jyh-Pin; Hsing, Cheng-Rong; Wei, Ching-Ming; Zotov, Andrey V.; Saranin, Alexander A.

2018-02-01

Metastable double-atomic layer of Tl on Si(111) has recently been found to display interesting electric properties, namely superconductivity below 0.96 K and magnetic-field-induced transition into an insulating phase intermediated by a quantum metal state. In the present work, using a set of experimental techniques, including low-energy electron diffraction, scanning tunneling microscopy, angle-resolved photoelectron spectroscopy, in a combination with density-functional-theory calculations, we have characterized atomic and electronic properties of the Tl double layer on Si(111). The double Tl layer has been concluded to contain ∼ 2.4 monolayer of Tl. A top Tl layer has a '1 × 1' basic structure and displays 6 × 6 moiré pattern which originates from various residence sites of Tl atoms. Upon cooling below ∼ 140 K, the 6 × 6 moiré pattern changes to that having a 6√{ 3} × 6√{ 3} periodicity. However, the experimentally determined electron band dispersions show a 1 × 1 periodicity. The calculated band structure unfolded into the 1 × 1 surface Brillouin zone reproduces well the main features of the photoelectron spectra.

Application of composite dictionary multi-atom matching in gear fault diagnosis.

PubMed

Cui, Lingli; Kang, Chenhui; Wang, Huaqing; Chen, Peng

2011-01-01

The sparse decomposition based on matching pursuit is an adaptive sparse expression method for signals. This paper proposes an idea concerning a composite dictionary multi-atom matching decomposition and reconstruction algorithm, and the introduction of threshold de-noising in the reconstruction algorithm. Based on the structural characteristics of gear fault signals, a composite dictionary combining the impulse time-frequency dictionary and the Fourier dictionary was constituted, and a genetic algorithm was applied to search for the best matching atom. The analysis results of gear fault simulation signals indicated the effectiveness of the hard threshold, and the impulse or harmonic characteristic components could be separately extracted. Meanwhile, the robustness of the composite dictionary multi-atom matching algorithm at different noise levels was investigated. Aiming at the effects of data lengths on the calculation efficiency of the algorithm, an improved segmented decomposition and reconstruction algorithm was proposed, and the calculation efficiency of the decomposition algorithm was significantly enhanced. In addition it is shown that the multi-atom matching algorithm was superior to the single-atom matching algorithm in both calculation efficiency and algorithm robustness. Finally, the above algorithm was applied to gear fault engineering signals, and achieved good results.

Quantitative characterization of the atomic-scale structure of oxyhydroxides in rusts formed on steel surfaces

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

Saito, M.; Suzuki, S.; Kimura, M.

Quantitative X-ray structural analysis coupled with anomalous X-ray scattering has been used for characterizing the atomic-scale structure of rust formed on steel surfaces. Samples were prepared from rust layers formed on the surfaces of two commercial steels. X-ray scattered intensity profiles of the two samples showed that the rusts consisted mainly of two types of ferric oxyhydroxide, {alpha}-FeOOH and {gamma}-FeOOH. The amounts of these rust components and the realistic atomic arrangements in the components were estimated by fitting both the ordinary and the environmental interference functions with a model structure calculated using the reverse Monte Carlo simulation technique. The twomore » rust components were found to be the network structure formed by FeO{sub 6} octahedral units, the network structure itself deviating from the ideal case. The present results also suggest that the structural analysis method using anomalous X-ray scattering and the reverse Monte Carlo technique is very successful in determining the atomic-scale structure of rusts formed on the steel surfaces.« less

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

PubMed

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

2015-01-01

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

Σ 3 (111 ) grain boundary of body-centered cubic Ti-Mo and Ti-V alloys: First-principles and model calculations

NASA Astrophysics Data System (ADS)

Yan, Jia-Yi; Ehteshami, Hossein; Korzhavyi, Pavel A.; Borgenstam, Annika

2017-07-01

The energetics and atomic structures of Σ 3 [1 1 ¯0 ] (111 ) grain boundary (GB) of body-centered cubic (bcc) Ti-Mo and Ti-V alloys are investigated using density-functional-theory calculations and virtual crystal approximation. The electron density in bcc structure and the atomic displacements and excess energy of the GB are correlated to bcc-ω phase stability. Model calculations based on pairwise interplanar interactions successfully reproduce the chemical part of GB energy. The chemical GB energy can be expressed as a sum of excess pairwise interactions between bcc (111) layers, which are obtained from Gaussian elimination of the total energies of a number of periodic structures. The energy associated with the relaxation near the GB is solved by numerical minimization using the derivatives of the excess interactions. Anharmonic interlayer interactions are necessary for obtaining accurate relaxation energy and excess GB volume from model calculations. The effect of GB on vibrational spectrum is also investigated. Segregation energies of B and Y to a substitutional site on the GB plane are calculated. Preliminary results suggest that Y tends to segregate, while B tends to antisegregate.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

PubMed

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

PubMed Central

van de Streek, Jacco; Neumann, Marcus A.

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom. PMID:25449625

Extended X-ray absorption fine structure investigation of Sn local environment in strained and relaxed epitaxial Ge{sub 1−x}Sn{sub x} films

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

Gencarelli, F., E-mail: federica.gencarelli@imec.be; Heyns, M.; Department of Metallurgy and Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, B-3001 Leuven

2015-03-07

We present an extended X-ray absorption fine structure investigation of the local environment of Sn atoms in strained and relaxed Ge{sub 1−x}Sn{sub x} layers with different compositions. We show that the preferred configuration for the incorporation of Sn atoms in these Ge{sub 1−x}Sn{sub x} layers is that of a α-Sn defect, with each Sn atom covalently bonded to four Ge atoms in a classic tetrahedral configuration. Sn interstitials, Sn-split vacancy complexes, or Sn dimers, if present at all, are not expected to involve more than 2.5% of the total Sn atoms. This finding, along with a relative increase of Snmore » atoms in the second atomic shell around a central Sn atom in Ge{sub 1−x}Sn{sub x} layers with increasing Sn concentrations, suggests that the investigated materials are homogeneous random substitutional alloys. Within the accuracy of the measurements, the degree of strain relaxation of the Ge{sub 1−x}Sn{sub x} layers does not have a significant impact on the local atomic surrounding of the Sn atoms. Finally, the calculated topological rigidity parameter a** = 0.69 ± 0.29 indicates that the strain due to alloying in Ge{sub 1−x}Sn{sub x} is accommodated via bond stretching and bond bending, with a slight predominance of the latter, in agreement with ab initio calculations reported in literature.« less

Scalability improvements to NRLMOL for DFT calculations of large molecules

NASA Astrophysics Data System (ADS)

Diaz, Carlos Manuel

Advances in high performance computing (HPC) have provided a way to treat large, computationally demanding tasks using thousands of processors. With the development of more powerful HPC architectures, the need to create efficient and scalable code has grown more important. Electronic structure calculations are valuable in understanding experimental observations and are routinely used for new materials predictions. For the electronic structure calculations, the memory and computation time are proportional to the number of atoms. Memory requirements for these calculations scale as N2, where N is the number of atoms. While the recent advances in HPC offer platforms with large numbers of cores, the limited amount of memory available on a given node and poor scalability of the electronic structure code hinder their efficient usage of these platforms. This thesis will present some developments to overcome these bottlenecks in order to study large systems. These developments, which are implemented in the NRLMOL electronic structure code, involve the use of sparse matrix storage formats and the use of linear algebra using sparse and distributed matrices. These developments along with other related development now allow ground state density functional calculations using up to 25,000 basis functions and the excited state calculations using up to 17,000 basis functions while utilizing all cores on a node. An example on a light-harvesting triad molecule is described. Finally, future plans to further improve the scalability will be presented.

Sulfur Adsorption on the Goethite (110) Surface

NASA Astrophysics Data System (ADS)

Simonetti, S.; Damiani, D.; Brizuela, G.; Juan, A.

The electronic structure of S adsorption on goethite (110) surface has been studied by ASED-MO cluster calculations. For S location, the most exposed surface atoms of goethite surface were selected. The calculations show that the surface offers several places for S adsorption. The most energetically stable system corresponds to S location above H atom. We studied in detail the configurations that correspond to the higher OP values. For these configurations, the H-S and Fe-S computed distances are 2.1 and 3.7 Å, respectively. The H-S and Fe-S are mainly bonding interaction with OP values of 0.156 and 0.034, respectively. The Fe-S interaction mainly involves Fe 3dx2-y2 atomic orbitals with lesser participation of Fe 4py and Fe 3dyz atomic orbitals. The O-S interaction shows the same bonding and antibonding contributions giving a small OP value. The O-S interaction involves O 2p orbitals. There is an electron transfer to the Fe atom from the S atom. On the other hand, there is an electron transfer to S atom from the H and O atoms, respectively.

Synthesis, crystal structure and DFT studies of a novel dinuclear copper(I) complex with triphenylphosphine and 2-mercaptonicotinic acid

NASA Astrophysics Data System (ADS)

Ahmad, Tayyaba; Mahmood, Rashid; Georgieva, Ivelina; Zahariev, Tsvetan; Tahir, Muhammad Nawaz; Shaheen, Muhammad Ashraf; Gilani, Mazhar Amjad; Ahmad, Saeed

2018-02-01

A novel dinuclear copper(I) complex, {[Cu2(Mnt)2(PPh3)2Cl2].2H2O.CH3CN}2 (1) (Mnt = Mercaptonicotinic acid, PPh3 = triphenylphosphine) was prepared and its structure was determined by X-ray crystallography. The complex 1 consists of two dinuclear molecules and in each molecule, the two copper atoms are bridged by S atoms of N-protonated mercaptonicotinic acid forming a four-membered ring. The planar Cu2S2 core is characterized by significant cuprophilic interactions (Cusbnd Cu distance = 2.7671(8), 2.8471(8) Å). Each copper atom in 1 is coordinated by two sulfur atoms of Mnt, one phosphorus atom of PPh3 and a chloride ion adopting a tetrahedral geometry. The calculated Gibbs energies for reaction in CH3CN supported the experimental structure and predicted more favorable formation of dinuclear Cu(I) complex as compared to the mononuclear Cu(I) complex. The dinuclear complex is stabilized by 65.98 kJ mol-1 by coupling of two mononuclear Cu(I) complexes. The IR spectra of 1 and Mnt ligand were reliably interpreted and the Mnt vibrations, which are sensitive to the ligand coordination to Cu(I) ion in 1 were selected with the help of DFT/ωB97XD calculations.

Efficient grid-based techniques for density functional theory

NASA Astrophysics Data System (ADS)

Rodriguez-Hernandez, Juan Ignacio

Understanding the chemical and physical properties of molecules and materials at a fundamental level often requires quantum-mechanical models for these substance's electronic structure. This type of many body quantum mechanics calculation is computationally demanding, hindering its application to substances with more than a few hundreds atoms. The supreme goal of many researches in quantum chemistry---and the topic of this dissertation---is to develop more efficient computational algorithms for electronic structure calculations. In particular, this dissertation develops two new numerical integration techniques for computing molecular and atomic properties within conventional Kohn-Sham-Density Functional Theory (KS-DFT) of molecular electronic structure. The first of these grid-based techniques is based on the transformed sparse grid construction. In this construction, a sparse grid is generated in the unit cube and then mapped to real space according to the pro-molecular density using the conditional distribution transformation. The transformed sparse grid was implemented in program deMon2k, where it is used as the numerical integrator for the exchange-correlation energy and potential in the KS-DFT procedure. We tested our grid by computing ground state energies, equilibrium geometries, and atomization energies. The accuracy on these test calculations shows that our grid is more efficient than some previous integration methods: our grids use fewer points to obtain the same accuracy. The transformed sparse grids were also tested for integrating, interpolating and differentiating in different dimensions (n = 1,2,3,6). The second technique is a grid-based method for computing atomic properties within QTAIM. It was also implemented in deMon2k. The performance of the method was tested by computing QTAIM atomic energies, charges, dipole moments, and quadrupole moments. For medium accuracy, our method is the fastest one we know of.

Stabilization of golden cages by encapsulation of a single transition metal atom

PubMed Central

Li, Hui-Fang

2018-01-01

Golden cage-doped nanoclusters have attracted great attention in the past decade due to their remarkable electronic, optical and catalytic properties. However, the structures of large golden cage doped with Mo and Tc are still not well known because of the challenges in global structural searches. Here, we report anionic and neutral golden cage doped with a transition metal atom MAu16 (M = Mo and Tc) using Saunders ‘Kick' stochastic automation search method associated with density-functional theory (DFT) calculation (SK-DFT). The geometric structures and electronic properties of the doped clusters, MAu16q (M = Mo and Tc; q = 0 and −1), are investigated by means of DFT theoretical calculations. Our calculations confirm that the 4d transition metals Mo and Tc can be stably encapsulated in the Au16− cage, forming three different configurations, i.e. endohedral cages, planar structures and exohedral derivatives. The ground-state structures of endohedral cages C2v Mo@Au16−-(a) and C1 Tc@Au16−-(b) exhibit a marked stability, as judged by their high binding energy per atom (greater than 2.46 eV), doping energy (0.29 eV) as well as a large HOMO–LUMO gap (greater than 0.40 eV). The predicted photoelectron spectra should aid in future experimental characterization of MAu16− (M = Mo and Tc). PMID:29410813

Synthesis, crystal structure and electronic structure of the binary phase Rh{sub 2}Cd{sub 5}

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

Koley, Biplab; Chatterjee, S.; Jana, Partha P., E-mail: ppj@chem.iitkgp.ernet.in

2017-02-15

A new phase in the Rh-Cd binary system - Rh{sub 2}Cd{sub 5} has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh{sub 2}Cd{sub 5} crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh{sub 2}Cd{sub 5} can be described as a defect form of the In{sub 3}Pd{sub 5} structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist ofmore » (3{sup 5}) (3{sup 7})- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh{sub 2}Cd{sub 5}. - Graphical abstract: (3.6.3.6)-Kagomé nets of cadmium atoms (top) and (3{sup 5}) (3{sup 7})- nets of both cadmium and rhodium atoms (bottom) in the structure of Rh{sub 2}Cd{sub 5}.« less

Structural stability and O{sub 2} dissociation on nitrogen-doped graphene with transition metal atoms embedded: A first-principles study

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

Yang, Mingye; Wang, Lu, E-mail: lwang22@suda.edu.cn, E-mail: yyli@suda.edu.cn; Li, Min

2015-06-15

By using first-principles calculations, we investigate the structural stability of nitrogen-doped (N-doped) graphene with graphitic-N, pyridinic-N and pyrrolic-N, and the transition metal (TM) atoms embedded into N-doped graphene. The structures and energetics of TM atoms from Sc to Ni embedded into N-doped graphene are studied. The TM atoms at N{sub 4}V {sub 2} forming a 4N-centered structure shows the strongest binding and the binding energies are more than 7 eV. Finally, we investigate the catalytic performance of N-doped graphene with and without TM embedding for O{sub 2} dissociation, which is a fundamental reaction in fuel cells. Compared to the pyridinic-N,more » the graphitic-N is more favorable to dissociate O{sub 2} molecules with a relatively low reaction barrier of 1.15 eV. However, the catalytic performance on pyridinic-N doped structure can be greatly improved by embedding TM atoms, and the energy barrier can be reduced to 0.61 eV with V atom embedded. Our results provide the stable structure of N-doped graphene and its potential applications in the oxygen reduction reactions.« less

Discrepancy between experimental and theoretical excitation transfer rates in LH2 bacteriochlorophyll-protein complexes of purple bacteria.

PubMed

Borisov, A Y

2008-02-01

Discrepancy is revealed between the values of excitation transfer times measured experimentally, and those calculated, for the atomic structures of B800 --> B850 bacteriochlorophylls within the LH2 light-harvesting pigment-protein complex of the purple bacterium Rhodopseudomonas acidophila. The value 2.9-3.2 ps for the B800 --> B850 excitation transfer, calculated on the basis of atomic structure of LH2, is about 4-times longer than that measured for this bacterium (0.7 ps). This discrepancy appears common in at least two purple bacteria. Possible sources responsible for this discrepancy are discussed. It may either signify some drawback/s/ in our notions about the precise in vivo structure of LH2 complexes, for example, possible changes of LH2 structure during crystallization, or it may reflect our ignorance of some mechanisms involved in excitation migration.

Atomic structure and electronic properties of MgO grain boundaries in tunnelling magnetoresistive devices

PubMed Central

Bean, Jonathan J.; Saito, Mitsuhiro; Fukami, Shunsuke; Sato, Hideo; Ikeda, Shoji; Ohno, Hideo; Ikuhara, Yuichi; McKenna, Keith P.

2017-01-01

Polycrystalline metal oxides find diverse applications in areas such as nanoelectronics, photovoltaics and catalysis. Although grain boundary defects are ubiquitous their structure and electronic properties are very poorly understood since it is extremely challenging to probe the structure of buried interfaces directly. In this paper we combine novel plan-view high-resolution transmission electron microscopy and first principles calculations to provide atomic level understanding of the structure and properties of grain boundaries in the barrier layer of a magnetic tunnel junction. We show that the highly [001] textured MgO films contain numerous tilt grain boundaries. First principles calculations reveal how these grain boundaries are associated with locally reduced band gaps (by up to 3 eV). Using a simple model we show how shunting a proportion of the tunnelling current through grain boundaries imposes limits on the maximum magnetoresistance that can be achieved in devices. PMID:28374755

The Calculation Study of Electronic Properties of Doped RE (Eu, Er and Tm)-GaN using Density Functional Theory

NASA Astrophysics Data System (ADS)

Zaharo, Aflah; Purqon, Acep

2017-07-01

The calculation of the structure and electronic properties of Rare Earth (RE) at the wurtzite Gallium Nitride (GaN) based on DFT has completed. GGA approximation used for exchange correlation and Ultra soft pseudo potential too. The stability structure of GaN is seen that difference lattice parameter 11% lower than another calculation and experiment result. It is shown the stability structure GaN have direct band gap energy on Gamma point hexagonal lattice Brillouin zone. The width Eg is 2.6 eV. When one atom Ga is substituted with one atom RE, the bond length is change 12 % longest. An in good agreement with theoretical doping RE concentration increases, the edge of energy level shifted towards to make the band gap narrow which is allow the optical transitions and help to improve the optical performance of GaN. The RE doped GaN is potentially applicable for various color of LED with lower energy consumption and potentially energy saving application

All-atom four-body knowledge-based statistical potential to distinguish native tertiary RNA structures from nonnative folds.

PubMed

Masso, Majid

2018-09-14

Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions. Here we develop an all-atom four-body statistical potential and evaluate its capacity to distinguish native RNA 3D structures from nonnative folds based on calculated free energy scores. Atomic four-body nearest-neighbors are objectively identified by their occurrence as tetrahedral vertices in the Delaunay tessellations of RNA structures, and rates of atomic quadruplet interactions expected by chance are obtained from a multinomial reference distribution. Our four-body energy function, referred to as RAMP (ribonucleic acids multibody potential), is subsequently derived by applying the inverted Boltzmann principle to the frequency data, yielding an energy score for each type of atomic quadruplet interaction. Several well-known benchmark datasets reveal that RAMP is comparable with, and often outperforms, existing knowledge- and physics-based energy functions. To the best of our knowledge, this is the first study detailing an RNA tertiary structure-based multibody statistical potential and its comparative evaluation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Calculation and Specification of the Multiple Chirality Displayed by Sugar Pyranoid Ring Structures.

ERIC Educational Resources Information Center

Shallenberger, Robert S.; And Others

1981-01-01

Describes a method, using simple algebraic notation, for calculating the nature of the salient features of a sugar pyranoid ring, the steric disposition of substituents about the reference, and the anomeric carbon atoms contained within the ring. (CS)

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

Kaur, Sandeep, E-mail: sipusukhn@gmail.com; Sharma, Amrish; Mudahar, Isha, E-mail: isha@pbi.ac.in

First principle calculations based on density functional theory were performed to calculate the structural and electronic properties of C{sub 20}-N{sub m}@C{sub n} dimer complexes. The calculated binding energies of the complexes formed are comparable to C{sub 60} dimer which ensures their stability. The bond lengths of these dimer complexes were found to be nearly same as pure complexes C{sub 20}-C{sub n}. Further, nitrogen (N) atoms were encapsulated inside the secondary cage (C{sub n}) of dimer complexes and the number of N atoms depends on diameter of the cage. The HOMO-LUMO gaps of new proposed complexes indicate the increase in gapmore » as compared to pure complexes. Mulliken charge analysis of these complexes has been studied which shows the significant charge transfer from the N atoms to the secondary cage of these complexes. The study propose the formation of the new dimer complexes which are stable and are able to encapsulate atoms which are otherwise reactive in free space.« less

Complexes of carboxyl-containing polymer and monosubstituted bipyridinium salts

NASA Astrophysics Data System (ADS)

Merekalova, N. D.; Bondarenko, G. N.; Krylsky, D. W.; Zakirov, M. I.; Talroze, R. V.

2013-09-01

Semi-empirical PM3 method for the quantum calculations of molecular electronic structure based on NDDO integral approximation is used to investigate the complex formation of monosubstituted 4,4‧-bipyridinium salts BpyR (Hal) containing a halide anion interacting with the quaternary nitrogen atom and carboxylic group of the two-units construct. Significant effect of the BpyR (Hal) electronic structure is unveiled that contributes in two different structures of these salts, namely, partial charge transfer complex and ion pair structure, both having stable energy minima. We demonstrate that (i) the structure of the N-substituent modulates the energy and electronic characteristics of monosubstituted salts BpyR with chlorine and bromine anions and (ii) the coulomb interactions between quaternary N-atom, halogen anion, and the proton of carboxylic group stimulate the transformation of the charge transfer complex into the ion pair structure. Results of calculations are compared with the experimental FTIR spectra of blends of BpyR(Hal) with Eudragit copolymer.

Neutron powder diffraction studies as a function of temperature of structure II hydrate formed from propane

USGS Publications Warehouse

Rawn, C.J.; Rondinone, A.J.; Chakoumakos, B.C.; Circone, S.; Stern, L.A.; Kirby, S.H.; Ishii, Y.

2003-01-01

Neutron powder diffraction data confirm that hydrate samples synthesized with propane crystallize as structure type II hydrate. The structure has been modeled using rigid-body constraints to describe C3H8 molecules located in the eight larger polyhedral cavities of a deuterated host lattice. Data were collected at 12, 40, 100, 130, 160, 190, 220, and 250 K and used to calculate the thermal expansivity from the temperature dependence of the lattice parameters. The data collected allowed for full structural refinement of atomic coordinates and the atomic-displacement parameters.

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…

Structural and magnetic evolution of bimetallic MnAu clusters driven by asymmetric atomic migration.

PubMed

Wei, Xiaohui; Zhou, Rulong; Lefebvre, Williams; He, Kai; Le Roy, Damien; Skomski, Ralph; Li, Xingzhong; Shield, Jeffrey E; Kramer, Matthew J; Chen, Shuang; Zeng, Xiao Cheng; Sellmyer, David J

2014-03-12

The nanoscale structural, compositional, and magnetic properties are examined for annealed MnAu nanoclusters. The MnAu clusters order into the L1(0) structure, and monotonic size-dependences develop for the composition and lattice parameters, which are well reproduced by our density functional theory calculations. Simultaneously, Mn diffusion forms 5 Å nanoshells on larger clusters inducing significant magnetization in an otherwise antiferromagnetic system. The differing atomic mobilities yield new cluster nanostructures that can be employed generally to create novel physical properties.

Unusual structures of MgF5- superhalogen anion

NASA Astrophysics Data System (ADS)

Anusiewicz, Iwona; Skurski, Piotr

2007-05-01

The vertical electron detachment energies (VDE) of three MgF5- anions were calculated at the outer valence Green function level with the 6-311 + G(3df) basis sets. This species was found to form unusual geometrical structures each of which corresponds to an anionic state exhibiting superhalogen nature. The global minimum structure was described as a system in which two central magnesium atoms are linked via symmetrical triangle formed by three fluorine atoms. Extremely large electron binding energies of these anions (exceeding 8.5 eV in all cases) were predicted and discussed.

Ultra-small rhenium clusters supported on graphene.

PubMed

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J; Mariscal, Marcelo M; Yacaman, Miguel José

2015-03-28

The adsorption of very small rhenium clusters (2-13 atoms) supported on graphene was studied by high-angle annular dark field-scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional theory calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones.

Ultra-small rhenium clusters supported on graphene

PubMed Central

Miramontes, Orlando; Bonafé, Franco; Santiago, Ulises; Larios-Rodriguez, Eduardo; Velázquez-Salazar, Jesús J.; Mariscal, Marcelo M.; Yacaman, Miguel José

2015-01-01

The adsorption of very small rhenium clusters (2 – 13 atoms) supported on graphene was studied with high annular dark field - scanning transmission electron microscopy (HAADF-STEM). The atomic structure of the clusters was fully resolved with the aid of density functional calculations and STEM simulations. It was found that octahedral and tetrahedral structures work as seeds to obtain more complex morphologies. Finally, a detailed analysis of the electronic structure suggested that a higher catalytic effect can be expected in Re clusters when adsorbed on graphene than in isolated ones. PMID:25721176

Synthesis and Stability of Lanthanum Superhydrides

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

Geballe, Zachary M.; Liu, Hanyu; Mishra, Ajay K.

Recent theoretical calculations predict that megabar pressure stabilizes very hydrogen-rich simple compounds having new clathrate-like structures and remarkable electronic properties including room-temperature superconductivity. X-ray diffraction and optical studies demonstrate that superhydrides of lanthanum can be synthesized with La atoms in an fcc lattice at 170 GPa upon heating to about 1000 K. The results match the predicted cubic metallic phase of LaH10 having cages of thirty-two hydrogen atoms surrounding each La atom. Upon decompression, the fcc-based structure undergoes a rhombohedral distortion of the La sublattice. The superhydride phases consist of an atomic hydrogen sublattice with H-H distances of about 1.1more » Å, which are close to predictions for solid atomic metallic hydrogen at these pressures. With stability below 200 GPa, the superhydride is thus the closest analogue to solid atomic metallic hydrogen yet to be synthesized and characterized.« less

Linear indices of the "molecular pseudograph's atom adjacency matrix": definition, significance-interpretation, and application to QSAR analysis of flavone derivatives as HIV-1 integrase inhibitors.

PubMed

Marrero-Ponce, Yovani

2004-01-01

This report describes a new set of molecular descriptors of relevance to QSAR/QSPR studies and drug design, atom linear indices fk(xi). These atomic level chemical descriptors are based on the calculation of linear maps on Rn[fk(xi): Rn--> Rn] in canonical basis. In this context, the kth power of the molecular pseudograph's atom adjacency matrix [Mk(G)] denotes the matrix of fk(xi) with respect to the canonical basis. In addition, a local-fragment (atom-type) formalism was developed. The kth atom-type linear indices are calculated by summing the kth atom linear indices of all atoms of the same atom type in the molecules. Moreover, total (whole-molecule) linear indices are also proposed. This descriptor is a linear functional (linear form) on Rn. That is, the kth total linear indices is a linear map from Rn to the scalar R[ fk(x): Rn --> R]. Thus, the kth total linear indices are calculated by summing the atom linear indices of all atoms in the molecule. The features of the kth total and local linear indices are illustrated by examples of various types of molecular structures, including chain-lengthening, branching, heteroatoms-content, and multiple bonds. Additionally, the linear independence of the local linear indices to other 0D, 1D, 2D, and 3D molecular descriptors is demonstrated by using principal component analysis for 42 very heterogeneous molecules. Much redundancy and overlapping was found among total linear indices and most of the other structural indices presently in use in the QSPR/QSAR practice. On the contrary, the information carried by atom-type linear indices was strikingly different from that codified in most of the 229 0D-3D molecular descriptors used in this study. It is concluded that the local linear indices are an independent indices containing important structural information to be used in QSPR/QSAR and drug design studies. In this sense, atom, atom-type, and total linear indices were used for the prediction of pIC50 values for the cleavage process of a set of flavone derivatives inhibitors of HIV-1 integrase. Quantitative models found are significant from a statistical point of view (R of 0.965, 0.902, and 0.927, respectively) and permit a clear interpretation of the studied properties in terms of the structural features of molecules. A LOO cross-validation procedure revealed that the regression models had a fairly good predictability (q2 of 0.679, 0.543, and 0.721, respectively). The comparison with other approaches reveals good behavior of the method proposed. The approach described in this paper appears to be an excellent alternative or guides for discovery and optimization of new lead compounds.

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.

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.

Adiabatic perturbation theory for atoms and molecules in the low-frequency regime

NASA Astrophysics Data System (ADS)

Martiskainen, Hanna; Moiseyev, Nimrod

2017-12-01

There is an increasing interest in the photoinduced dynamics in the low frequency, ω, regime. The multiphoton absorptions by molecules in strong laser fields depend on the polarization of the laser and on the molecular structure. The unique properties of the interaction of atoms and molecules with lasers in the low-frequency regime imply new concepts and directions in strong-field light-matter interactions. Here we represent a perturbational approach for the calculations of the quasi-energy spectrum in the low-frequency regime, which avoids the construction of the Floquet operator with extremely large number of Floquet channels. The zero-order Hamiltonian in our perturbational approach is the adiabatic Hamiltonian where the atoms/molecules are exposed to a dc electric field rather than to ac-field. This is in the spirit of the first step in the Corkum three-step model. The second-order perturbation correction terms are obtained when i ℏ ω ∂/∂ τ serves as a perturbation and τ is a dimensionless variable. The second-order adiabatic perturbation scheme is found to be an excellent approach for calculating the ac-field Floquet solutions in our test case studies of a simple one-dimensional time-periodic model Hamiltonian. It is straightforward to implement the perturbation approach presented here for calculating atomic and molecular energy shifts (positions) due to the interaction with low-frequency ac-fields using high-level electronic structure methods. This is enabled since standard quantum chemistry packages allow the calculations of atomic and molecular energy shifts due to the interaction with dc-fields. In addition to the shift of the energy positions, the energy widths (inverse lifetimes) can be obtained at the same level of theory. These energy shifts are functions of the laser parameters (low frequency, intensity, and polarization).

Tailoring Dirac Fermions in Molecular Graphene

NASA Astrophysics Data System (ADS)

Gomes, Kenjiro K.; Mar, Warren; Ko, Wonhee; Camp, Charlie D.; Rastawicki, Dominik K.; Guinea, Francisco; Manoharan, Hari C.

2012-02-01

The dynamics of electrons in solids is tied to the band structure created by a periodic atomic potential. The design of artificial lattices, assembled through atomic manipulation, opens the door to engineer electronic band structure and to create novel quantum states. We present scanning tunneling spectroscopic measurements of a nanoassembled honeycomb lattice displaying a Dirac fermion band structure. The artificial lattice is created by atomic manipulation of single CO molecules with the scanning tunneling microscope on the surface of Cu(111). The periodic potential generated by the assembled CO molecules reshapes the band structure of the two-dimensional electron gas, present as a surface state of Cu(111), into a ``molecular graphene'' system. We create local defects in the lattice to observe the quasiparticle interference patterns that unveil the underlying band structure. We present direct comparison between the tunneling data, first-principles calculations of the band structure, and tight-binding models.

Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-12-21

With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn-Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve a conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number of degrees of freedom required to represent the Kohn-Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, results in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as their dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080-10,800 atoms is only 10-25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5000-50,000 processors. We use DGDFT based ab initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 × 1 edge reconstruction appears in ACPNRs at room temperature.

Optimal packing size of non-ligated CdSe nanoclusters for microstructure synthesis

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

Tefera, Anteneh G.; Mochena, Mogus D.; Johnson, Elijah

2014-09-14

Structural and electrostatic properties of nanoclusters of CdSe of diameter 1–2 nm are studied with first principle calculations to determine the optimal size for synthesizing microstructures. Based on robustness of the core structure, i.e., the retention of tetrahedral geometry, hexagonal ring structure, and overall wu{sup ¨}rtzite structure to surface relaxations, we conclude that nanoclusters of ~2 nm diameter are the best candidates to form a dense microstructure with minimal interstitial space. Se-terminated surfaces retain a zigzag structure as Se atoms are pulled out and Cd atoms are pulled in due to relaxation, therefore, are best suited for inter-nanocluster formations.

Linear Scaling Density Functional Calculations with Gaussian Orbitals

NASA Technical Reports Server (NTRS)

Scuseria, Gustavo E.

1999-01-01

Recent advances in linear scaling algorithms that circumvent the computational bottlenecks of large-scale electronic structure simulations make it possible to carry out density functional calculations with Gaussian orbitals on molecules containing more than 1000 atoms and 15000 basis functions using current workstations and personal computers. This paper discusses the recent theoretical developments that have led to these advances and demonstrates in a series of benchmark calculations the present capabilities of state-of-the-art computational quantum chemistry programs for the prediction of molecular structure and properties.

Molecular dynamics simulation of coarse-grained poly(L-lysine) dendrimers.

PubMed

Rahimi, Ali; Amjad-Iranagh, Sepideh; Modarress, Hamid

2016-03-01

Poly(L-lysine) (PLL) dendrimer are amino acid based macromolecules and can be used as drug delivery agents. Their branched structure allows them to be functionalized by various groups to encapsulate drug agents into their structure. In this work, at first, an attempt was made on all-atom simulation of PLL dendrimer of different generations. Based on all-atom results, a course-grained model of this dendrimer was designed and its parameters were determined, to be used for simulation of three generations of PLL dendrimer, at two pHs. Similar to the all-atom, the coarse-grained results indicated that by increasing the generation, the dendrimer becomes more spherical. At pH 7, the dendrimer had larger size, whereas at pH 12, due to back folding of branching chains, they had the tendency to penetrate into the inner layers. The calculated radial probability and radial distribution functions confirm that at pH 7, the PLL dendrimer has more cavities and as a result it can encapsulate more water molecules into its inner structure. By calculating the moment of inertia and the aspect ratio, the formation of spherical structure for PLL dendrimer was confirmed.

Mn induced 1 × 2 reconstruction in the τ-MnAl(0 0 1) surface

NASA Astrophysics Data System (ADS)

Guerrero-Sánchez, J.; Takeuchi, Noboru

2018-05-01

We report on first principles total energy calculations to describe the structural, electronic and magnetic properties of MnAl(0 0 1) surfaces. We have concentrated in structural models having 1 × 1 and 1 × 2 periodicities, since recent experiments of the similar MnGa(0 0 1) surface have found 1 × 1 and 1 × 2 reconstructions. Our calculations show the existence of two stable structures for different ranges of chemical potential. A 1 × 1 surface is stable for Al-rich conditions, whereas a Mn-induced 1 × 2 reconstruction appears after increasing the Mn chemical potential up to Mn-rich conditions. It is important to notice that experimentally, Mn rich conditions are important for improved magnetic properties. The Mn layers in both structures have ferromagnetic arrangements, but they are aligned antiferromagnetically with the almost no magnetic Al atoms. Moreover, the on top Mn atoms, which produce the 1 × 2 reconstruction, align antiferromagnetically with the second layer Mn atoms. These findings are similar to those obtained experimentally in MnGa thin films grown by molecular beam epitaxy. Therefore, this method could also be used to grow the proposed MnAl films.

Real-space localization and quantification of hole distribution in chain-ladder Sr3Ca11Cu24O41 superconductor.

PubMed

Bugnet, Matthieu; Löffler, Stefan; Hawthorn, David; Dabkowska, Hanna A; Luke, Graeme M; Schattschneider, Peter; Sawatzky, George A; Radtke, Guillaume; Botton, Gianluigi A

2016-03-01

Understanding the physical properties of the chain-ladder Sr3Ca11Cu24O41 hole-doped superconductor has been precluded by the unknown hole distribution among chains and ladders. We use electron energy-loss spectrometry (EELS) in a scanning transmission electron microscope (STEM) at atomic resolution to directly separate the contributions of chains and ladders and to unravel the hole distribution from the atomic scale variations of the O-K near-edge structures. The experimental data unambiguously demonstrate that most of the holes lie within the chain layers. A quantitative interpretation supported by inelastic scattering calculations shows that about two holes are located in the ladders, and about four holes in the chains, shedding light on the electronic structure of Sr3Ca11Cu24O41. Combined atomic resolution STEM-EELS and inelastic scattering calculations is demonstrated as a powerful approach toward a quantitative understanding of the electronic structure of cuprate superconductors, offering new possibilities for elucidating their physical properties.

Stabilization of a Metastable Fibrous Bi 21.2(1)(Mn 1–xCo x ) 20 Phase with Pseudo-Pentagonal Symmetry Prepared Using a Bi Self-Flux

DOE PAGES

Thimmaiah, Srinivasa; Taufour, Valentin; Iowa State Univ., Ames, IA; ...

2016-11-15

Bi 21.2(1)(Mn 1–xCo x ) 20 is a new metastable phase which is synthesized via Bi self-flux, adopts a highly fibrous morpholo-gy, and decomposes endothermically near 168 °C. It crystallizes in the orthorhombic space group Imma with unit cell parameters α = 19.067(4) Å, $b$ = 4.6071(10) Å and c = 11.583(4) Å, adopting a low-temperature modification of BiNi-type structure by forming columns along the b-axis. Wave-length-dispersive X-ray spectroscopy (WDS) confirms the presence of Co in the structure, which is found to be 7 at.%. In each column, the transition metal (T) and Bi atoms construct a double-walled nanotubular arrangementmore » of atoms around the disordered central Bi atoms. Electronic structure calculations (LMTO-ASA, LSDA) show that the calculated Fermi level falls into a pseudogap and also indicate a possible low-temperature magnetic ordering in the phase.« less

Structure of 1-butylpyridinium tetrafluoroborate ionic liquid: quantum chemistry and molecular dynamic simulation studies.

PubMed

Sun, Hui; Qiao, Baofu; Zhang, Dongju; Liu, Chengbu

2010-03-25

Density functional theory (DFT) calculations combined with molecular dynamic (MD) simulations have been performed to show in detail the structure characteristic of 1-butylpyridinium tetrafluoroborate ([BPy(+)][BF(4)(-)]), a representative of pyridinium-based ionic liquids (ILs). It is found that the relative stability for ion pair configurations is synergically determined by the electrostatic attractions and the H-bond interactions between the ions of opposite charge. [BPy(+)][BF(4)(-)] IL possesses strong long-range ordered structure with cations and anions alternately arranging. The spatial distributions of anions and cations around the given cations are clearly shown, and T-shaped orientation is indicated to play a key role in the interaction between two pyridine rings. DFT calculations and MD simulations uniformly suggest that the H-bonds of the fluorine atoms with the hydrogen atoms on the pyridine rings are stronger than those of the fluorine atoms with the butyl chain hydrogens. The present results can offer useful information for understanding the physicochemical properties of [BPy(+)][BF(4)(-)] IL and further designing new pyridinium-based ILs.

Real-space localization and quantification of hole distribution in chain-ladder Sr3Ca11Cu24O41 superconductor

PubMed Central

Bugnet, Matthieu; Löffler, Stefan; Hawthorn, David; Dabkowska, Hanna A.; Luke, Graeme M.; Schattschneider, Peter; Sawatzky, George A.; Radtke, Guillaume; Botton, Gianluigi A.

2016-01-01

Understanding the physical properties of the chain-ladder Sr3Ca11Cu24O41 hole-doped superconductor has been precluded by the unknown hole distribution among chains and ladders. We use electron energy-loss spectrometry (EELS) in a scanning transmission electron microscope (STEM) at atomic resolution to directly separate the contributions of chains and ladders and to unravel the hole distribution from the atomic scale variations of the O-K near-edge structures. The experimental data unambiguously demonstrate that most of the holes lie within the chain layers. A quantitative interpretation supported by inelastic scattering calculations shows that about two holes are located in the ladders, and about four holes in the chains, shedding light on the electronic structure of Sr3Ca11Cu24O41. Combined atomic resolution STEM-EELS and inelastic scattering calculations is demonstrated as a powerful approach toward a quantitative understanding of the electronic structure of cuprate superconductors, offering new possibilities for elucidating their physical properties. PMID:27051872

Systematic investigation of structural, electronic, optical and thermal properties of ternary MoAlB; an ab initio approach

NASA Astrophysics Data System (ADS)

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

2018-02-01

Structural, electronic, optical and thermal properties of molybdenum aluminum boride (MoAlB) have been analyzed systematically using the full potential linearized augmented plane wave method based on density functional theory at ambient condition as well as high pressure and high temperature. Density of states and band structure calculation reflect the metallic character of MoAlB. In addition to this, the electron charge density calculation reveals the strong covalent bonding, in between ‘B’ atoms as well as ‘Mo’ and ‘B’ atoms. Optical parameters exhibit anisotropic nature and MoAlB become transparent in ultraviolet region for the radiation of energy above 25 eV. The thermal properties were investigated by using the quasi-harmonic Debye model at high temperature and high pressure.

Cryosolution infrared study of hydrogen bonded halothane acetylene complex

NASA Astrophysics Data System (ADS)

Melikova, S. M.; Rutkowski, K. S.; Rospenk, M.

2018-05-01

The interactions between halothane (2-bromo-2-chloro-1,1,1-trifluoroethane) and acetylene (C2H2) are studied by FTIR spectroscopy. Results obtained in liquid cryosolutions in Kr suggest weak complex formation stabilized by H - bond. The complexation enthalpy (∼11 kJ/mol) is evaluated in a series of temperature measurements (T ∼ 120-160 K) of integrated intensity of selected bands performed in liquefied Kr. The quantum chemical MP2/6-311++G(2d,2p) calculations predict four different structures of the complex. The most stable and populated (94% at T∼120 K) structure corresponds to the H - bond between H atom of halothane and pi-electron of triple bond between C atoms of acetylene. Wave numbers of vibrational bands of the most stable structure are calculated in anharmonic approximation implemented in Gaussian program.

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

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.

Al-centered icosahedral ordering in Cu46Zr46Al8 bulk metallic glass

NASA Astrophysics Data System (ADS)

Fang, H. Z.; Hui, X.; Chen, G. L.; Liu, Z. K.

2009-03-01

Icosahedral short-range order, of which Al atoms are caged in the center of icosahedra with Cu and Zr atoms being the vertices, has been evidenced in the Cu46Zr46Al8 glassy structure by ab initio molecular dynamics simulation. These Al-centered clusters distribute irregularly in the three-dimensional space and form a "backbone" structure of the Cu46Zr46Al8 glass alloy. It is suggested that this kind of local structural feature is attributed to the requirement of efficient dense packing and the chemical affinity between Zr-Zr, Zr-Al, and Cu-Zr atoms. Our calculated results are found to be in good agreement with the experimental data.

Influence of Cr doping on the stability and structure of small cobalt oxide clusters.

PubMed

Tung, Nguyen Thanh; Tam, Nguyen Minh; Nguyen, Minh Tho; Lievens, Peter; Janssens, Ewald

2014-07-28

The stability of mass-selected pure cobalt oxide and chromium doped cobalt oxide cluster cations, ConO+m and Con-1CrO+m (n = 2, 3; m = 2-6 and n = 4; m = 3-8), has been investigated using photodissociation mass spectrometry. Oxygen-rich ConO+m clusters (m ≥ n + 1 for n = 2, 4 and m ≥ n + 2 for n = 3) prefer to photodissociate via the loss of an oxygen molecule, whereas oxygen poorer clusters favor the evaporation of oxygen atoms. Substituting a single Co atom by a single Cr atom alters the dissociation behavior. All investigated Con-1 CrO+m clusters, except CoCrO+2 and CoCrO+3, prefer to decay by eliminating a neutral oxygen molecule. Co2O+2, Co4O+3, Co4O+4, and CoCrO+2 are found to be relatively difficult to dissociate and appear as fragmentation product of several larger clusters, suggesting that they are particularly stable. The geometric structures of pure and Cr doped cobalt oxide species are studied using density functional theory calculations. Dissociation energies for different evaporation channels are calculated and compared with the experimental observations. The influence of the dopant atom on the structure and the stability of the clusters is discussed.

Structure and conformation of N-(2-methyl-5-chlorophenyl)salicylaldimine

NASA Astrophysics Data System (ADS)

Elmali, A.; Elerman, Y.

1998-02-01

N-(2-methyl-5-chlorophenyl)salicylaldimine (C 14H 12ClNO) has been studied by X-ray analysis and AM1 molecular orbital methods. It crystallises in the orthorhombic space group P2 12 12 1 with a = 7.474(1) Å, b = 12.155(1) Å, c = 13.378(1) Å, V = 1215.3(2) Å3, Z = 4, Dc = 1.343 g cm -3 and μ(Mo Kα) = 0.296 mm -1. The structure was solved by direct methods and refined to R = 0.0374 for 1689 reflections [ I > 2 σ( I)]. The title compound is photochromic and the molecule is not planar. There is a strong intramolecular hydrogen bond of distance 2.604(3) Å between the hydroxyl oxygen atom and imine nitrogen atom, the hydrogen atom essentially being bonded to the oxygen atom. Minimum energy conformations from AM1 were calculated as a function of the three torsion angles θ1(C8N1C7C6), θ2(C9C8N1C7) and θ3(N1C7C6C5), varied every 10°. The optimised geometry of the crystal structure corresponding to a non-planar conformation is the most stable conformation in all calculations.

Correlation between the resistivity and the atomic clusters in liquid Cu-Sn alloys

NASA Astrophysics Data System (ADS)

Jia, Peng; Zhang, Jinyang; Hu, Xun; Li, Cancan; Zhao, Degang; Teng, XinYing; Yang, Cheng

2018-05-01

The liquid structure of CuxSn100-x (x = 0, 10, 20, 33, 40, 50, 60, 75, 80 and 100) alloys with atom percentage were investigated with resistivity and viscosity methods. It can be found from the resistivity data that the liquid Cu75Sn25 and Cu80Sn20 alloys had a negative temperature coefficient of resistivity (TCR), and liquid Cu75Sn25 alloy had a minimum value of -9.24 μΩ cm K-1. While the rest of liquid Cu-Sn alloys had a positive TCR. The results indicated that the Cu75Sn25 atomic clusters existed in Cu-Sn alloys. In addition, the method of calculating the percentage of Cu75Sn25 atomic clusters was established on the basis of resistivity theory and the law of conservation of mass. The Cu75Sn25 alloy had a maximum volume of the atomic clusters and a highest activation energy. The results further proved the existence of Cu75Sn25 atomic clusters. Furthermore, the correlation between the liquid structure and the resistivity was established. These results provide a useful reference for the investigation of liquid structure via the sensitive physical properties to the liquid structure.

Tunable electronic structures of germanium monochalcogenide nanosheets via light non-metallic atom functionalization: a first-principles study.

PubMed

Ding, Yi; Wang, Yanli

2016-08-17

Germanium monochalcogenides, i.e. GeS and GeSe sheets, are isoelectronic analogues of phosphorene, which have been synthesized in recent experiments (P. Ramasamy et al., J. Mater. Chem. C, 2016, 4, 479). Utilizing first-principles calculations, we have investigated their tunable electronic and magnetic properties via light non-metallic atom (B, C, N, O, Si, P, S) functionalization. We find that on these GeS and GeSe sheets O and S adatoms prefer to locate at the top site above the Ge atom, while the other ones like to occupy the anion site, which push the original S/Se atom to the hollow site instead. O and S adatoms slightly affect the semiconducting behaviour of the doped systems, while B, C, N, Si, P ones will drastically modify their band structures and induce versatile spintronic properties. Through the supercell calculations, B and C adatoms are found to induce a bipolar semiconducting behaviour in the decorated systems, while the N/P adatom will cause a spin-gapless-semiconducting/nearly-half-metallic feature in them. The B/C/N/Si/P-substituted GeS/GeSe sheet can be formed by removing the hollow-site S/Se atom from the adatom-decorated structures, which exhibit an opposite semiconducting/metallic behaviour to their phosphorene counterparts. A general odd-even rule is proposed for this phenomenon, which shows that an odd (even) number of valence electron difference between the substitution and host atoms would cause a metallic (semiconducting) feature in the substituted systems. Our study demonstrates that atom functionalization is an efficient way to tailor the properties of GeS and GeSe nanosheets, which have adaptable electronic properties for potential applications in nanoelectronics and spintronics.

First-principles calculations of the thermodynamic properties of transuranium elements in a molten salt medium

NASA Astrophysics Data System (ADS)

Noh, Seunghyo; Kwak, Dohyun; Lee, Juseung; Kang, Joonhee; Han, Byungchan

2014-03-01

We utilized first-principles density-functional-theory (DFT) calculations to evaluate the thermodynamic feasibility of a pyroprocessing methodology for reducing the volume of high-level radioactive materials and recycling spent nuclear fuels. The thermodynamic properties of transuranium elements (Pu, Np and Cm) were obtained in electrochemical equilibrium with a LiCl-KCl molten salt as ionic phases and as adsorbates on a W(110) surface. To accomplish the goal, we rigorously calculated the double layer interface structures on an atomic resolution, on the thermodynamically most stable configurations on W(110) surfaces and the chemical activities of the transuranium elements for various coverages of those elements. Our results indicated that the electrodeposition process was very sensitive to the atomic level structures of Cl ions at the double-layer interface. Our studies are easily expandable to general electrochemical applications involving strong redox reactions of transition metals in non-aqueous solutions.

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

Seña, N.; Dussan, A.; Mesa, F.

We have carried out first-principles spin polarized calculations to obtain comprehensive information regarding the structural, magnetic, and electronic properties of the Mn-doped GaSb compound with dopant concentrations: x = 0.062, 0.083, 0.125, 0.25, and 0.50. The plane-wave pseudopotential method was used in order to calculate total energies and electronic structures. It was found that the Mn{sub Ga} substitution is the most stable configuration with a formation energy of ∼1.60 eV/Mn-atom. The calculated density of states shows that the half-metallic ferromagnetism is energetically stable for all dopant concentrations with a total magnetization of about 4.0 μ{sub B}/Mn-atom. The results indicate that the magnetic ground statemore » originates from the strong hybridization between Mn-d and Sb-p states, which agree with previous studies on Mn-doped wide gap semiconductors. This study gives new clues to the fabrication of diluted magnetic semiconductors.« less

Investigation of ionic transport in sodium scandium phosphate (NSP) and related compounds

NASA Astrophysics Data System (ADS)

Bhat, Kaustubh; Blügel, Stefan; Lustfeld, Hans

Sodium ionic conductors offer significant advantages for application in large scale energy storage systems. In this study, we investigate the different pathways available for sodium ion conduction in NSP and calculate energy barriers for ionic transport using Density Functional Theory (DFT) and the Nudged Elastic Band Method. We identify the structural parameters that reduce the energy barrier, by calculating the influence of positive and negative external pressure on the energy barrier. Lattice strain can be introduced by cation or anion substitution within the NASICON structure. We substitute the scandium atom with other trivalent atoms such as aluminium and yttrium, and calculate the resulting energy barriers. Sodium thiophosphate (Na3PS4) has previously shown about two orders of magnitude higher ionic conductivity than sodium phosphate (Na3PO4). We investigate the effect of substituting oxygen with sulphur in NSP. We acknowledge discussions with our experimental colleagues F. Tietz and M. Guin toward this work

Predicting the properties of the lead alloys from DFT calculations

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

Buimaga-Iarinca, L., E-mail: luiza.iarinca@itim-cj.ro; Calborean, A.

2015-12-23

We provide qualitative results for the physical properties of the lead alloys at atomic scale by using DFT calculations. Our approach is based on the two assumptions: (i) the geometric structure of lead atoms provides a matrix where the alloying elements can take their positions in the structure as substitutions and (ii) there is a small probability of a direct interaction between the alloying elements, thus the interactions of each alloying element may be approximated by the interactions to the lead matrix. DFT calculations are used to investigate the interaction between several types of impurities and the lead matrix formore » low concentrations of the alloying element. We report results such as the enthalpy of formation, charge transfer and mechanical stress induced by the impurities in the lead matrix; these results can be used as qualitative guide in tuning the physico-chemical properties of the lead alloys.« less

Optical conductivity of partially oxidized graphene from first principles

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

Nasehnia, F., E-mail: f.nasehnia@gmail.com; Seifi, M., E-mail: Seifi@guilan.ac.ir

2015-07-07

We investigate the geometry, electronic structure, and optical properties of partially oxidized graphene using density functional theory. Our calculations show that oxygen atoms are chemisorbed on graphene plane and distort carbon atoms vertically, with almost no change in the in-plane structure. The ground state configurations for different oxygen coverages ranging from 2% to 50% (O/C ratio) are calculated and show the strong tendency of oxygen adatoms to aggregate and form discrete islands on graphene plane. It is found that the opened band gap due to oxygen functionalization depends on the oxygen density and the adsorption configuration. The gap is notmore » significant for oxygen densities lower than 8%. The optical conductivities are calculated in the infrared, visible, and ultraviolet regions and show different characteristic features depending on the degree of oxidation. These results imply that optical measurement techniques can be employed to monitor oxidation (or reduction) process as contact-free methods.« less

Time-dependent first-principles study of angle-resolved secondary electron emission from atomic sheets

NASA Astrophysics Data System (ADS)

Ueda, Yoshihiro; Suzuki, Yasumitsu; Watanabe, Kazuyuki

2018-02-01

Angle-resolved secondary electron emission (ARSEE) spectra were analyzed for two-dimensional atomic sheets using a time-dependent first-principles simulation of electron scattering. We demonstrate that the calculated ARSEE spectra capture the unoccupied band structure of the atomic sheets. The excitation dynamics that lead to SEE have also been revealed by the time-dependent Kohn-Sham decomposition scheme. In the present study, the mechanism for the experimentally observed ARSEE from atomic sheets is elucidated with respect to both energetics and the dynamical aspects of SEE.

Ab initio prediction of stable nanotwin double layers and 4O structure in Ni2MnGa

NASA Astrophysics Data System (ADS)

Zelený, Martin; Straka, Ladislav; Sozinov, Alexei; Heczko, Oleg

2016-12-01

The ab initio electronic structure calculations of the Ni2MnGa alloy indicate that the orthorhombic 4O structure exhibits the lowest energy compared to all known martensitic structures. The 4O structure is formed by nanotwin double layers, i.e., oppositely oriented nanotwins consisting of two (101) lattice planes of nonmodulated martensitic structure. It exhibits the lowest occupation of density of states at the Fermi level. The total energy 1.98 meV/atom below the energy of nonmodulated martensite is achieved within structural relaxation by shifting Mn and Ga atoms at the nanotwin boundaries. The same atomic shift can also be found in other martensitic nanotwinned or modulated structures such as 10M and 14M, which indicates the importance of the nanotwin double layer for the stability of these structures. Our discovery shows that the nanotwinning or modulation is a natural property of low-temperature martensitic phases in Ni-Mn-Ga alloys.

NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary.

PubMed

Yilmaz, Emel Maden; Güntert, Peter

2015-09-01

An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

Interfacial Structure and Chemistry of GaN on Ge(111)

NASA Astrophysics Data System (ADS)

Zhang, Siyuan; Zhang, Yucheng; Cui, Ying; Freysoldt, Christoph; Neugebauer, Jörg; Lieten, Ruben R.; Barnard, Jonathan S.; Humphreys, Colin J.

2013-12-01

The interface of GaN grown on Ge(111) by plasma-assisted molecular beam epitaxy is resolved by aberration corrected scanning transmission electron microscopy. A novel interfacial structure with a 5∶4 closely spaced atomic bilayer is observed that explains why the interface is flat, crystalline, and free of GeNx. Density functional theory based total energy calculations show that the interface bilayer contains Ge and Ga atoms, with no N atoms. The 5∶4 bilayer at the interface has a lower energy than a direct stacking of GaN on Ge(111) and enables the 5∶4 lattice-matching growth of GaN.

Solution of the comoving-frame equation of transfer in spherically symmetric flows. V - Multilevel atoms. [in early star atmospheres

NASA Technical Reports Server (NTRS)

Mihalas, D.; Kunasz, P. B.

1978-01-01

The coupled radiative transfer and statistical equilibrium equations for multilevel ionic structures in the atmospheres of early-type stars are solved. Both lines and continua are treated consistently; the treatment is applicable throughout a transonic wind, and allows for the presence of background continuum sources and sinks in the transfer. An equivalent-two-level-atoms approach provides the solution for the equations. Calculations for simplified He (+)-like model atoms in parameterized isothermal wind models indicate that subordinate line profiles are sensitive to the assumed mass-loss rate, and to the assumed structure of the velocity law in the atmospheres.

Si-centered capped trigonal prism ordering in liquid Pd 82Si 18 alloy study by first-principles calculations

DOE PAGES

Dong, F.; Yue, G. Q.; Ames Lab. and Iowa State Univ., Ames, IA; ...

2017-03-24

First-principles molecular dynamic (MD) simulation and X-ray diffraction were employed to study the local structures of Pd–Si liquid at the eutectic composition (Pd 82Si 18). Here, a strong repulsion is found between Si atoms, and Si atoms prefer to be evenly distributed in the liquid. The dominate local structures around Si atoms are found to be with of a trigonal prism capped by three half-octahedra and an archimedean anti-prism. The populations of these clusters increase significantly upon cooling, and may play an important role in the formation of Pd 82Si 18 alloy glass.

Si-centered capped trigonal prism ordering in liquid Pd 82Si 18 alloy study by first-principles calculations

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

Dong, F.; Yue, G. Q.; Ames Lab. and Iowa State Univ., Ames, IA

First-principles molecular dynamic (MD) simulation and X-ray diffraction were employed to study the local structures of Pd–Si liquid at the eutectic composition (Pd 82Si 18). Here, a strong repulsion is found between Si atoms, and Si atoms prefer to be evenly distributed in the liquid. The dominate local structures around Si atoms are found to be with of a trigonal prism capped by three half-octahedra and an archimedean anti-prism. The populations of these clusters increase significantly upon cooling, and may play an important role in the formation of Pd 82Si 18 alloy glass.

Atomic Defects and Doping of Monolayer NbSe2.

PubMed

Nguyen, Lan; Komsa, Hannu-Pekka; Khestanova, Ekaterina; Kashtiban, Reza J; Peters, Jonathan J P; Lawlor, Sean; Sanchez, Ana M; Sloan, Jeremy; Gorbachev, Roman V; Grigorieva, Irina V; Krasheninnikov, Arkady V; Haigh, Sarah J

2017-03-28

We have investigated the structure of atomic defects within monolayer NbSe 2 encapsulated in graphene by combining atomic resolution transmission electron microscope imaging, density functional theory (DFT) calculations, and strain mapping using geometric phase analysis. We demonstrate the presence of stable Nb and Se monovacancies in monolayer material and reveal that Se monovacancies are the most frequently observed defects, consistent with DFT calculations of their formation energy. We reveal that adventitious impurities of C, N, and O can substitute into the NbSe 2 lattice stabilizing Se divacancies. We further observe evidence of Pt substitution into both Se and Nb vacancy sites. This knowledge of the character and relative frequency of different atomic defects provides the potential to better understand and control the unusual electronic and magnetic properties of this exciting two-dimensional material.

Optical properties of an indium doped CdSe nanocrystal: A density functional approach

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

Salini, K.; Mathew, Vincent, E-mail: vincent@cukerala.ac.in; Mathew, Thomas

2016-05-06

We have studied the electronic and optical properties of a CdSe nanocrystal doped with n-type impurity atom. First principle calculations of the CdSe nanocrystal based on the density functional theory (DFT), as implemented in the Vienna Ab Initio Simulation Package (VASP) was used in the calculations. We have introduced a single Indium impurity atom into CdSe nanocrystal with 1.3 nm diameter. Nanocrystal surface dangling bonds are passivated with hydrogen atom. The band-structure, density of states and absorption spectra of the doped and undopted nanocrystals were discussed. Inclusion of the n-type impurity atom introduces an additional electron in conduction band, and significantlymore » alters the electronic and optical properties of undoped CdSe nanocrystal. Indium doped CdSe nannocrystal have potential applications in optoelectronic devices.« less

When Anatase Nanoparticles Become Bulklike: Properties of Realistic TiO2 Nanoparticles in the 1-6 nm Size Range from All Electron Relativistic Density Functional Theory Based Calculations.

PubMed

Lamiel-Garcia, Oriol; Ko, Kyoung Chul; Lee, Jin Yong; Bromley, Stefan T; Illas, Francesc

2017-04-11

All electron relativistic density functional theory (DFT) based calculations using numerical atom-centered orbitals have been carried out to explore the relative stability, atomic, and electronic structure of a series of stoichiometric TiO 2 anatase nanoparticles explicitly containing up to 1365 atoms as a function of size and morphology. The nanoparticles under scrutiny exhibit octahedral or truncated octahedral structures and span the 1-6 nm diameter size range. Initial structures were obtained using the Wulff construction, thus exhibiting the most stable (101) and (001) anatase surfaces. Final structures were obtained from geometry optimization with full relaxation of all structural parameters using both generalized gradient approximation (GGA) and hybrid density functionals. Results show that, for nanoparticles of a similar size, octahedral and truncated octahedral morphologies have comparable energetic stabilities. The electronic structure properties exhibit a clear trend converging to the bulk values as the size of the nanoparticles increases but with a marked influence of the density functional employed. Our results suggest that electronic structure properties, and hence reactivity, for the largest anatase nanoparticles considered in this study will be similar to those exhibited by even larger mesoscale particles or by bulk systems. Finally, we present compelling evidence that anatase nanoparticles become effectively bulklike when reaching a size of ∼20 nm diameter.

Transformation of γ-alumina to θ-alumina

NASA Astrophysics Data System (ADS)

Cai, Shuhui; Sohlberg, Karl; Rashkeev, Sergey; Pantelides, Sokrates T.

2002-03-01

γ- and θ-alumina are two metastable phases of aluminum oxide observed along the dehydration sequence of boehmite upon thermal treatment before conversion to the final product α-alumina. The transformation from the γ to the θ phase can best be studied by using Al_16O_24 cells. Motion of eight Al atoms from their γ-alumina positions to new positions and no O motions result in an approximate structure that, upon relaxation by first-principles calculations, becomes the known θ-alumina structure. Total-energy calculations along the paths of atomic motions have been used to map out possible synergistic transformation pathways. This work was supported in part by the USDoE and a NSF GOALI Grant with Alcoa, Inc.

Linking Chemical Electron–Proton Transfer to Proton Pumping in Cytochrome c Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron–Copper Dinuclear Complex

PubMed Central

2015-01-01

After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3–CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185–190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment. PMID:24960612

Magnetism of a relaxed single atom vacancy in graphene

NASA Astrophysics Data System (ADS)

Wu, Yunyi; Hu, Yonghong; Xue, Li; Sun, Tieyu; Wang, Yu

2018-04-01

It has been suggested in literature that defects in graphene (e.g. absorbed atoms and vacancies) may induce magnetizations due to unpaired electrons. The nature of magnetism, i.e. ferromagnetic or anti-ferromagnetic, is dependent on a number of structural factors including locations of magnetic moments and lattice symmetry. In the present work we investigated the influence of a relaxed single atom vacancy in garphnene on magnetization which were obtained under different pinning boundary conditions, aiming to achieve a better understanding of the magnetic behaviors of graphene. Through first principles calculations, we found that major spin polarizations occur on atoms that deviate slightly from their original lattice positions, and pinning boundaries could also affect the relaxed positions of atoms and determine which atom(s) would become the main source(s) of total spin polarizations and magnetic moments. When the pinning boundary condition is free, a special non-magnetic and semi-conductive structure may be obtained, suggesting that magnetization should more readily occur under pinning boundary conditions.

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

NASA Astrophysics Data System (ADS)

Belianinov, Alex; Ganesh, Panchapakesan; Lin, Wenzhi; Sales, Brian C.; Sefat, Athena S.; Jesse, Stephen; Pan, Minghu; Kalinin, Sergei V.

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1-xSex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.

Atomic dynamics and the problem of the structural stability of free clusters of solidified inert gases

NASA Astrophysics Data System (ADS)

Verkhovtseva, É. T.; Gospodarev, I. A.; Grishaev, A. V.; Kovalenko, S. I.; Solnyshkin, D. D.; Syrkin, E. S.; Feodos'ev, S. B.

2003-05-01

The dependence of the rms amplitudes of atoms in free clusters of solidified inert gases on the cluster size is investigated theoretically and experimentally. Free clusters are produced by homogeneous nucleation in an adiabatically expanding supersonic stream. Electron diffraction is used to measure the rms amplitudes of the atoms; the Jacobi-matrix method is used for theoretical calculations. A series of distinguishing features of the atomic dynamics of microclusters was found. This was necessary to determine the character of the formation and the stability conditions of the crystal structure. It wass shown that for clusters consisting of less than N˜103 atoms, as the cluster size decreases, the rms amplitudes grow much more rapidly than expected from the increase in the specific contribution of the surface. It is also established that an fcc structure of a free cluster, as a rule, contains twinning defects (nuclei of an hcp phase). One reason for the appearance of such defects is the so-called vertex instability (anomalously large oscillation amplitudes) of the atoms in coordination spheres.

Grown from lithium flux, the ErCo5Si(3.17) silicide is a combination of disordered derivatives of the UCo5Si3 and Yb6Co30P19 structure types.

PubMed

Stetskiv, Andrij; Rozdzynska-Kielbik, Beata; Misztal, Renata; Pavlyuk, Volodymyr

2015-06-01

A ternary hexaerbium triacontacobalt enneakaidecasilicide, ErCo5Si(3.17), crystallizes as a combination of disordered variants of the hexagonal UCo5Si3 (P6₃/m) and Yb6Co30P19 (P6) structure types and is closely related to the Sc6Co30Si19 and Ce6Rh30Si19 types. The Er, Co and three of the Si atoms occupy sites of m.. symmetry and a fourth Si atom occupies a site of -6.. symmetry. The environment of the Er atom is a 21-vertex pseudo-Frank-Kasper polyhedron. Trigonal prismatic coordination is observed for the Si atoms. The Co atoms are enclosed in heavily deformed cuboctahedra and 11-vertex polyhedra. Crystallochemistry analysis and the data from electronic structure calculations (TB-LMTO-ASA) suggest that the Er atoms form positively charged cations which compensate the negative charge of the [Co12Si9](m-) polyanions.

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

Li, Rong; Wu, Yongquan, E-mail: yqwu@shu.edu.cn; Xiao, Junjiang

We observed homogeneous nucleation process of supercooled liquid Fe by molecular dynamics simulations. Using bond-orientational order parameters together with Voronoi polyhedron method, we characterized local structure, calculated the volume of Voronoi polyhedra of atoms and identified the structure and density fluctuations. We monitored the formation of nucleus and analyzed its inner structure. The birth and growth of the pre-nucleus and nucleus are accompanied with aggregating and disaggregating processes in the time scale of femtosecond. Only the initial solid-like clusters (ISLC), ranging from 1 to 7 atoms, pop up directly from liquid. The relation between the logarithm of number of clustersmore » and the cluster size was found to be linear for ISLCs and was observed to be parabolic for all solid-like clusters (SLC) due to aggregating and disaggregating effects. The nucleus and pre-nuclei mainly consist of body centered cubic (BCC) and hexagonal close packed atoms, while the BCC atoms tend to be located at the surface. Medium-range structure fluctuations induce the birth of ISLCs, benefit the aggregation of embryos and remarkably promote the nucleation. But density fluctuations contribute little to nucleation. The lifetime of most icosahedral-like atoms (ICO) is shorter than 0.7 ps. No obvious relationship was found between structure/density fluctuations and the appearance of ICO atoms.« less

Calculating hyperfine couplings in large ionic crystals containing hundreds of QM atoms: subsystem DFT is the key.

PubMed

Kevorkyants, Ruslan; Wang, Xiqiao; Close, David M; Pavanello, Michele

2013-11-14

We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.

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.

Ag@ZnO core-shell nanoparticles study by first principle: The structural, magnetic and optical properties

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

Cheng, Hai-Xia; Wang, Xiao-Xu; Beijing Computing Center, Beijing 100094

Ag@ZnO core-shell nanoparticles of around 72 atoms have been investigated by the density functional theory, revealing proving for the first time that the core-shell structure exhibits a shrinkage phenomenon from outer shell in agreement with the other studies in literatures. Our calculations predict that the Ag@ZnO core-shell structure is a ferromagnetic spin polarized state, and the magnetism mainly stems from the spin splitting of 2p electrons of O atoms. In addition, the total and partial DOS of Ag@ZnO indicate that the nanostructure is a half-metallic nanoparticle and has the characters of the p-type semiconductor. Furthermore, the optical properties calculations showmore » that the absorption edge of Ag@ZnO have a red shift and good photocatalysis compare to that of the bulk ZnO. These results of the Ag@ZnO core-shell structure obtain a well agreement with the experimental measurement. - Graphical abstract: Geometric structure of (a) Ag@ZnO core-shell nanostructure; (b) the core of Ag; (c) the shell of ZnO The core-shell nanoparticle Ag@ZnO contains Ag inner core of radius of 4 Å and ZnO outer shell with thickness of 2 Å. Ag@ZnO core-shell nanoparticles of around 72 atoms have been proved for the first time that the core-shell structure exhibit a shrinkage phenomenon from outer shell. Our calculations predict that the Ag@ZnO core-shell structure is a half-metallic nanoparticle and has the characters of the p-type semiconductor. The absorption edge of Ag@ZnO have a red shift and get good photo-catalysis compare to that of the bulk ZnO.« less

TED analysis of the Si(113) surface structure

NASA Astrophysics Data System (ADS)

Suzuki, T.; Minoda, H.; Tanishiro, Y.; Yagi, K.

1999-09-01

We carried out a TED (transmission electron diffraction) analysis of the Si(113) surface structure. The TED patterns taken at room temperature showed reflections due to the 3×2 reconstructed structure. The TED pattern indicated that a glide plane parallel to the <332> direction suggested in some models is excluded. We calculated the R-factors (reliability factors) for six surface structure models proposed previously. All structure models with energy-optimized atomic positions have large R-factors. After revision of the atomic positions, the R-factors of all the structure models decreased below 0.3, and the revised version of Dabrowski's 3×2 model has the smallest R-factor of 0.17.

Hybrid platforms of graphane-graphene 2D structures: prototypes for atomically precise nanoelectronics.

PubMed

Mota, F de B; Rivelino, R; Medeiros, P V C; Mascarenhas, A J S; de Castilho, C M C

2014-11-21

First-principles calculations demonstrate that line/ribbon defects, resulting from a controlled dehydrogenation in graphane, lead to the formation of low-dimensional electron-rich tracks in a monolayer. The present simulations point out that hybrid graphane-graphene nanostructures exhibit important elements, greatly required for the fabrication of efficient electronic circuits at the atomic level.

Theoretical investigations on the d-p hybridized aromaticity, photoelectron spectroscopy and neutral salts of the LaX2- (X=Al, Ga, In) clusters.

PubMed

Chen, Jing; Yang, Huan; Wang, Jing; Cheng, Shi-Bo

2018-05-30

We present an extensive density functional theory (DFT) calculations on the geometrical and electronic structures of the triatomic LaX 2 - (X=Al, Ga, In) clusters. Various trail structures and spin states have been attempted to determine the lowest-energy geometries of these La-doped metal clusters. The ground states of all three clusters are calculated to possess the trigonal structures with the singlet multiplicities. The calculations on molecular orbitals (MOs) and nucleus-independent chemical shift (NICS) values have been performed to examine the aromatic characteristics of the LaX 2 - (X=Al, Ga, In) clusters. The present calculations disclose that all these metal clusters are doubly aromatic, namely d-p hybridized σ and π aromaticity resulting from the effective overlap between the 5d atomic orbital of the La atom and the p orbitals of the IIIA group elements. Theoretical vertical detachment energies (VDEs) were also calculated to simulate the photoelectron spectra (PES) of the clusters. In addition, by adding the alkali cations (Li + and Na + ) into the LaX 2 - (X=Al, Ga, In) clusters, the geometries and electronic structures of the corresponding neutral salts have also been investigated to gain more insights in the potential of using these aromatic anions as building blocks. Copyright © 2018 Elsevier B.V. All rights reserved.

TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid

NASA Astrophysics Data System (ADS)

Kononova, Olga; Maksudov, Farkhad; Marx, Kenneth A.; Barsegov, Valeri

2018-01-01

A new computational methodology for the accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and C_α -based coarse-grained structural models of biological particles. The methodology mapped into the software package TensorCalculator was successfully applied to the empty cowpea chlorotic mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid. We found an inhomogeneous stress distribution in various portions of the CCMV structure and stress transfer from one portion of the virus structure to another, which also points to the importance of entropic effects, often ignored in finite element analysis and elastic network modeling. We formulate a criterion for elastic deformation using the first principal stress components. Furthermore, we show that von Mises and Tresca stress tensors can be used to predict the onset of a viral capsid’s mechanical failure, which leads to total structural collapse. TensorCalculator can be used to study stress evolution and dynamics of defects in viral capsids and other large-size protein assemblies.

Reduced interface spin polarization by antiferromagnetically coupled Mn segregated to the C o2MnSi /GaAs (001) interface

NASA Astrophysics Data System (ADS)

Rath, Ashutosh; Sivakumar, Chockalingam; Sun, C.; Patel, Sahil J.; Jeong, Jong Seok; Feng, J.; Stecklein, G.; Crowell, Paul A.; Palmstrøm, Chris J.; Butler, William H.; Voyles, Paul M.

2018-01-01

We have investigated the interfacial structure and its correlation with the calculated spin polarization in C o2MnSi /GaAs(001) lateral spin valves. C o2MnSi (CMS) films were grown on As-terminated c(4 ×4 ) GaAs(100) by molecular beam epitaxy using different first atomic layers: MnSi, Co, and Mn. Atomically resolved Z -contrast scanning transmission electron microscopy (STEM) imaging and electron energy loss spectroscopy (EELS) were used to develop atomic structural models of the CMS/GaAs interfaces that were used as inputs for first-principles calculations to understand the magnetic and electronic properties of the interface. First-principles structures were relaxed and then validated by comparing experimental and simulated high-resolution STEM images. STEM-EELS results show that all three films have similar six atomic layer thick, Mn- and As-rich multilayer interfaces. However, the Co-initiated interface contains a M n2As -like layer, which is antiferromagnetic, and which is not present in the other two interfaces. Density functional theory calculations show a higher degree of interface spin polarization in the Mn- and MnSi-initiated cases, compared to the Co-initiated case, although none of the interfaces are half-metallic. The loss of half-metallicity is attributed, at least in part, to the segregation of Mn at the interface, which leads to the formation of interface states. The implications for the performance of lateral spin valves based on these interfaces are discussed briefly.

Correlating electronic transport to atomic structures in self-assembled quantum wires.

PubMed

Qin, Shengyong; Kim, Tae-Hwan; Zhang, Yanning; Ouyang, Wenjie; Weitering, Hanno H; Shih, Chih-Kang; Baddorf, Arthur P; Wu, Ruqian; Li, An-Ping

2012-02-08

Quantum wires, as a smallest electronic conductor, are expected to be a fundamental component in all quantum architectures. The electronic conductance in quantum wires, however, is often dictated by structural instabilities and electron localization at the atomic scale. Here we report on the evolutions of electronic transport as a function of temperature and interwire coupling as the quantum wires of GdSi(2) are self-assembled on Si(100) wire-by-wire. The correlation between structure, electronic properties, and electronic transport are examined by combining nanotransport measurements, scanning tunneling microscopy, and density functional theory calculations. A metal-insulator transition is revealed in isolated nanowires, while a robust metallic state is obtained in wire bundles at low temperature. The atomic defects lead to electron localizations in isolated nanowire, and interwire coupling stabilizes the structure and promotes the metallic states in wire bundles. This illustrates how the conductance nature of a one-dimensional system can be dramatically modified by the environmental change on the atomic scale. © 2012 American Chemical Society

Planar CoB18- Cluster: a New Motif for - and Metallo-Borophenes

NASA Astrophysics Data System (ADS)

Chen, Teng-Teng; Jian, Tian; Lopez, Gary; Li, Wan-Lu; Chen, Xin; Li, Jun; Wang, Lai-Sheng

2016-06-01

Combined Photoelectron Spectroscopy (PES) and theoretical calculations have found that anion boron clusters (Bn-) are planar and quasi-planar up to B25-. Recent works show that anion pure boron clusters continued to be planar at B27-,B30-,B35- and B36-. B35- and B36- provide the first experimental evidence for the viability of the two-dimensional (2D) boron sheets (Borophene). The 2D to three-dimensional (3D) transitions are shown to happen at B40-,B39- and B28-, which possess cage-like structures. These fullerene-like boron cage clusters are named as Borospherene. Recently, borophenes or similar structures are claimed to be synthesized by several groups. Following an electronic design principle, a series of transition-metal-doped boron clusters (M©Bn-, n=8-10) are found to possess the monocyclic wheel structures. Meanwhile, CoB12- and RhB12- are revealed to adopt half-sandwich-type structures with the quasi-planar B12 moiety similar to the B12- cluster. Very lately, we show that the CoB16- cluster possesses a highly symmetric Cobalt-centered drum-like structure, with a new record of coordination number at 16. Here we report the CoB18- cluster to possess a unique planar structure, in which the Co atom is doped into the network of a planar boron cluster. PES reveals that the CoB18- cluster is a highly stable electronic system with the first adiabatic detachment energy (ADE) at 4.0 eV. Global minimum searches along with high-level quantum calculations show the global minimum for CoB18- is perfectly planar and closed shell (1A1) with C2v symmetry. The Co atom is bonded with 7 boron atoms in the closest coordination shell and the other 11 boron atoms in the outer coordination shell. The calculated vertical detachment energy (VDE) values match quite well with our experimental results. Chemical bonding analysis by the Adaptive Natural Density Partitioning (AdNDP) method shows the CoB18- cluster is π-aromatic with four 4-centered-2-electron (4c-2e) π bonds and one 19-centered-2-electron (19c-2e) π bond, 10 π electrons in total. This perfectly planar structure reveals the viability of creating a new class of hetero-borophenes and metallo-borophenes by doping metal atoms into the plane of monolayer boron atoms. This gives a new approach to design perspective hetero-borophenes and metallo-borophenes materials with tunable chemical, magnetic and optical properties.

Reconstructing Solvent Density of Myoglobin Unit Cell from Proximal Radial Distribution Functions of Amino Acids

NASA Astrophysics Data System (ADS)

Galbraith, Madeline; Lynch, Gc; Pettitt, Bm

Understanding the solvent density around a protein crystal structure is an important step for refining accurate crystal structures for use in dynamics simulations or in free energy calculations. The free energy of solvation has typically been approximated using an implicit continuum solvent model or an all atom MD simulation, with a trade-off between accuracy and computation time. For proteins, using precomputed proximal radial distribution functions (pRDFs) of the solvent to reconstruct solvent density on a grid is much faster than all atom MD simulations and more accurate than using implicit solvent models. MD simulations were run for the 20 common amino acids and pRDFs were calculated for several atom type data sets with and without hydrogens, using atom types representative of amino acid side chain atoms. Preliminary results from reconstructions suggest using a data set with 15 heavy atoms and 3 hydrogen yields results with the lowest error without a tradeoff on time. The results of using precomputed pRDFs to reconstruct the solvent density of water for the myoglobin (pdb ID 2mgk) unit cell quantifies the accuracy of the method in comparison with the crystallographic data. Funding Acknowledgement: This research was funded by the CPRIT Summer Undergraduate Program in Computational Cancer Biology, training Grant award RP 140113 from the Cancer Prevention & Research Institute of Texas (CPRIT).

Mechanical, electronic, and thermodynamic properties of zirconium carbide from first-principles calculations

NASA Astrophysics Data System (ADS)

Yang, Xiao-Yong; Lu, Yong; Zheng, Fa-Wei; Zhang, Ping

2015-11-01

Mechanical, electronic, and thermodynamic properties of zirconium carbide have been systematically studied using the ab initio calculations. The calculated equilibrium lattice parameter, bulk modulus, and elastic constants are all well consistent with the experimental data. The electronic band structure indicates that the mixture of C 2p and Zr 4d and 4p orbitals around the Fermi level makes a large covalent contribution to the chemical bonds between the C and Zr atoms. The Bader charge analysis suggests that there are about 1.71 electrons transferred from each Zr atom to its nearest C atom. Therefore, the Zr-C bond displays a mixed ionic/covalent character. The calculated phonon dispersions of ZrC are stable, coinciding with the experimental measurement. A drastic expansion in the volume of ZrC is seen with increasing temperature, while the bulk modulus decreases linearly. Based on the calculated phonon dispersion curves and within the quasi-harmonic approximation, the temperature dependence of the heat capacities is obtained, which gives a good description compared with the available experimental data. Project supported by the National Natural Science Foundation of China (Grant No. 51071032).

DFT investigation of electronic structures and magnetic properties of halides family MeHal3 (Me=Ti, Mo,Zr,Nb, Ru, Hal=Cl,Br,I) one dimensional structures

NASA Astrophysics Data System (ADS)

Kuzubov, A. A.; Kovaleva, E. A.; Popova, M. I.; Kholtobina, A. S.; Mikhaleva, N. S.; Visotin, M. A.; Fedorov, A. S.

2017-10-01

Using DFT GGA calculations, electronic structure and magnetic properties of wide family of transition metal trihalides (TMHal3) (Zr, Ti and Nb iodides, Mo, Ru, Ti and Zr bromides and Ti or Zr chlorides) are investigated. These structures consist of transition metal atoms chains surrounded by halides atoms. Chains are connected to each other by weak interactions. All TMHal3 compounds were found to be conductive along chain axis except of MoBr3 which is indirect gap semiconductor. It was shown that NbI3 and MoBr3 have large magnetic moments on metal atoms (1.17 and 1.81 μB, respectively) but other TMHal3 materials have small or zero magnetic moments. For all structures ferromagnetic and anti-ferromagnetic phases have almost the same energies. The causes of these properties are debated.

sp3-hybridized framework structure of group-14 elements discovered by genetic algorithm

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

Nguyen, Manh Cuong; Zhao, Xin; Wang, Cai-Zhuang

2014-05-01

Group-14 elements, including C, Si, Ge, and Sn, can form various stable and metastable structures. Finding new metastable structures of group-14 elements with desirable physical properties for new technological applications has attracted a lot of interest. Using a genetic algorithm, we discovered a new low-energy metastable distorted sp3-hybridized framework structure of the group-14 elements. It has P42/mnm symmetry with 12 atoms per unit cell. The void volume of this structure is as large as 139.7Å3 for Si P42/mnm, and it can be used for gas or metal-atom encapsulation. Band-structure calculations show that P42/mnm structures of Si and Ge are semiconductingmore » with energy band gaps close to the optimal values for optoelectronic or photovoltaic applications. With metal-atom encapsulation, the P42/mnm structure would also be a candidate for rattling-mediated superconducting or used as thermoelectric materials.« less

First-principles calculation of the polarization-dependent force driving the Eg mode in bismuth under optical excitation.

NASA Astrophysics Data System (ADS)

Murray, Eamonn; Fahy, Stephen

2014-03-01

Using first principles electronic structure methods, we calculate the induced force on the Eg (zone centre transverse optical) phonon mode in bismuth immediately after absorption of polarized light. When radiation with polarization perpendicular to the c-axis is absorbed in bismuth, the distribution of excited electrons and holes breaks the three-fold rotational symmetry and leads to a net force on the atoms in the direction perpendicular to the axis. We calculate the initial excited electronic distribution as a function of photon energy and polarization and find the resulting transverse and longitudinal forces experienced by the atoms. Using the measured, temperature-dependent rate of decay of the transverse force[2], we predict the approximate amplitude of induced atomic motion in the Eg mode as a function of temperature and optical fluence. This work is supported by Science Foundation Ireland and a Marie Curie International Incoming Fellowship.

Multipolar electrostatics for proteins: atom-atom electrostatic energies in crambin.

PubMed

Yuan, Yongna; Mills, Matthew J L; Popelier, Paul L A

2014-02-15

Accurate electrostatics necessitates the use of multipole moments centered on nuclei or extra point charges centered away from the nuclei. Here, we follow the former alternative and investigate the convergence behavior of atom-atom electrostatic interactions in the pilot protein crambin. Amino acids are cut out from a Protein Data Bank structure of crambin, as single amino acids, di, or tripeptides, and are then capped with a peptide bond at each side. The atoms in the amino acids are defined through Quantum Chemical Topology (QCT) as finite volume electron density fragments. Atom-atom electrostatic energies are computed by means of a multipole expansion with regular spherical harmonics, up to a total interaction rank of L = ℓA+ ℓB + 1 = 10. The minimum internuclear distance in the convergent region of all the 15 possible types of atom-atom interactions in crambin that were calculated based on single amino acids are close to the values calculated from di and tripeptides. Values obtained at B3LYP/aug-cc-pVTZ and MP2/aug-cc-pVTZ levels are only slightly larger than those calculated at HF/6-31G(d,p) level. This convergence behavior is transferable to the well-known amyloid beta polypeptide Aβ1-42. Moreover, for a selected central atom, the influence of its neighbors on its multipole moments is investigated, and how far away this influence can be ignored is also determined. Finally, the convergence behavior of AMBER becomes closer to that of QCT with increasing internuclear distance. Copyright © 2013 Wiley Periodicals, Inc.

A comparative experimental and quantum chemical study on monomeric and dimeric structures of 3,5-dibromoanthranilic acid.

PubMed

Karabacak, Mehmet; Cinar, Mehmet

2012-10-01

This study presents the structural and spectroscopic characterization of 3,5-dibromoanthranilic acid with help of experimental techniques (FT-IR, FT-Raman, UV, NMR) and quantum chemical calculations. The vibrational spectra of title compound were recorded in solid state with FT-IR and FT-Raman in the range of 4000-400 and 4000-50 cm(-1), respectively. The vibrational frequencies were also computed using B3LYP method of DFT with 6-311++G(d,p) basis set. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The (1)H, (13)C and DEPT NMR spectra were recorded in DMSO solution and calculated by gauge-invariant atomic orbitals (GIAO) method. The UV absorption spectra of the compound were recorded in the range of 200-400 nm in ethanol, water and DMSO solutions. Solvent effects were calculated using time-dependent density functional theory and CIS method. The ground state geometrical structure of compound was predicted by B3LYP method and compared with the crystallographic structure of similar compounds. All calculations were made for monomeric and dimeric structure of compound. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken atomic charges of neutral and anionic form of the molecule were computed and compared with anthranilic acid. Copyright © 2012 Elsevier B.V. All rights reserved.

Electronic structure of graphene nanoribbons doped with nitrogen atoms: a theoretical insight.

PubMed

Torres, A E; Fomine, S

2015-04-28

The electronic structure of graphene nanoribbons doped with a graphitic type of nitrogen atoms has been studied using B3LYP, B2PLYP and CAS methods. In all but one case the restricted B3LYP solutions were unstable and the CAS calculations provided evidence for the multiconfigurational nature of the ground state with contributions from two dominant configurations. The relative stability of the doped nanoribbons depends mostly on the mutual position of the dopant atoms and notably less on the position of nitrogen atoms within the nanoribbon. N-graphitic doping affects cationic states much more than anionic ones due the participation of the nitrogen atoms in the stabilization of the positive charge, resulting in a drop in ionization energies (IPs) for N-graphitic doped systems. Nitrogen atoms do not participate in the negative charge stabilization of anionic species and, therefore, the doping does not affect the electron affinities (EAs). The unrestricted B3LYP method is the method of choice for the calculation of IPs and EAs. Restricted B3LYP and B2PLYP produces unreliable results for both IPs and EAs while CAS strongly underestimates the electron affinities. This is also true for the reorganization energies where restricted B3LYP produces qualitatively incorrect results. Doping changes the reorganization energy of the nanoribbons; the hole reorganization energy is generally higher than the corresponding electron reorganization energy due to the participation of nitrogen atoms in the stabilization of the positive charge.

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

PubMed

Shen, Lin; Yang, Weitao

2016-04-12

We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

Atomic kinetic energy, momentum distribution, and structure of solid neon at zero temperature

NASA Astrophysics Data System (ADS)

Cazorla, C.; Boronat, J.

2008-01-01

We report on the calculation of the ground-state atomic kinetic energy Ek and momentum distribution of solid Ne by means of the diffusion Monte Carlo method and Aziz HFD-B pair potential. This approach is shown to perform notably for this crystal since we obtain very good agreement with respect to experimental thermodynamic data. Additionally, we study the structural properties of solid Ne at densities near the equilibrium by estimating the radial pair-distribution function, Lindemann’s ratio, and atomic density profile around the positions of the perfect crystalline lattice. Our value for Ek at the equilibrium density is 41.51(6)K , which agrees perfectly with the recent prediction made by Timms , 41(2)K , based on their deep-inelastic neutron scattering experiments carried out over the temperature range 4-20K , and also with previous path integral Monte Carlo results obtained with the Lennard-Jones and Aziz HFD-C2 atomic pairwise interactions. The one-body density function of solid Ne is calculated accurately and found to fit perfectly, within statistical uncertainty, to a Gaussian curve. Furthermore, we analyze the degree of anharmonicity of solid Ne by calculating some of its microscopic ground-state properties within traditional harmonic approaches. We provide insightful comparison to solid He4 in terms of the Debye model in order to assess the relevance of anharmonic effects in Ne.

Thermodynamic properties of arsenic compounds and the heat of formation of the As atom from high level electronic structure calculations.

PubMed

Feller, David; Vasiliu, Monica; Grant, Daniel J; Dixon, David A

2011-12-29

Structures, vibrational frequencies, atomization energies at 0 K, and heats of formation at 0 and 298 K are predicted for the compounds As(2), AsH, AsH(2), AsH(3), AsF, AsF(2), and AsF(3) from frozen core coupled cluster theory calculations performed with large correlation consistent basis sets, up through augmented sextuple zeta quality. The coupled cluster calculations involved up through quadruple excitations. For As(2) and the hydrides, it was also possible to examine the impact of full configuration interaction on some of the properties. In addition, adjustments were incorporated to account for extrapolation to the frozen core complete basis set limit, core/valence correlation, scalar relativistic effects, the diagonal Born-Oppenheimer correction, and atomic spin orbit corrections. Based on our best theoretical D(0)(As(2)) and the experimental heat of formation of As(2), we propose a revised 0 K arsenic atomic heat of formation of 68.86 ± 0.8 kcal/mol. While generally good agreement was found between theory and experiment, the heat of formation of AsF(3) was an exception. Our best estimate is more than 7 kcal/mol more negative than the single available experimental value, which argues for a re-examination of that measurement. © 2011 American Chemical Society

Geometry at the aliphatic tertiary carbon atom: computational and experimental test of the Walsh rule.

PubMed

Böhm, Stanislav; Exner, Otto

2004-02-01

The geometrical parameters of molecules of 2-substituted 2-methylpropanes and 1-substituted bicyclo[2.2.2]octanes were calculated at the B3LYP/6-311+G(d,p) level. They agreed reasonably well with the mean crystallographic values retrieved from the Cambridge Structural Database for a set of diverse non-cyclic structures with a tertiary C atom. The angle deformations at this C atom produced by the immediately bonded substituent are also closely related to those observed previously in benzene mono derivatives (either as calculated or as derived from crystallographic data). The calculated geometrical parameters were used to test the classical Walsh rule: It is evidently true that an electron-attracting substituent increases the proportion of C-atom p-electrons in the bond to the substituent and leaves more s-electrons to the remaining bonds; as a consequence the C-C-C angles at a tertiary carbon are widened and the C-C bonds shortened. However, this rule describes only part of the reality since the bond angles and lengths are controlled by other factors as well, for instance by steric crowding. Another imperfection of the Walsh rule is that the sequence of substituents does not correspond to their electronegativities, as measured by any known scale; more probably it is connected with the inductive effect, but then only very roughly.

X-ray photoelectron spectrum and electronic properties of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4): LDA, GGA, and EV-GGA.

PubMed

Reshak, Ali Hussain; Khenata, R; Kityk, I V; Plucinski, K J; Auluck, S

2009-04-30

An all electron full potential linearized augmented plane wave method has been applied for a theoretical study of the band structure, density of states, and electron charge density of a noncentrosymmetric chalcopyrite compound HgGa(2)S(4) using three different approximations for the exchange correlation potential. Our calculations show that the valence band maximum (VBM) and conduction band minimum (CBM) are located at Gamma resulting in a direct energy gap of about 2.0, 2.2, and 2.8 eV for local density approximation (LDA), generalized gradient approximation (GGA), and Engel-Vosko (EVGGA) compared to the experimental value of 2.84 eV. We notice that EVGGA shows excellent agreement with the experimental data. This agreement is attributed to the fact that the Engel-Vosko GGA formalism optimizes the corresponding potential for band structure calculations. We make a detailed comparison of the density of states deduced from the X-ray photoelectron spectra with our calculations. We find that there is a strong covalent bond between the Hg and S atoms and Ga and S atoms. The Hg-Hg, Ga-Ga, and S-S bonds are found to be weaker than the Hg-S and Ga-S bonds showing that a covalent bond exists between Hg and S atoms and Ga and S atoms.

Geometric structure of anatase Ti O2(101 )

NASA Astrophysics Data System (ADS)

Treacy, Jon P. W.; Hussain, Hadeel; Torrelles, Xavier; Grinter, David C.; Cabailh, Gregory; Bikondoa, Oier; Nicklin, Christopher; Selcuk, Sencer; Selloni, Annabella; Lindsay, Robert; Thornton, Geoff

2017-02-01

Surface x-ray diffraction has been used to determine the quantitative structure of the (101) termination of anatase Ti O2 . The atomic displacements from the bulk-terminated structure are significantly different from those previously calculated with density functional theory (DFT) methods with discrepancies for the Ti displacements in the [10 1 ¯] direction of up to 0.3 Å . DFT calculations carried out as part of the current paper provide a much better agreement through improved accuracy and thicker slab models.

Electronic structure of ruthenium-doped iron chalcogenides

NASA Astrophysics Data System (ADS)

Winiarski, M. J.; Samsel-Czekała, M.; Ciechan, A.

2014-12-01

The structural and electronic properties of hypothetical RuxFe1-xSe and RuxFe1-xTe systems have been investigated from first principles within the density functional theory (DFT). Reasonable values of lattice parameters and chalcogen atomic positions in the tetragonal unit cell of iron chalcogenides have been obtained with the use of norm-conserving pseudopotentials. The well known discrepancies between experimental data and DFT-calculated results for structural parameters of iron chalcogenides are related to the semicore atomic states which were frozen in the used here approach. Such an approach yields valid results of the electronic structures of the investigated compounds. The Ru-based chalcogenides exhibit the same topology of the Fermi surface (FS) as that of FeSe, differing only in subtle FS nesting features. Our calculations predict that the ground states of RuSe and RuTe are nonmagnetic, whereas those of the solid solutions RuxFe1-xSe and RuxFe1-xTe become the single- and double-stripe antiferromagnetic, respectively. However, the calculated stabilization energy values are comparable for each system. The phase transitions between these magnetic arrangements may be induced by slight changes of the chalcogen atom positions and the lattice parameters a in the unit cell of iron selenides and tellurides. Since the superconductivity in iron chalcogenides is believed to be mediated by the spin fluctuations in single-stripe magnetic phase, the RuxFe1-xSe and RuxFe1-xTe systems are good candidates for new superconducting iron-based materials.

Atomic-scale recognition of surface structure and intercalation mechanism of Ti3C2X.

PubMed

Wang, Xuefeng; Shen, Xi; Gao, Yurui; Wang, Zhaoxiang; Yu, Richeng; Chen, Liquan

2015-02-25

MXenes represent a large family of functionalized two-dimensional (2D) transition-metal carbides and carbonitrides. However, most of the understanding on their unique structures and applications stops at the theoretical suggestion and lack of experimental support. Herein, the surface structure and intercalation chemistry of Ti3C2X are clarified at the atomic scale by aberration-corrected scanning transmission electron microscope (STEM) and density functional theory (DFT) calculations. The STEM studies show that the functional groups (e.g., OH(-), F(-), O(-)) and the intercalated sodium (Na) ions prefer to stay on the top sites of the centro-Ti atoms and the C atoms of the Ti3C2 monolayer, respectively. Double Na-atomic layers are found within the Ti3C2X interlayer upon extensive Na intercalation via two-phase transition and solid-solution reactions. In addition, aluminum (Al)-ion intercalation leads to horizontal sliding of the Ti3C2X monolayer. On the basis of these observations, the previous monolayer surface model of Ti3C2X is modified. DFT calculations using the new modeling help to understand more about their physical and chemical properties. These findings enrich the understanding of the MXenes and shed light on future material design and applications. Moreover, the Ti3C2X exhibits prominent rate performance and long-term cycling stability as an anode material for Na-ion batteries.

Inductive electronegativity scale. Iterative calculation of inductive partial charges.

PubMed

Cherkasov, Artem

2003-01-01

A number of novel QSAR descriptors have been introduced on the basis of the previously elaborated models for steric and inductive effects. The developed "inductive" parameters include absolute and effective electronegativity, atomic partial charges, and local and global chemical hardness and softness. Being based on traditional inductive and steric substituent constants these 3D descriptors provide a valuable insight into intramolecular steric and electronic interactions and can find broad application in structure-activity studies. Possible interpretation of physical meaning of the inductive descriptors has been suggested by considering a neutral molecule as an electrical capacitor formed by charged atomic spheres. This approximation relates inductive chemical softness and hardness of bound atom(s) with the total area of the facings of electrical capacitor formed by the atom(s) and the rest of the molecule. The derived full electronegativity equalization scheme allows iterative calculation of inductive partial charges on the basis of atomic electronegativities, covalent radii, and intramolecular distances. A range of inductive descriptors has been computed for a variety of organic compounds. The calculated inductive charges in the studied molecules have been validated by experimental C-1s Electron Core Binding Energies and molecular dipole moments. Several semiempirical chemical rules, such as equalized electronegativity's arithmetic mean, principle of maximum hardness, and principle of hardness borrowing could be explicitly illustrated in the framework of the developed approach.

The application of quasi-steady approximation in atomic kinetics in simulation of hohlraum radiation drive

NASA Astrophysics Data System (ADS)

Ren, Guoli; Pei, Wenbing; Lan, Ke; Li, Xin; Hohlraum Physics Team

2014-10-01

In current routine 2D simulation of hohlraum physics, we adopt the principal-quantum-number (n-level) average atom model (AAM) in NLTE plasma description. The more sophisticated atomic kinetics description is better choice, but the in-line calculation consumes much more resource. By distinguishing the much more fast bound-bound atomic processes from the relative slow bound-free atomic processes, we found a method to built up a bound electron distribution (n-level or nl-level) using in-line n-level calculated plasma condition (such as temperature, density, average ionization degree). We name this method ``quasi-steady approximation.'' Using this method and the plasma condition calculated under n-level, we re-build the nl-level bound electron distribution (Pnl), and acquire a new hohlraum radiative drive by post-processing. Comparison with the n-level post-processed hohlraum drive shows that we get an almost identical radiation flux but with more-detailed frequency-dependant structures. Also we use this method in the benchmark gold sphere experiment, the constructed nl-level radiation drive resembles the experimental results and DCA results, while the n-level raditation does not.

Phase stability and electronic structure of UMo2Al20: A first-principles study

NASA Astrophysics Data System (ADS)

Liu, Peng-Chuang; Xian, Ya-Jiang; Wang, Xin; Zhang, Yu-Ting; Zhang, Peng-Cheng

2017-09-01

In this paper, the phase stability of UMo2Al20 was explored using cluster formula in combination with first-principles calculations. Cluster formula analysis uncovered that the compound was composed of two principal clusters, i.e. [Mo-Al12] and [U-Al16]. The electronic interactions between U, Mo and Al atoms in this compound were discussed using elastic property, Bader charges and energy-resolved local bonding analysis, as well as the electronic interactions between Mo and Al atoms in [Mo-Al12] cluster and between U and Al atoms in [U-Al16] cluster. It revealed that UMo2Al20 satisfied the mechanical stability criterion for cubic system, and exhibited near ionic bonding character with weak bonding directionality. The calculations within both standard DFT and HSE frameworks demonstrated that U and Al atoms acted as an electron donor while Mo atoms acted as electron acceptor. The intrinsic stability of UMo2Al20 mainly stemmed from the bonding states of Mo-Al bonds and Al-Al bonds in [Mo-Al12] cluster. These calculations provide a further insight on the CeCr2Al20-type ternary compounds.

Linear-scaling implementation of molecular response theory in self-consistent field electronic-structure theory.

PubMed

Coriani, Sonia; Høst, Stinne; Jansík, Branislav; Thøgersen, Lea; Olsen, Jeppe; Jørgensen, Poul; Reine, Simen; Pawłowski, Filip; Helgaker, Trygve; Sałek, Paweł

2007-04-21

A linear-scaling implementation of Hartree-Fock and Kohn-Sham self-consistent field theories for the calculation of frequency-dependent molecular response properties and excitation energies is presented, based on a nonredundant exponential parametrization of the one-electron density matrix in the atomic-orbital basis, avoiding the use of canonical orbitals. The response equations are solved iteratively, by an atomic-orbital subspace method equivalent to that of molecular-orbital theory. Important features of the subspace method are the use of paired trial vectors (to preserve the algebraic structure of the response equations), a nondiagonal preconditioner (for rapid convergence), and the generation of good initial guesses (for robust solution). As a result, the performance of the iterative method is the same as in canonical molecular-orbital theory, with five to ten iterations needed for convergence. As in traditional direct Hartree-Fock and Kohn-Sham theories, the calculations are dominated by the construction of the effective Fock/Kohn-Sham matrix, once in each iteration. Linear complexity is achieved by using sparse-matrix algebra, as illustrated in calculations of excitation energies and frequency-dependent polarizabilities of polyalanine peptides containing up to 1400 atoms.

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.

Impact of Coulomb potential on peak structures arising in momentum and low-energy photoelectron spectra produced in strong-field ionization of laser-irradiated atoms

NASA Astrophysics Data System (ADS)

Pyak, P. E.; Usachenko, V. I.

2018-03-01

The phenomenon of pronounced peak structure(s) of longitudinal momentum distributions as well as a spike-like structure of low-energy spectra of photoelectrons emitted from laser-irradiated Ar and Ne atoms in a single ionization process is theoretically studied in the tunneling and multiphoton regimes of ionization. The problem is addressed assuming only the direct above-threshold ionization (ATI) as a physical mechanism underlying the phenomenon under consideration (viz. solely contributing to observed photoelectron momentum distributions (PMD)) and using the Coulomb-Volkov (CV) ansatz within the frame of conventional strong-field approximation (SFA) applied in the length-gauge formulation. The developed CV-SFA approach also incorporates the density functional theory essentially exploited for numerical composition of initial (laser-free) atomic state(s) constructed from atomic orbitals of Gaussian type. Our presented CV-SFA based (and laser focal-volume averaged) calculation results proved to be well reproducing both the pronounced double-peak and/or ATI-like multi-peak structure(s) experimentally observed in longitudinal PMD under conditions of tunneling and/or multiphoton regime, respectively. In addition, our CV-SFA results presented for tunneling regime also suggest and remarkably reproduce a pronounced structure observed in relevant experiments as a ‘spike-like’ enhanced maximum arising in low-energy region (around the value of about 1 eV) of photoelectron spectra. The latter consistency allows to identify and interpret these results as the so-called low-energy structure (LES) since the phenomenon proved to appear as the most prominent if the influence of Coulomb potential on photoelectron continuum states is maximally taken into account under calculations (viz. if the parameter Z in CV’s functions is put equal to 1). Moreover, the calculated LES proved to correspond (viz., established as closely related) to the mentioned double-peak structure arising in the low-momentum region ({p}| | ≤slant | 0.2| a.u.) of longitudinal PMDs calculated under condition of the tunneling regime. Thus, the phenomena under consideration can be well understood and adequately interpreted beyond the terms and/or concepts of various different alternative strong-field approaches and models (such as e.g., extensively invoked and exploited nowadays though, more sophisticated SFA-based ‘rescattering’ mechanism) compared to which, the currently applied CV-SFA model (through the same underlying physical mechanism of solely direct ATI suggested) is additionally able to provide and reveal an intimate and transparent interrelation between the phenomena of LES and double-peak structure arising in PMDs observed in the tunneling regime.

DFT study of structural and electronic properties of MoS2(1-x)Se2x alloy (x = 0.25)

NASA Astrophysics Data System (ADS)

Gusakova, Julia; Gusakov, Vasilii; Tay, Beng Kang

2018-04-01

First-principles calculations have been performed to study the structural features of the monolayer MoS2(1-x)Se2x (x = 0.25) alloy and its electronic properties. We studied the effects of the relative positions of Se atoms in a real monolayer alloy. It was demonstrated that the distribution of the Se atoms between the top and bottom chalcogen planes was most energetically favorable. For a more probable distribution of Se atoms, a MoS2(1-x)Se2x (x = 0.25) monolayer alloy is a direct semiconductor with a fundamental band gap equal to 2.35 eV (calculated with the GVJ-2e method). We also evaluated the optical band gap of the alloy at 77 K (1.86 eV) and at room temperature (1.80 eV), which was in good agreement with the experimentally measured band gap of 1.79 eV.

Ab initio calculations of the concentration dependent band gap reduction in dilute nitrides

NASA Astrophysics Data System (ADS)

Rosenow, Phil; Bannow, Lars C.; Fischer, Eric W.; Stolz, Wolfgang; Volz, Kerstin; Koch, Stephan W.; Tonner, Ralf

2018-02-01

While being of persistent interest for the integration of lattice-matched laser devices with silicon circuits, the electronic structure of dilute nitride III/V-semiconductors has presented a challenge to ab initio computational approaches. The origin of the computational problems is the strong distortion exerted by the N atoms on most host materials. Here, these issues are resolved by combining density functional theory calculations based on the meta-GGA functional presented by Tran and Blaha (TB09) with a supercell approach for the dilute nitride Ga(NAs). Exploring the requirements posed to supercells, it is shown that the distortion field of a single N atom must be allowed to decrease so far that it does not overlap with its periodic images. This also prevents spurious electronic interactions between translational symmetric atoms, allowing us to compute band gaps in very good agreement with experimentally derived reference values. In addition to existing approaches, these results offer a promising ab initio avenue to the electronic structure of dilute nitride semiconductor compounds.

Impact of stoichiometry and disorder on the electronic structure of the PbBi2Te4 -xSex topological insulator

NASA Astrophysics Data System (ADS)

Shvets, I. A.; Klimovskikh, I. I.; Aliev, Z. S.; Babanly, M. B.; Sánchez-Barriga, J.; Krivenkov, M.; Shikin, A. M.; Chulkov, E. V.

2017-12-01

Detailed comparative theoretical and experimental study of electronic properties and spin structure was carried out for a series of Pb-based quaternary compounds PbBi2Te4 -xSex . For all values of x , these compounds are theoretically predicted to be topological insulators, possessing at high Se content a remarkably large band gap and a Dirac point isolated from bulk states. Using spin- and angle-resolved photoemission spectroscopy, it was shown that the PbBi2Te2Se2 and PbBi2Te1.4Se2.6 compounds are characterized by well-defined spin-polarized topological surface state in the bulk gap. To define the probable distribution of atoms over the atomic sites for these samples, we performed ab initio calculations in ordered and disordered configurations of the unit cell. We found that theoretical calculations better reproduce photoemission data when Te atoms are placed in the outermost layers of the septuple layer block.

Achieving atomic resolution magnetic dichroism by controlling the phase symmetry of an electron probe

DOE PAGES

Rusz, Jan; Idrobo, Juan -Carlos; Bhowmick, Somnath

2014-09-30

The calculations presented here reveal that an electron probe carrying orbital angular momentum is just a particular case of a wider class of electron beams that can be used to measure electron magnetic circular dichroism (EMCD) with atomic resolution. It is possible to obtain an EMCD signal with atomic resolution by simply breaking the symmetry of the electron probe phase front using the aberration-corrected optics of a scanning transmission electron microscope. The probe’s required phase distribution depends on the sample’s magnetic symmetry and crystal structure. The calculations indicate that EMCD signals that use the electron probe’s phase are as strongmore » as those obtained by nanodiffraction methods.« less

MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling.

PubMed

Song, Yifan; Mao, Junjun; Gunner, M R

2009-11-15

Multiconformation continuum electrostatics (MCCE) explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand pK(a)s. Explicit changes in side chain conformations throughout a titration create a position dependent, heterogeneous dielectric response giving a more accurate picture of coupled ionization and position changes. The MCCE2 methods for choosing a group of input heavy atom and proton positions are described. The pK(a)s calculated with different isosteric conformers, heavy atom rotamers and proton positions, with different degrees of optimization are tested against a curated group of 305 experimental pK(a)s in 33 proteins. QUICK calculations, with rotation around Asn and Gln termini, sampling His tautomers and torsion minimum hydroxyls yield an RMSD of 1.34 with 84% of the errors being <1.5 pH units. FULL calculations adding heavy atom rotamers and side chain optimization yield an RMSD of 0.90 with 90% of the errors <1.5 pH unit. Good results are also found for pK(a)s in the membrane protein bacteriorhodopsin. The inclusion of extra side chain positions distorts the dielectric boundary and also biases the calculated pK(a)s by creating more neutral than ionized conformers. Methods for correcting these errors are introduced. Calculations are compared with multiple X-ray and NMR derived structures in 36 soluble proteins. Calculations with X-ray structures give significantly better pK(a)s. Results with the default protein dielectric constant of 4 are as good as those using a value of 8. The MCCE2 program can be downloaded from http://www.sci.ccny.cuny.edu/~mcce. 2009 Wiley Periodicals, Inc.

FT-IR, FT-Raman, UV-visible, and NMR spectroscopy and vibrational properties of the labdane-type diterpene 13-epi-sclareol.

PubMed

Chain, Fernando E; Leyton, Patricio; Paipa, Carolina; Fortuna, Mario; Brandán, Silvia A

2015-03-05

In this work, FT-IR, FT-Raman, UV-Visible and NMR spectroscopies and density functional theory (DFT) calculations were employed to study the structural and vibrational properties of the labdane-type diterpene 13-epi-sclareol using the hybrid B3LYP method together with the 6-31G(∗) basis set. Three stable structures with minimum energy found on the potential energy curves (PES) were optimized, and the corresponding molecular electrostatic potentials, atomic charges, bond orders, stabilization energies and topological properties were computed at the same approximation level. The complete assignment of the bands observed in the vibrational spectrum of 13-epi-sclareol was performed taking into account the internal symmetry coordinates for the three structures using the scaled quantum mechanical force field (SQMFF) methodology at the same level of theory. In addition, the force constants were calculated and compared with those reported in the literature for similar compounds. The predicted vibrational spectrum and the calculated (1)H NMR and (13)C NMR chemical shifts are in good agreement with the corresponding experimental results. The theoretical UV-Vis spectra for the most stable structure of 13-epi-sclareol demonstrate a better correlation with the corresponding experimental spectrum. The study of the three conformers by means of the theory of atoms in molecules (AIM) revealed different H bond interactions and a strong dependence of the interactions on the distance between the involved atoms. Furthermore, the natural bond orbital (NBO) calculations showed the characteristics of the electronic delocalization for the two six-membered rings with chair conformations. Copyright © 2014 Elsevier B.V. All rights reserved.

Anion Exchange in II-VI Semiconducting Nanostructures via Atomic Templating.

PubMed

Agarwal, Rahul; Krook, Nadia M; Ren, Ming-Liang; Tan, Liang Z; Liu, Wenjing; Rappe, Andrew M; Agarwal, Ritesh

2018-03-14

Controlled chemical transformation of nanostructures is a promising technique to obtain precisely designed novel materials, which are difficult to synthesize otherwise. We report high-temperature vapor-phase anion-exchange reactions to chemically transform II-VI semiconductor nanostructures (100-300 nm length scale) while retaining the single crystallinity, crystal structure, morphology, and even defect distribution of the parent material via atomic templating. The concept of atomic templating is employed to obtain kinetically controlled, thermodynamically metastable structural phases such as zincblende CdSe and CdS from zincblende CdTe upon complete chemical replacement of Te with Se or S. The underlying transformation mechanisms are explained through first-principles density functional theory calculations. Atomic templating is a unique path to independently tune materials' phase and composition at the nanoscale, allowing the synthesis of novel materials.

Atomic Scale Structure of (001) Hydrogen-Induced Platelets in Germanium

NASA Astrophysics Data System (ADS)

David, Marie-Laure; Pizzagalli, Laurent; Pailloux, Fréderic; Barbot, Jean François

2009-04-01

An accurate characterization of the structure of hydrogen-induced platelets is a prerequisite for investigating both hydrogen aggregation and formation of larger defects. On the basis of quantitative high resolution transmission electron microscopy experiments combined with extensive first principles calculations, we present a model for the atomic structure of (001) hydrogen-induced platelets in germanium. It involves broken Ge-Ge bonds in the [001] direction that are dihydride passivated, vacancies, and trapped H2 molecules, showing that the species involved in platelet formation depend on the habit plane. This model explains all previous experimental observations.

Structural paradox in submonolayer chlorine coverage on Au(111)

NASA Astrophysics Data System (ADS)

Zheltov, V. V.; Cherkez, V. V.; Andryushechkin, B. V.; Zhidomirov, G. M.; Kierren, B.; Fagot-Revurat, Y.; Malterre, D.; Eltsov, K. N.

2014-05-01

In this work, we present a combined low-temperature scanning tunneling microscopy (STM) and density functional theory (DFT) study of chlorine adsorption on Au(111) at low coverages. Our STM study of Cl/Au(111) system has shown that at submonolayer coverages (θ < 0.1 ML) chlorine atoms form chainlike structures with abnormally short distances of 3.8 Å between them. Our DFT calculations have shown that chlorine atoms can interact with each other through distortion of the substrate and this indirect elastic interaction is strong enough to affect their arrangement in the chainlike structures.

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs

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

Mannix, A. J.; Zhou, X. -F.; Kiraly, B.

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal.

Nature of adsorption on TiC(111) investigated with density-functional calculations

NASA Astrophysics Data System (ADS)

Ruberto, Carlo; Lundqvist, Bengt I.

2007-06-01

Extensive density-functional calculations are performed for chemisorption of atoms in the three first periods (H, B, C, N, O, F, Al, Si, P, S, and Cl) on the polar TiC(111) surface. Calculations are also performed for O on TiC(001), for full O(1×1) monolayer on TiC(111), as well as for bulk TiC and for the clean TiC(111) and (001) surfaces. Detailed results concerning atomic structures, energetics, and electronic structures are presented. For the bulk and the clean surfaces, previous results are confirmed. In addition, detailed results are given on the presence of C-C bonds in the bulk and at the surface, as well as on the presence of a Ti-based surface resonance (TiSR) at the Fermi level and of C-based surface resonances (CSR’s) in the lower part of the surface upper valence band. For the adsorption, adsorption energies Eads and relaxed geometries are presented, showing great variations characterized by pyramid-shaped Eads trends within each period. An extraordinarily strong chemisorption is found for the O atom, 8.8eV /adatom. On the basis of the calculated electronic structures, a concerted-coupling model for the chemisorption is proposed, in which two different types of adatom-substrate interactions work together to provide the obtained strong chemisorption: (i) adatom-TiSR and (ii) adatom-CSR’s. This model is used to successfully describe the essential features of the calculated Eads trends. The fundamental nature of this model, based on the Newns-Anderson model, should make it apt for general application to transition-metal carbides and nitrides and for predictive purposes in technological applications, such as cutting-tool multilayer coatings and MAX phases.

Atomically-thick two-dimensional crystals: electronic structure regulation and energy device construction.

PubMed

Sun, Yongfu; Gao, Shan; Xie, Yi

2014-01-21

Atomically-thick two-dimensional crystals can provide promising opportunities to satisfy people's requirement of next-generation flexible and transparent nanodevices. However, the characterization of these low-dimensional structures and the understanding of their clear structure-property relationship encounter many great difficulties, owing to the lack of long-range order in the third dimensionality. In this review, we survey the recent progress in fine structure characterization by X-ray absorption fine structure spectroscopy and also overview electronic structure modulation by density-functional calculations in the ultrathin two-dimensional crystals. In addition, we highlight their structure-property relationship, transparent and flexible device construction as well as wide applications in photoelectrochemical water splitting, photodetectors, thermoelectric conversion, touchless moisture sensing, supercapacitors and lithium ion batteries. Finally, we outline the major challenges and opportunities that face the atomically-thick two-dimensional crystals. It is anticipated that the present review will deepen people's understanding of this field and hence contribute to guide the future design of high-efficiency energy-related devices.

SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

PubMed

Vaguine, A A; Richelle, J; Wodak, S J

1999-01-01

In this paper we present SFCHECK, a stand-alone software package that features a unified set of procedures for evaluating the structure-factor data obtained from X-ray diffraction experiments and for assessing the agreement of the atomic coordinates with these data. The evaluation is performed completely automatically, and produces a concise PostScript pictorial output similar to that of PROCHECK [Laskowski, MacArthur, Moss & Thornton (1993). J. Appl. Cryst. 26, 283-291], greatly facilitating visual inspection of the results. The required inputs are the structure-factor amplitudes and the atomic coordinates. Having those, the program summarizes relevant information on the deposited structure factors and evaluates their quality using criteria such as data completeness, structure-factor uncertainty and the optical resolution computed from the Patterson origin peak. The dependence of various parameters on the nominal resolution (d spacing) is also given. To evaluate the global agreement of the atomic model with the experimental data, the program recomputes the R factor, the correlation coefficient between observed and calculated structure-factor amplitudes and Rfree (when appropriate). In addition, it gives several estimates of the average error in the atomic coordinates. The local agreement between the model and the electron-density map is evaluated on a per-residue basis, considering separately the macromolecule backbone and side-chain atoms, as well as solvent atoms and heterogroups. Among the criteria are the normalized average atomic displacement, the local density correlation coefficient and the polymer chain connectivity. The possibility of computing these criteria using the omit-map procedure is also provided. The described software should be a valuable tool in monitoring the refinement procedure and in assessing structures deposited in databases.

Electronic and crystal structure of NiTi martensite

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

Sanati, M.; Albers, R.C.; Pinski, F.J.

1998-11-01

All of the first-principles electronic-structure calculations for the martensitic structure of NiTi have used the experimental atomic parameters reported by Michal and Sinclair [Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. {bold B37}, 1803 (1981)]. We have used first-principles, full-potential, linear muffin-tin orbital calculations to examine the total energy of all the experimental martensitic structures reported in the literature. We find that another crystal structure, that of Kudoh {ital et al.} [Acta Metall. Mater. {bold 33}, 2049 (1985)], has the lowest total energy at zero temperature. Ground-state and formation energies were calculated for all of the experimental structures. Total andmore » local densities of states were calculated and compared with each other for the structures of both Kudoh {ital et al.} and Michal and Sinclair thinsp {copyright} {ital 1998} {ital The American Physical Society}« less

Structural evolution study of 1-2 nm gold clusters

NASA Astrophysics Data System (ADS)

Beltrán, M. R.; Suárez Raspopov, R.; González, G.

2011-12-01

We have explored lowest energy minima structures of gold atom clusters both, charged and neutral (Aun^{ν}νn with n = 20, 28, 34, 38, 55, 75, 101, 146, 147, 192, 212 atoms and ν = 0, ±1). The structures have been obtained from first principles generalized gradient approximation, density functional theory (DFT) calculations based on norm-conserving pseudopotentials and numerical atomic basis sets. We have found two new disordered or defective isomers lower in energy than their ordered counterparts for n = 101, 147. The purpose of this work is to systematically study the difference between the electronic properties of the two lowest ordered and disordered isomers for each size. Our results agree with previous first principle calculations and with some recent experimental results (Au20 and Au101). For each case we report total energies, binding energies, ionization potentials, electron affinities, density of states, highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps, Housdorff chirality measure index and their simulated image in a high resolution transmission electron microscopy (HRTEM). The calculated properties of the two low lying (ordered and disordered) isomers show clear differences as to be singled out in a suitable experimental setting. An extensive discussion on the evolution with size of the cohesive energy, the ionization potentials, the electron affinities, the HOMO-LUMO gaps and their index of chirality to determine the crossover between them is given.

First-principles study of uranium carbide: Accommodation of point defects and of helium, xenon, and oxygen impurities

NASA Astrophysics Data System (ADS)

Freyss, Michel

2010-01-01

Point defects and volatile impurities (helium, xenon, oxygen) in uranium monocarbide UC are studied by first-principles calculations. Preliminarily, bulk properties of UC and of two other uranium carbide phases, UC2 and U2C3 , are calculated in order to compare them to experimental data and to get confidence in the use of the generalized gradient approximation for this class of compounds. The subsequent study of different types of point defects shows that the carbon sublattice best accommodates the defects. The perturbation of the crystal structure induced by the defects is weak and the interaction between defects is found short range. Interstitial carbon dumbbells possibly play an important role in the diffusion of carbon atoms. The most favorable location of diluted helium, xenon, and oxygen impurities in the UC crystal lattice is then determined. The rare-gas atoms occupy preferably a uranium substitution site or a uranium site in a U-C bivacancy. But their incorporation in UC is, however, not energetically favorable, especially for xenon, suggesting their propensity to diffuse in the material and/or form bubbles. On the other hand, oxygen atoms are very favorably incorporated as diluted atoms in the UC lattice, confirming the easy oxidation of UC. The oxygen atoms preferably occupy a carbon substitution site or the carbon site of a U-C bivacancy. Our results are compared to available experimental data on UC and to similar studies by first-principles calculations for other carbides and nitrides with the rock-salt structure.

Short and medium range structures of 80GeSe2–20Ga2Se3 chalcogenide glasses

NASA Astrophysics Data System (ADS)

Petracovschi, Elena; Calvez, Laurent; Cormier, Laurent; Le Coq, David; Du, Jincheng

2018-05-01

The short and medium range structures of 80GeSe2–20Ga2Se3 (or Ge23.5Ga11.8Se64.7) chalcogenide glasses have been studied by combining ab initio molecular dynamics (AIMD) simulations and experimental neutron diffraction studies. The structure factor and total correlation function were calculated from glass structures generated from AIMD simulations and compared with neutron diffraction experiments showing reasonable agreement. The atomic structures of ternary chalcogenide glasses were analyzed in detail, and it was found that gallium atoms are four-fold coordinated by selenium (Se) and form [GaSe4] tetrahedra. Germanium atoms on average also have four-fold coordination, among which Se is 3.5 with the remaining being Ge–Ge homo-nuclear bonds. Ga and Ge tetrahedra link together mainly through corner-sharing and some edge-sharing of Se. No homo-nuclear bonds were observed among Ga atoms or between Ge and Ga. In addition, Se–Se homo-nuclear bonds and Se chains with various lengths were observed. A small fraction of Se atom triclusters that bond to three cations of Ge and Ga were also observed, confirming earlier proposals from 77Se solid state nuclear magnetic resonance studies. Furthermore, the electronic structures of ternary chalcogenide glasses were studied in terms of atomic charge and electronic density of states in order to gain insights into the chemical bonding and electronic properties, as well as to provide an explanation of the observed atomic structures in these ternary chalcogenide glasses.

Intermetallic structures with atomic precision for selective hydrogenation of nitroarenes

DOE PAGES

Pei, Yuchen; Qi, Zhiyuan; Goh, Tian Wei; ...

2017-11-14

It is essential to bridge the structure-properties relationship of bimetallic catalysts for the rational design of heterogeneous catalysts. Different from random alloys, intermetallic compounds (IMCs) present atomically-ordered structures, which is advantageous for catalytic mechanism studies. Here, we used Pt-based intermetallic nanoparticles (iNPs), individually encapsulated in mesoporous silica shells, as catalysts for the hydrogenation of nitroarenes to functionalized anilines. With the capping-free nature and ordered atomic structure, PtSn iNPs show >99% selectivity to hydrogenate the nitro group of 3-nitrostyrene albeit with a lower activity, in contrast to Pt 3Sn iNPs and Pt NPs. The geometric structure of PtSn iNPs in eliminatingmore » Pt threefold sites hampers the adsorption/dissociation of molecular H 2 and leads to a non-Horiuti-Polanyi hydrogenation pathway, while Pt 3Sn and Pt surfaces are saturated by atomic H. Calculations using density functional theory (DFT) suggest a preferential adsorption of the nitro group on the intermetallic PtSn surface contributing to its high selectivity.« less

Conformational structures of a decapeptide validated by first principles calculations and cold ion spectroscopy.

PubMed

Roy, Tapta Kanchan; Kopysov, Vladimir; Nagornova, Natalia S; Rizzo, Thomas R; Boyarkin, Oleg V; Gerber, R Benny

2015-05-18

Calculated structures of the two most stable conformers of a protonated decapeptide gramicidin S in the gas phase have been validated by comparing the vibrational spectra, calculated from first- principles and measured in a wide spectral range using infrared (IR)-UV double resonance cold ion spectroscopy. All the 522 vibrational modes of each conformer were calculated quantum mechanically and compared with the experiment without any recourse to an empirical scaling. The study demonstrates that first-principles calculations, when accounting for vibrational anharmonicity, can reproduce high-resolution experimental spectra well enough for validating structures of molecules as large as of 200 atoms. The validated accurate structures of the peptide may serve as templates for in silico drug design and absolute calibration of ion mobility measurements. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Incorporating isolated molybdenum (Mo) atoms into Bilayer Epitaxial Graphene on 4H-SiC(0001)

NASA Astrophysics Data System (ADS)

Huang, Han; Wan, Wen; Li, Hui; Wong, Swee Liang; Lv, Lu; Gao, Yongli; Wee, Andrew T. S.

2014-03-01

The atomic structures and electronic properties of isolated Mo atoms in bilayer epitaxial graphene (BLEG) on 4H-SiC(0001) are investigated by low temperature scanning tunneling microscopy (LT-STM). LT-STM results reveal that isolated Mo dopants prefer to substitute C atoms at α-sites, and preferentially locate between the graphene bilayers. First-principles calculations confirm that the embedding of single Mo dopants within BLEG is energetically favorable as compared to monolayer graphene. The calculated bandstructures show that Mo-doped BLEG is n-doped, and each Mo atom introduces a local magnetic moment of 1.81 μB. Our findings demonstrate a simple and stable method to incorporate single transition metal dopants into the graphene lattice to tune its electronic and magnetic properties for possible use in graphene spin devices. NRF-CRP (Singapore) grants R-143-000-360-281and R-144-000-295-281. ``Shenghua Professorship'' startup funding from CSU and the support from the NSF of China (Grant No.11304398).

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors

PubMed Central

Thorwart, Michael

2018-01-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing. PMID:29756034

Toward tailoring Majorana bound states in artificially constructed magnetic atom chains on elemental superconductors.

PubMed

Kim, Howon; Palacio-Morales, Alexandra; Posske, Thore; Rózsa, Levente; Palotás, Krisztián; Szunyogh, László; Thorwart, Michael; Wiesendanger, Roland

2018-05-01

Realizing Majorana bound states (MBS) in condensed matter systems is a key challenge on the way toward topological quantum computing. As a promising platform, one-dimensional magnetic chains on conventional superconductors were theoretically predicted to host MBS at the chain ends. We demonstrate a novel approach to design of model-type atomic-scale systems for studying MBS using single-atom manipulation techniques. Our artificially constructed atomic Fe chains on a Re surface exhibit spin spiral states and a remarkable enhancement of the local density of states at zero energy being strongly localized at the chain ends. Moreover, the zero-energy modes at the chain ends are shown to emerge and become stabilized with increasing chain length. Tight-binding model calculations based on parameters obtained from ab initio calculations corroborate that the system resides in the topological phase. Our work opens new pathways to design MBS in atomic-scale hybrid structures as a basis for fault-tolerant topological quantum computing.

Atomicrex—a general purpose tool for the construction of atomic interaction models

NASA Astrophysics Data System (ADS)

Stukowski, Alexander; Fransson, Erik; Mock, Markus; Erhart, Paul

2017-07-01

We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands of atoms or more, because electronic structure methods become computationally too expensive at this scale. atomicrex covers a wide range of interatomic potential types and fulfills many needs in atomistic model development. As inputs, it supports experimental property values as well as ab initio energies and forces, to which models can be fitted using various optimization algorithms. The open architecture of atomicrex allows it to be used in custom model development scenarios beyond classical interatomic potentials while thanks to its Python interface it can be readily integrated e.g., with electronic structure calculations or machine learning algorithms.

Experimental validation of calculated atomic charges in ionic liquids

NASA Astrophysics Data System (ADS)

Fogarty, Richard M.; Matthews, Richard P.; Ashworth, Claire R.; Brandt-Talbot, Agnieszka; Palgrave, Robert G.; Bourne, Richard A.; Vander Hoogerstraete, Tom; Hunt, Patricia A.; Lovelock, Kevin R. J.

2018-05-01

A combination of X-ray photoelectron spectroscopy and near edge X-ray absorption fine structure spectroscopy has been used to provide an experimental measure of nitrogen atomic charges in nine ionic liquids (ILs). These experimental results are used to validate charges calculated with three computational methods: charges from electrostatic potentials using a grid-based method (ChelpG), natural bond orbital population analysis, and the atoms in molecules approach. By combining these results with those from a previous study on sulfur, we find that ChelpG charges provide the best description of the charge distribution in ILs. However, we find that ChelpG charges can lead to significant conformational dependence and therefore advise that small differences in ChelpG charges (<0.3 e) should be interpreted with care. We use these validated charges to provide physical insight into nitrogen atomic charges for the ILs probed.

On the Functionality of Complex Intermetallics: Frustration, Chemical Pressure Relief, and Potential Rattling Atoms in Y11Ni60C6.

PubMed

Guo, Yiming; Fredrickson, Daniel C

2016-10-17

Intermetallic carbides provide excellent model systems for exploring how frustration can shape the structures and properties of inorganic materials. Combinations of several metals with carbon can be designed in which the formation of tetrahedrally close-packed (TCP) intermetallics conflicts with the C atoms' requirement of trigonal prismatic or octahedral coordination environments, as offered by the simple close-packings (SCP) of equally sized spheres. In this Article, we explore the driving forces that lead to the coexistence of these incompatible arrangements in the Yb 11 Ni 60 C 6 -type compound Y 11 Ni 60 C 6 (cI154), as well as potential consequences of this intergrowth for the phase's physical properties. Our focus begins on the structure's SCP regions, which appear as C-stuffed versions of a AuCu 3 -type YNi 3 phase that is not observed on its own in the Y-Ni system. DFT-Chemical Pressure (DFT-CP) calculations on this hypothetical YNi 3 phase reveal large negative pressures within the Ni sublattice, as it is stretched to accommodate the size requirements of the Y atoms. In the Y 11 Ni 60 C 6 structure, two structural mechanisms for addressing these CP issues appear: the incorporation of interstitial C atoms, and the presence of interfaces with CaCu 5 -type domains. The relative roles of these two mechanisms are investigated with the CP analysis on a hypothetical YNi 3 C x series of C-stuffed AuCu 3 -type phases, the Y-Ni sublattice of Y 11 Ni 60 C 6 , and finally the full Y 11 Ni 60 C 6 structure. Through these calculations, the C atoms appear to play the roles of relieving positive Y CPs and supporting relaxation at the AuCu 3 -type/CaCu 5 -type interfaces, where the cancellation occurs between opposite CPs experienced by the Y atoms in the two parent structures (following the epitaxial stabilization mechanism). The CP analysis of Y 11 Ni 60 C 6 also highlights a sublattice of Y and Ni atoms with large negative CPs (and thus the potential for soft vibrational modes), illustrating how frustrated structures could lead to the full realization of the phonon glass-electron crystal concept.

Hyperfine structure parametrisation in Maple

NASA Astrophysics Data System (ADS)

Gaigalas, G.; Scharf, O.; Fritzsche, S.

2006-02-01

In hyperfine structure examinations, routine high resolution spectroscopy methods have to be combined with exact fine structure calculations. The so-called magnetic A and electric B factor of the fine structure levels allow to check for a correct fine structure analysis, to find errors in the level designation, to find new levels and to probe the electron wavefunctions and its mixing coefficients. This is done by parametrisation of these factors into different contributions of the subshell electrons, which are split further into their radial and spin-angular part. Due to the routine with which hyperfine structure measurements are done, a tool for keeping the necessary information together, performing checks online with the experiment and deriving standard quantities is of great help. MAPLE [Maple is a registered trademark of Waterloo Maple Inc.] is a highly-developed symbolic programming language, often referred to as the pocket calculator of the future. Packages for theoretical atomic calculation exist ( RACAH and JUCYS) and the language meets all the requirements to keep and present information accessible for the user in a fast and practical way. We slightly extended the RACAH package [S. Fritzsche, Comput. Phys. Comm. 103 (1997) 51] and set up an environment for experimental hyperfine structure calculations, the HFS package. Supplying the fine structure and nuclear data, one is in the position to obtain information about the hyperfine spectrum, the different contributions to the splitting and to perform a least square fit of the radial parameters based on the semiempirical method. Experimentalist as well as theoretical physicist can do a complete hyperfine structure analysis using MAPLE. Program summaryTitle of program: H FS Catalogue number: ADXD Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXD Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: none Computers for which the program is designed: All computers with a license of the computer algebra package MAPLE Installations: University of Kassel (Germany) Operating systems under which the program has been tested: Linux 9.0 Program language used:MAPLE, Release 7, 8 and 9 Memory required to execute with typical data: 5 MB No. of lines in distributed program, including test data, etc.: 34 300 No. of bytes in distributed program, including test data, etc.: 954 196 Distribution format: tar.gz Nature of the physical problem: Atomic state functions of an many configuration many electron atom with several open shells are defined by a number of quantum numbers, by their coupling and selection rules such as the Pauli exclusion principal or parity conservation. The matrix elements of any one-particle operator acting on these wavefunctions can be analytically integrated up to the radial part [G. Gaigalas, O. Scharf, S. Fritzsche, Central European J. Phys. 2 (2004) 720]. The decoupling of the interacting electrons is general, the obtained submatrix element holds all the peculiarities of the operator in question. These so-called submatrix elements are the key to do hyperfine structure calculations. The interaction between the electrons and the atomic nucleus leads to an additional splitting of the fine structure lines, the hyperfine structure. The leading components are the magnetic dipole interaction defining the so-called A factor and the electric quadrupole interaction, defining the so-called B factor. They express the energetic splitting of the spectral lines. Moreover, they are obtained directly by experiments and can be calculated theoretically in an ab initio approach. A semiempirical approach allows the fitting of the radial parts of the wavefunction to the experimentally obtained A and B factors. Method of solution: Extending the existing csf_LS() and asf_LS() to several open shells and implementing a data structure level_LS() for the fine structure level, the atomic environment is defined in MAPLE. It is used in a general approach to decouple the interacting shells for any one-particle operator. Further submatrix elements for the magnetic dipole and electric quadrupole interaction are implemented, allowing to calculate the A and B factors up to the radial part. Several procedures for standard quantities of the hyperfine structure are defined, too. The calculations are accelerated by using a hyper-geometric approach for three, six and nine symbols. Restrictions onto the complexity of the problem: Only atomic state functions in nonrelativistic LS-coupling with states having l⩽3 are supported. Typical running time: The program replies promptly on most requests. The least square fit depends heavily on the number of levels and can take a few minutes.

Atoms and Molecules Interacting with Light

NASA Astrophysics Data System (ADS)

van der Straten, Peter; Metcalf, Harold

2016-02-01

Part I. Atom-Light Interaction: 1. The classical physics pathway; Appendix 1.A. Damping force on an accelerating charge; Appendix 1.B. Hanle effect; Appendix 1.C. Optical tweezers; 2. Interaction of two-level atoms and light; Appendix 2.A. Pauli matrices for motion of the bloch vector; Appendix 2.B. The Ramsey method; Appendix 2.C. Echoes and interferometry; Appendix 2.D. Adiabatic rapid passage; Appendix 2.E Superposition and entanglement; 3. The atom-light interaction; Appendix 3.A. Proof of the oscillator strength theorem; Appendix 3.B. Electromagnetic fields; Appendix 3.C. The dipole approximation; Appendix 3.D. Time resolved fluorescence from multi-level atoms; 4. 'Forbidden' transitions; Appendix 4.A. Higher order approximations; 5. Spontaneous emission; Appendix 5.A. The quantum mechanical harmonic oscillator; Appendix 5.B. Field quantization; Appendix 5.C. Alternative theories to QED; 6. The density matrix; Appendix 6.A. The Liouville-von Neumann equation; Part II. Internal Structure: 7. The hydrogen atom; Appendix 7.A. Center-of-mass motion; Appendix 7.B. Coordinate systems; Appendix 7.C. Commuting operators; Appendix 7.D. Matrix elements of the radial wavefunctions; 8. Fine structure; Appendix 8.A. The Sommerfeld fine-structure constant; Appendix 8.B. Measurements of the fine structure 9. Effects of the nucleus; Appendix 9.A. Interacting magnetic dipoles; Appendix 9.B. Hyperfine structure for two spin =2 particles; Appendix 9.C. The hydrogen maser; 10. The alkali-metal atoms; Appendix 10.A. Quantum defects for the alkalis; Appendix 10.B. Numerov method; 11. Atoms in magnetic fields; Appendix 11.A. The ground state of atomic hydrogen; Appendix 11.B. Positronium; Appendix 11.C. The non-crossing theorem; Appendix 11.D. Passage through an anticrossing: Landau-Zener transitions; 12. Atoms in electric fields; 13. Rydberg atoms; 14. The helium atom; Appendix 14.A. Variational calculations; Appendix 14.B. Detail on the variational calculations of the ground state; 15. The periodic system of the elements; Appendix 15. A paramagnetism; Appendix 15.B. The color of gold; 16. Molecules; Appendix 16.A. Morse potential; 17. Binding in the hydrogen molecule; Appendix 17.A. Confocal elliptical coordinates; Appendix 17.B. One-electron two-center integrals; Appendix 17.C. Electron-electron interaction in molecular hydrogen; 18. Ultra-cold chemistry; Part III. Applications: 19. Optical forces and laser cooling; 20. Confinement of neutral atoms; 21. Bose-Einstein condensation; Appendix 21.A. Distribution functions; Appendix 21.B. Density of states; 22. Cold molecules; 23. Three level systems; Appendix 23.A. General Case for _1 , _2; 24. Fundamental physics; Part IV. Appendices: Appendix A. Notation and definitions; Appendix B. Units and notation; Appendix C. Angular momentum in quantum mechanics; Appendix D. Transition strengths; References; Index.

Ab initio prediction of superdense tetragonal and monoclinic polymorphs of carbon

DOE PAGES

Li, Zhen -Zhen; Wang, Jian -Tao; Xu, Li -Fang; ...

2016-11-02

The design and synthesis of three-dimensional denser carbons are one of the hot issues in condensed matter physics because of their fascinating properties. Here we identify by ab initio calculations several tetragonal and monoclinic polymorphs of carbon that adopt the t32, t32*, m32, and m32* structures in P4¯2 1c, P4 32 12, P2 1/c, and C2 symmetry, respectively. These carbon polymorphs have large 32-atom unit cells in all-sp 3 bonding networks comprising five- and six-membered rings that are dynamically stable, as verified by a phonon mode analysis. Electronic band structure calculations show that they are insulators with band gaps inmore » the range of 5.19–5.41 eV, close to the calculated band gap of 5.34 eV for diamond. Remarkably, these carbon phases possess an extremely high atom number density exceeding that of diamond. Lastly, the present results establish different types of carbon phases and offer insights into their outstanding structural and electronic properties.« less

Achieving DFT accuracy with a machine-learning interatomic potential: Thermomechanics and defects in bcc ferromagnetic iron

NASA Astrophysics Data System (ADS)

Dragoni, Daniele; Daff, Thomas D.; Csányi, Gábor; Marzari, Nicola

2018-01-01

We show that the Gaussian Approximation Potential (GAP) machine-learning framework can describe complex magnetic potential energy surfaces, taking ferromagnetic iron as a paradigmatic challenging case. The training database includes total energies, forces, and stresses obtained from density-functional theory in the generalized-gradient approximation, and comprises approximately 150,000 local atomic environments, ranging from pristine and defected bulk configurations to surfaces and generalized stacking faults with different crystallographic orientations. We find the structural, vibrational, and thermodynamic properties of the GAP model to be in excellent agreement with those obtained directly from first-principles electronic-structure calculations. There is good transferability to quantities, such as Peierls energy barriers, which are determined to a large extent by atomic configurations that were not part of the training set. We observe the benefit and the need of using highly converged electronic-structure calculations to sample a target potential energy surface. The end result is a systematically improvable potential that can achieve the same accuracy of density-functional theory calculations, but at a fraction of the computational cost.

Formation, Fragmentation, and Structures of YxOy(+) (x = 1, 2, y = 1 - 13) Clusters: Collision-Induced Dissociation Experiments and Density Functional Theory Calculations.

PubMed

Glodić, Pavle; Mihesan, Claudia; Klontzas, Emmanouel; Velegrakis, Michalis

2016-02-25

Yttrium oxide cluster cations have been experimentally and theoretically studied. We produced small, oxygen-rich yttrium oxide clusters, YxOy+ (x = 1, 2, y = 1–13), by mixing the laser-produced yttrium plasma with a molecular oxygen jet. Mass spectrometry measurements showed that the most stable clusters are those consisting of one yttrium and an odd number of oxygen atoms of the form YO(+)(2k+1) (k = 0–6). Additionally, we performed collision induced dissociation experiments, which indicated that the loss of pairs of oxygen atoms down to a YO+ core is the preferred fragmentation channel for all clusters investigated. Furthermore, we conduct DFT calculations and we obtained two types of low-energy structures: one containing an yttrium cation core and the other composed of YO+ core and O2 ligands, being in agreement with the observed fragmentation pattern. Finally, from the fragmentation studies, total collision cross sections are obtained and these are compared with geometrical cross sections of the calculated structures.

Ionic structures and transport properties of hot dense W and U plasmas

NASA Astrophysics Data System (ADS)

Hou, Yong; Yuan, Jianmin

2016-10-01

We have combined the average-atom model with the hyper-netted chain approximation (AAHNC) to describe the electronic and ionic structure of uranium and tungsten in the hot dense matter regime. When the electronic structure is described within the average-atom model, the effects of others ions on the electronic structure are considered by the correlation functions. And the ionic structure is calculated though using the hyper-netted chain (HNC) approximation. The ion-ion pair potential is calculated using the modified Gordon-Kim model based on the electronic density distribution in the temperature-depended density functional theory. And electronic and ionic structures are determined self-consistently. On the basis of the ion-ion pair potential, we perform the classical (CMD) and Langevin (LMD) molecular dynamics to simulate the ionic transport properties, such as ionic self-diffusion and shear viscosity coefficients, through the ionic velocity correlation functions. Due that the free electrons become more and more with increasing the plasma temperature, the influence of the electron-ion collisions on the transport properties become more and more important.

Configuration interaction in charge exchange spectra of tin and xenon

NASA Astrophysics Data System (ADS)

D'Arcy, R.; Morris, O.; Ohashi, H.; Suda, S.; Tanuma, H.; Fujioka, S.; Nishimura, H.; Nishihara, K.; Suzuki, C.; Kato, T.; Koike, F.; O'Sullivan, G.

2011-06-01

Charge-state-specific extreme ultraviolet spectra from both tin ions and xenon ions have been recorded at Tokyo Metropolitan University. The electron cyclotron resonance source spectra were produced from charge exchange collisions between the ions and rare gas target atoms. To identify unknown spectral lines of tin and xenon, atomic structure calculations were performed for Sn14+-Sn17+ and Xe16+-Xe20+ using the Hartree-Fock configuration interaction code of Cowan (1981 The Theory of Atomic Structure and Spectra (Berkeley, CA: University of California Press)). The energies of the capture states involved in the single-electron process that occurs in these slow collisions were estimated using the classical over-barrier model.

On the Nature of Disorder in Solid 4He

NASA Astrophysics Data System (ADS)

Krainyukova, N. V.

2010-02-01

We apply a modified Debye approach to calculate the Gibbs free energy for different structural phases and crystallite sizes in 4He. Atoms are assumed to interact via the Aziz potential. We have found that some intermediate (between hcp and bcc) phase predicted previously is more favorable than hcp at low temperatures and for small sizes. We show that it can exist in a wide pressure range up to 60 bar in 4He for crystallite sizes about 3,000 atoms. For larger sizes (10,000 atoms or more) this phase becomes unfavorable. In multidomain structures the intermediate phase competes with hcp and metastable fcc that can be a reason for disorder in solid 4He.

Energetics and solvation structure of a dihalogen dopant (I2) in (4)He clusters.

PubMed

Pérez de Tudela, Ricardo; Barragán, Patricia; Valdés, Álvaro; Prosmiti, Rita

2014-08-21

The energetics and structure of small HeNI2 clusters are analyzed as the size of the system changes, with N up to 38. The full interaction between the I2 molecule and the He atoms is based on analytical ab initio He-I2 potentials plus the He-He interaction, obtained from first-principle calculations. The most stable structures, as a function of the number of solvent He atoms, are obtained by employing an evolutionary algorithm and compared with CCSD(T) and MP2 ab initio computations. Further, the classical description is completed by explicitly including thermal corrections and quantum features, such as zero-point-energy values and spatial delocalization. From quantum PIMC calculations, the binding energies and radial/angular probability density distributions of the thermal equilibrium state for selected-size clusters are computed at a low temperature. The sequential formation of regular shell structures is analyzed and discussed for both classical and quantum treatments.

Structural and compositional evolution of Al{sub 3}(Zr,Y) precipitates in Al-Zr-Y alloy

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

Gao, Haiyan, E-mail: gaohaiyan@sjtu.edu.cn

Structural and compositional evolution of Al{sub 3}(Zr,Y) precipitates in aged Al-Zr-Y alloy was investigated through atom probe tomography (APT) and transmission electron microscope (TEM) analysis and first principles calculations. The results show that short-bar-shaped D0{sub 19}-Al{sub 3}Y with some Zr atoms dissolved in precipitated at the very beginning of decomposition and worked as heterogeneous nuclei for L1{sub 2}-Al{sub 3}Zr with spherical morphology after being aged at 400 °C for 2 h. Quasi-static coarsening happened as the aging treatment lasted from 2 h to 200 h. However, distribution of Zr and Y atoms in Al{sub 3}(Zr,Y) is nearly uniform and Al{submore » 3}(Zr,Y) do not have the typical “Al{sub 3}RE core-Al{sub 3}Zr shell” structure which observed in other RE containing Al-Zr-RE alloys with L1{sub 2}-Al{sub 3}RE as nuclei. First principles calculations revealed that binding energy between Y and Zr is strong during the growth of Al{sub 3}(Zr,Y), which led to the co-precipitation of Y and Zr atoms and attribute to the evolution of Al{sub 3}(Zr,Y). - Highlights: •Al{sub 3}Y precipitated firstly and then became nuclei for Al{sub 3}Zr during aging of Al-Zr-Y. •Al{sub 3}(Zr,Y) precipitates do not have the typical “Al{sub 3}Y core-Al{sub 3}Zr shell” structure. •Strong binding between Y and Zr led to the co-precipitation of Y and Zr atoms.« less

Simulated structure and imaging of NTCDI on Si(1 1 1)-7 × 7 : a combined STM, NC-AFM and DFT study

NASA Astrophysics Data System (ADS)

Jarvis, S. P.; Sweetman, A. M.; Lekkas, I.; Champness, N. R.; Kantorovich, L.; Moriarty, P.

2015-02-01

The adsorption of naphthalene tetracarboxylic diimide (NTCDI) on Si(1 1 1)-7 × 7 is investigated through a combination of scanning tunnelling microscopy (STM), noncontact atomic force microscopy (NC-AFM) and density functional theory (DFT) calculations. We show that NTCDI adopts multiple planar adsorption geometries on the Si(1 1 1)-7 × 7 surface which can be imaged with intramolecular bond resolution using NC-AFM. DFT calculations reveal adsorption is dominated by covalent bond formation between the molecular oxygen atoms and the surface silicon adatoms. The chemisorption of the molecule is found to induce subtle distortions to the molecular structure, which are observed in NC-AFM images.

Electronic structure of lead pyrophosphate

NASA Astrophysics Data System (ADS)

Suewattana, Malliga; Singh, David

2007-03-01

Lead Pyrophosphate Pb2P2O7 is of interest for potential radiation detection applications and use in long term waste storage. It forms in triclinic P1 crystals and can also be grown as glasses. We performed electronic structure calculations using the crystal structure which determined by Mullica et. al (J. Solid State Chem (1986)) using x-ray diffraction and found large forces on atoms suggesting that the refined atomic positions were not fully correct. Here we report first principles structure relaxation and a revised crystal structure for this compound. We analyze the resulting structure using pair distribution functions and discuss the implications for the electronic properties. This work was supported by DOE NA22 and the Office of Naval Research.

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

Chezhina, N.V., E-mail: chezhina@nc2490.spb.edu; Korolev, D.A.; Zhuk, N.A.

On the basis of the results of magnetic susceptibility and ESR studies of the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions iron atoms in the solid solutions of cubic modification of bismuth niobate were found to exist as Fe(III) monomers and exchange bound Fe(III)-O-Fe(III) dimers with antiferro- and ferromagnetic type of superexchange. The exchange parameters and the distribution of monomers and dimers in the solid solutions were calculated as a function of paramagnetic atom content. - Graphical abstract: The study of the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions showed that the introduction of iron atoms into the structure ofmore » Bi{sub 3}NbO{sub 7} stabilizes the cubic structure of bismuth niobate making the phase transition tetragonal ↔ cubic structure irreversible. In the Bi{sub 3}Nb{sub 1−x}Fe{sub x}O{sub 7−δ} solid solutions we observe the formation of dimers with antiferro- and ferromagnetic exchange. Such clusters are partially retained even at the infinite dilution of the solid solution, which testifies for their rigidity. A sufficiently high parameter of ferromagnetic exchange in a dimer (+53 cm{sup −1}) seems to result from iron atoms being located in the vicinity of oxygen vacancy. - Highlights: • The reversible transition cubic – tetragonal modifications in Bi{sub 3}NbO{sub 7} becomes irreversible. • Only cubic modification of Bi{sub 3}Nb{sub 1-x}Fe{sub x}O{sub 7-δ} is stable due to clusters of Fe atoms. • These clusters are sufficiently strong and retained even at the infinite dilution. • The calculations of magnetic susceptibility give the distribution of the clusters and single atoms.« less

Design of graphene nanoparticle undergoing axial compression: quantum study

NASA Astrophysics Data System (ADS)

Glukhova, O. E.; Kirillova, I. V.; Saliy, I. N.; Kolesnikova, A. S.; Slepchenkov, M. M.

2011-03-01

We report the results of quantum mechanical investigations of the atomic structure and deformations of graphene nanoparticle undergoing axial compression. We applied the tight-binding (TB) method. Our transferable tightbinding potential correctly reproduced tight-binding changes in the electronic configuration as a function of the local bonding geometry around each carbon atom. The tight-binding method applied provided the consideration and calculation of the rehybridization between σ- and π-orbitals. To research nanoribbons using tight-binding potential our own program was used. We adapted TB method to be able to run the algorithm on a parallel computing machine (computer cluster). To simulate axial compression of graphene nanoparticles the atoms on the ends were fixed on the plates. The plates were moved towards each other to decrease the length at some percent. Plane atomic network undergoing axial compression became wave-like. The amplitude of wave and its period were not constant and changed along axis. This is a phase transition. The strain energy collapse occurs at the value of axial compression 0.03-0.04. The strain energy increased up to the quantity compression 0.03, then collapsed sharply and decreased. So according to our theoretical investigation, the elasticity of graphene nanoparticles is more than the elasticity of nanotubes the same width and length. The curvature of the atomic network because of compression will decrease the reactivity of graphene nanoparticles. We have calculated the atomic structure and electronic structure of the compression graphene nanopaticle at each step of strain of axial compression. We have come to the conclusion that the wave-like graphenes adsorbing protein and nucleic acid are the effective nanosensors and bionanosensors.

Electronic stopping in oxides beyond Bragg additivity

NASA Astrophysics Data System (ADS)

Sigmund, P.; Schinner, A.

2018-01-01

We present stopping cross sections calculated by our PASS code for several ions in metal oxides and SiO2 over a wide energy range. Input takes into account changes in the valence structure by assigning two additional electrons to the 2p shell of oxygen and removing the appropriate number of electrons from the outer shells of the metal atom. Results are compared with tabulated experimental values and with two versions of Bragg's additivity rule. Calculated stopping cross sections are applied in testing a recently-proposed scaling rule, which relates the stopping cross section to the number of oxygen atoms per molecule.

Electronic structure and magnetism of epitaxial Ni-Mn-Ga(-Co) thin films with partial disorder: a view across the phase transition

NASA Astrophysics Data System (ADS)

Schleicher, B.; Klar, D.; Ollefs, K.; Diestel, A.; Walecki, D.; Weschke, E.; Schultz, L.; Nielsch, K.; Fähler, S.; Wende, H.; Gruner, M. E.

2017-11-01

The influence of Co-doping in off-stoichiometric Ni-Mn-Ga and Ni-Mn-Ga-Co thin films on the magnetic coupling of the atoms is investigated with x-ray magnetic circular dichroism in both the martensitic as well as austenitic phase, respectively. Additionally, first principles calculations were performed to compare the experimentally obtained absorption spectra with theoretical predictions. Calculated exchange constants and density of states for the different atomic sites underline the large influence of chemical and magnetic order on the magnetocaloric properties of the material.

Implementation of an approximate self-energy correction scheme in the orthogonalized linear combination of atomic orbitals method of band-structure calculations

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

Gu, Z.; Ching, W.Y.

Based on the Sterne-Inkson model for the self-energy correction to the single-particle energy in the local-density approximation (LDA), we have implemented an approximate energy-dependent and [bold k]-dependent [ital GW] correction scheme to the orthogonalized linear combination of atomic orbital-based local-density calculation for insulators. In contrast to the approach of Jenkins, Srivastava, and Inkson, we evaluate the on-site exchange integrals using the LDA Bloch functions throughout the Brillouin zone. By using a [bold k]-weighted band gap [ital E][sub [ital g

Tight-binding model for borophene and borophane

NASA Astrophysics Data System (ADS)

Nakhaee, M.; Ketabi, S. A.; Peeters, F. M.

2018-03-01

Starting from the simplified linear combination of atomic orbitals method in combination with first-principles calculations, we construct a tight-binding (TB) model in the two-centre approximation for borophene and hydrogenated borophene (borophane). The Slater and Koster approach is applied to calculate the TB Hamiltonian of these systems. We obtain expressions for the Hamiltonian and overlap matrix elements between different orbitals for the different atoms and present the SK coefficients in a nonorthogonal basis set. An anisotropic Dirac cone is found in the band structure of borophane. We derive a Dirac low-energy Hamiltonian and compare the Fermi velocities with that of graphene.

Atomically thin transition metal layers: Atomic layer stabilization and metal-semiconductor transition

NASA Astrophysics Data System (ADS)

Hwang, Jeongwoon; Oh, Young Jun; Kim, Jiyoung; Sung, Myung Mo; Cho, Kyeongjae

2018-04-01

We have performed first-principle calculations to explore the possibility of synthesizing atomically thin transition metal (TM) layers. Buckled structures as well as planar structures of elemental 2D TM layers result in significantly higher formation energies compared with sp-bonded elemental 2D materials with similar structures, such as silicene and phosphorene. It is shown that the TM layers can be stabilized by surface passivation with HS, C6H5S2, or O, and O passivation is most effective. The surface oxygen passivation can improve stability leading to thermodynamically stable TM monolayers except Au, which is the most non-reactive metal element. Such stabilized TM monolayers also show an electronic structure transition from metallic state of free-standing TM layer to semiconducting O-passivated Mo and W monolayers with band gaps of 0.20-1.38 eV.

Chemically directing d-block heterometallics to nanocrystal surfaces as molecular beacons of surface structure

DOE PAGES

Rosen, Evelyn L.; Gilmore, Keith; Sawvel, April M.; ...

2015-07-28

Our understanding of structure and bonding in nanoscale materials is incomplete without knowledge of their surface structure. Needed are better surveying capabilities responsive not only to different atoms at the surface, but also their respective coordination environments. We report here that d-block organometallics, when placed at nanocrystal surfaces through heterometallic bonds, serve as molecular beacons broadcasting local surface structure in atomic detail. This unique ability stems from their elemental specificity and the sensitivity of their d-orbital level alignment to local coordination environment, which can be assessed spectroscopically. Re-surfacing cadmium and lead chalcogenide nanocrystals with iron- or ruthenium-based molecular beacons ismore » readily accomplished with trimethylsilylated cyclopentadienyl metal carbonyls. For PbSe nanocrystals with iron-based beacons, we show how core-level X-ray spectroscopies and DFT calculations enrich our understanding of both charge and atomic reorganization at the surface when beacons are bound.« less

Atomic structure of a decagonal Al-Pd-Mn phase

NASA Astrophysics Data System (ADS)

Mihalkovič, Marek; Roth, Johannes; Trebin, Hans-Rainer

2017-12-01

We present a detailed structure solution for the 16 -Å decagonal quasicrystal in the Al-Pd-Mn system by means of cluster decoration and ab initio energy minimization. It is based on structure models of the ɛ and other approximant phases. The ɛ phases can be represented as subsets of a hexagon-boat-star (HBS) tiling. The decagonal phase comprises further HBS tiles. We have constructed several fictitious HBS approximants and optimized their structures individually. All tiles are decorated by two types of atomic clusters: the pseudo-Mackay icosahedron (PMI) and the large bicapped pentagonal prism (LBPP). It turns out that, whereas the PMI clusters can be kept essentially unchanged, the LBPP clusters must be adjusted in occupancy with Al atoms depending on their positions in the various tiles. In this way we obtain cluster decorations for all tiles of the decagonal quasicrystal. The calculations were confirmed by evaluation of an effective tile Hamiltonian.

Thermodynamic stability of boron: the role of defects and zero point motion.

PubMed

van Setten, Michiel J; Uijttewaal, Matthé A; de Wijs, Gilles A; de Groot, Robert A

2007-03-07

Its low weight, high melting point, and large degree of hardness make elemental boron a technologically interesting material. The large number of allotropes, mostly containing over a hundred atoms in the unit cell, and their difficult characterization challenge both experimentalists and theoreticians. Even the ground state of this element is still under discussion. For over 30 years, scientists have attempted to determine the relative stability of alpha- and beta-rhombohedral boron. We use density functional calculations in the generalized gradient approximation to study a broad range of possible beta-rhombohedral structures containing interstitial atoms and partially occupied sites within a 105 atoms framework. The two most stable structures are practically degenerate in energy and semiconducting. One contains the experimental 320 atoms in the hexagonal unit cell, and the other contains 106 atoms in the triclinic unit cell. When populated with the experimental 320 electrons, the 106 atom structure exhibits a band gap of 1.4 eV and an in-gap hole trap at 0.35 eV above the valence band, consistent with known experiments. The total energy of these two structures is 23 meV/B lower than the original 105 atom framework, but it is still 1 meV/B above the alpha phase. Adding zero point energies finally makes the beta phase the ground state of elemental boron by 3 meV/B. At finite temperatures, the difference becomes even larger.

Atomically resolved scanning force studies of vicinal Si(111)

NASA Astrophysics Data System (ADS)

Pérez León, Carmen; Drees, Holger; Wippermann, Stefan Martin; Marz, Michael; Hoffmann-Vogel, Regina

2017-06-01

Well-ordered stepped semiconductor surfaces attract intense attention owing to the regular arrangements of their atomic steps that makes them perfect templates for the growth of one-dimensional systems, e.g., nanowires. Here, we report on the atomic structure of the vicinal Si (111 ) surface with 10∘ miscut investigated by a joint frequency-modulation scanning force microscopy (FM-SFM) and ab initio approach. This popular stepped surface contains 7 ×7 -reconstructed terraces oriented along the Si (111 ) direction, separated by a stepped region. Recently, the atomic structure of this triple step based on scanning tunneling microscopy (STM) images has been subject of debate. Unlike STM, SFM atomic resolution capability arises from chemical bonding of the tip apex with the surface atoms. Thus, for surfaces with a corrugated density of states such as semiconductors, SFM provides complementary information to STM and partially removes the dependency of the topography on the electronic structure. Our FM-SFM images with unprecedented spatial resolution on steps coincide with the model based on a (7 7 10 ) orientation of the surface and reveal structural details of this surface. Two different FM-SFM contrasts together with density functional theory calculations explain the presence of defects, buckling, and filling asymmetries on the surface. Our results evidence the important role of charge transfers between adatoms, restatoms, and dimers in the stabilisation of the structure of the vicinal surface.

Magnetic behavior of Si-Ge bond in SixGe4-x nano-clusters

NASA Astrophysics Data System (ADS)

Nahali, Masoud; Mehri, Ali

2018-06-01

The structure of SixGe4-x nano-clusters were optimized by MPW1B95 level of theory using MG3S and SDB-aug-cc-PVTZ basis set. The agreement of the calculated ionization and dissociation energies with experimental values validates the reported structures of nano-clusters and justifies the use of hybrid meta density functional method. Since the Si-Si bond is stronger than Si-Ge and Ge-Ge bonds, the Si-Si, Si-Ge, and Ge-Ge diagonal bonds determine the precedence of the stability in these nano-clusters. The hybrid meta density functional calculations were carried out to investigate the adsorption of CO on all possible SixGe4-x nano-clusters. It was found that the silicon atom generally makes a stronger bond with CO than germanium and thereby preferentially affects the shape of structures having higher multiplicity. In Si-Ge structures with higher spin more than 95% of spins accumulate on positions with less bonds to other atoms of the cluster. Through CO adsorption on these clusters bridge structures are made that behave as spin bridge which conduct the spin from the nano-cluster surface to the adsorbate atoms. A better understanding of bridged structures was achieved upon introducing the 'spin bridge' concept. Based on exhaustive spin density analysis, it was found that the reason for the extra negative charge on oxygen in the bridged structures is the relocation of spin from the surface through the bridge.

Lifetime of a Chemically Bound Helium Compound

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Lundell, Jan; Gerber, R. Benny; Kwak, Dochan (Technical Monitor)

2001-01-01

The rare-gas atoms are chemically inert, to an extent unique among all elements. This is due to the stable electronic structure of the atoms. Stable molecules with chemically bound rare-gas atoms are, however, known. A first such compound, XePtF6, W2S prepared in 1962 and since then a range of molecules containing radon, xenon and krypton have been obtained. Most recently, a first stable chemically bound compound of argon was prepared, leaving neon and helium as the only elements for which stable chemically bound molecules are not yet known. Electronic structure calculations predict that a metastable species HHeF exists, but significance of the result depends on the unknown lifetime. Here we report quantum dynamics calculations of the lifetime of HHeF, using accurate interactions computed from electronic structure theory. HHeF is shown to disintegrate by tunneling through energy barriers into He + HF and H + He + F the first channel greatly dominating. The lifetime of HHeF is more than 120 picoseconds, that of DHeF is 14 nanoseconds. The relatively long lifetimes are encouraging for the preparation prospects of this first chemically bound helium compound.

Atomic mechanism for the growth of wafer-scale single-crystal graphene: theoretical perspective and scanning tunneling microscopy investigations

NASA Astrophysics Data System (ADS)

Niu, Tianchao; Zhang, Jialin; Chen, Wei

2017-12-01

Chemical vapor deposition (CVD) is the most promising approach for producing low-cost, high-quality, and large area graphene. Revealing the graphene growth mechanism at the atomic-scale is of great importance for realizing single crystal graphene (SCG) over wafer scale. Density functional theoretical (DFT) calculations are playing an increasingly important role in revealing the structure of the most stable carbon species, understanding the evolution processes, and disclosing the active sites. Scanning tunneling microscopy (STM) is a powerful surface characterization tool to illustrate the real space distribution and atomic structures of growth intermediates during the CVD process. Combining them together can provide valuable information to improve the atomically controlled growth of SCG. Starting from a basic concept of the substrate effect on realizing SCG, this review covers the progress made in theoretical investigations on various carbon species during graphene growth on different transition metal substrates, in the STM study of the structural intermediates on transition metal surfaces, and in synthesizing graphene nanoribbons with atomic-precise width and edge structure, ending with a perspective on the future development of 2D materials beyond graphene.

One-atom-layer 4×4 compound in (Tl, Pb)/Si(111) system

NASA Astrophysics Data System (ADS)

Mihalyuk, A. N.; Hsing, C. R.; Wei, C. M.; Gruznev, D. V.; Bondarenko, L. V.; Tupchaya, A. Y.; Zotov, A. V.; Saranin, A. A.

2017-03-01

An ordered 4×4-periodicity 2D compound has been found in the (Tl, Pb)/Si(111) system and its composition, structure and electronic properties have been characterized using low-energy electron diffraction, scanning tunneling microscopy observations and density-functional-theory calculations. The compound has been concluded to contain 9 Tl atoms and 12 Pb atoms per 4×4 unit cell, i.e., 0.56 ML of Tl and 0.75 ML of Pb. Structural model was proposed for the 4×4-(Tl, Pb) compound where building blocks are a hexagonal array of 12 Pb atoms, a triangular array of 6 Tl atoms and a Tl trimer. The proposed structure has a C3 symmetry and occurs in the two equivalent orientations. The electron band structure of the compound contains two metallic spin-split surface-state bands. Bearing in mind the advanced properties of the known √{ 3 } ×√{ 3 } 2D compound in the same (Tl, Pb)/Si(111) system (i.e., combination of giant Rashba effect and superconductivity), the found 4×4-(Tl, Pb) compound is believed to be a promising object for exploration of its superconductive properties.

Photoelectron spectroscopy and density functional theory study of TiAlO(y) (-) (y=1-3) and TiAl(2)O(y) (-) (y=2-3) clusters.

PubMed

Zhang, Zeng-Guang; Xu, Hong-Guang; Zhao, Yuchao; Zheng, Weijun

2010-10-21

Small titanium-aluminum oxide clusters, TiAlO(y) (-) (y=1-3) and TiAl(2)O(y) (-) (y=2-3), were studied by using anion photoelectron spectroscopy. The adiabatic detachment energies of TiAlO(y) (-) (y=1-3) were estimated to be 1.11±0.05, 1.70±0.08, and 2.47±0.08eV based on their photoelectron spectra; those of TiAl(2)O(2) (-) and TiAl(2)O(3) (-) were estimated to be 1.17±0.08 and 2.2±0.1eV, respectively. The structures of these clusters were determined by comparison of density functional calculations with the experimental results. The structure of TiAlO(-) is nearly linear with the O atom in the middle. That of TiAlO(2) (-) is a kite-shaped structure. TiAlO(3) (-) has a kite-shaped TiAlO(2) unit with the third O atom attaching to the Ti atom. TiAl(2)O(2) (-) has two nearly degenerate Al-O-Ti-O-Al chain structures that can be considered as cis and trans forms. TiAl(2)O(3) (-) has two low-lying isomers, kite structure and book structure. The structures of these clusters indicate that the Ti atom tends to bind to more O atoms.

To acquire more detailed radiation drive by use of ``quasi-steady'' approximation in atomic kinetics

NASA Astrophysics Data System (ADS)

Ren, Guoli; Pei, Wenbing; Lan, Ke; Gu, Peijun; Li, Xin

2012-10-01

In current routine 2D simulation of hohlraum physics, we adopt the principal-quantum- number(n-level) average atom model(AAM) in NLTE plasma description. However, the detailed experimental frequency-dependant radiative drive differs from our n-level simulated drive, which reminds us the need of a more detailed atomic kinetics description. The orbital-quantum- number(nl-level) average atom model is a natural consideration, however the nl-level in-line calculation needs much more computational resource. By distinguishing the rapid bound-bound atomic processes from the relative slow bound-free atomic processes, we found a method to build up a more detailed bound electron distribution(nl-level even nlm-level) using in-line n-level calculated plasma conditions(temperature, density, and average ionization degree). We name this method ``quasi-steady approximation'' in atomic kinetics. Using this method, we re-build the nl-level bound electron distribution (Pnl), and acquire a new hohlraum radiative drive by post-processing. Comparison with the n-level post-processed hohlraum drive shows that we get an almost identical radiation flux but with more fine frequency-denpending spectrum structure which appears only in nl-level transition with same n number(n=0) .

Hydroxyl migration disorders the surface structure of hydroxyapatite nanoparticles

NASA Astrophysics Data System (ADS)

Cheng, Xiajie; Wu, Hong; Zhang, Li; Ma, Xingtao; Zhang, Xingdong; Yang, Mingli

2017-09-01

The surface structure of nano-hydroxyapatite (HAP) was investigated using a combined simulated annealing and molecular dynamics method. The stationary structures of nano-HAP with 4-7 nm in diameter and annealed under different temperatures were analyzed in terms of pair distribution function, structural factor, mean square displacement and atomic coordination number. The particles possess different structures from bulk crystal. A clear radial change in their atomic arrangements was noted. From core to surface the structures change from ordered to disordered. A three-shell model was proposed to describe the structure evolution of nano-HAP. Atoms in the core zone keep their arrangements as in crystal, while atoms in the surface shell are in short-range order and long-range disorder, adopting a typically amorphous structure. Atoms in the middle shell have small displacements and/or deflections but basically retain their original locations as in crystal. The disordered shell is about 1 nm in thickness, in agreement with experimental observations. The disordering mainly stems from hydroxyl migration during which hydroxyls move to the surface and bond with the exposed Ca ions, and their left vacancies bring about a rearrangement of nearby atoms. The disordering is to some extent different for particles unannealed under different temperatures, resulting from fewer number of migrated hydroxyls at lower temperatures. Particles with different sizes have similar surface structures, and their surface energy decreases with increasing size. Moreover, the surface energy is reduced by hydroxyl migration because the exposed Ca ions on the surface are ionically bonded with the migrated hydroxyls. Our calculations proposed a new structure model for nano-HAP, which indicates a surface structure with activities different from those without surface reorganization. This is particularly interesting because most bioactivities of biomaterials are dominated by their surface activity.

A theoretical study of the omega-phase transformation in metals

NASA Astrophysics Data System (ADS)

Sanati, Mahdi

I have studied the formation of o-phase from electronic and mesoscopic (domain wall) points of view. To study the formation of domain walls, I have extended the Landau model of Cook for the o-phase transition by including a spatial gradient (Ginzburg) term of the scalar order parameter. In general, the Landau free energy is an asymmetric double-well potential. From the variational derivative of the total free energy I obtained a static equilibrium condition. By solving this equation for different physical parameters and boundary conditions, I obtained different quasi-one-dimensional soliton-like solutions. These solutions correspond to three different types of domain walls between the o-phase and the beta-matrix. These results are used to model the formation of the o-phase in bcc Ti. Canonical band model and first principles calculations confirmed the instability of the bcc-phase of group III and IV transition metals with respect to the o-phase transformation. I showed that the d-electron density is the controlling parameter for this type of the transformation. Also the possibility of formation of the o-phase for rare earth metals is discussed. First-principles full-potential linear muffin-tin orbital method (FPLMTO) calculations are performed for o-type displacement of the atoms to study the formation of the o-phase in TiAl and Ti 3Al2Nb alloys. The results of my calculations showed an instability in ordered B2 TiAl structure with respect to the o-phase when one third of the Al atoms are replaced by Nb atoms. These phenomena are explained, first by symmetry arguments; then a pair potential model is used to illustrate this instability based on interactions between different pair of atoms derived from the electronic structure. In addition, importance of the atomic arrangements on the structural stability of the Ti3Al2 Nb system is discussed.

A First Principles Study of H2 Adsorption on LaNiO3(001) Surfaces

PubMed Central

Pan, Changchang; Chen, Yuhong; Wu, Na; Zhang, Meiling; Yuan, Lihua; Zhang, Cairong

2017-01-01

The adsorption of H2 on LaNiO3 was investigated using density functional theory (DFT) calculations. The adsorption sites, adsorption energy, and electronic structure of LaNiO3(001)/H2 systems were calculated and indicated through the calculated surface energy that the (001) surface was the most stable surface. By looking at optimized structure, adsorption energy and dissociation energy, we found that there were three types of adsorption on the surface. First, H2 molecules completely dissociate and then tend to bind with the O atoms, forming two –OH bonds. Second, H2 molecules partially dissociate with the H atoms bonding to the same O atom to form one H2O molecule. These two types are chemical adsorption modes; however, the physical adsorption of H2 molecules can also occur. When analyzing the electron structure of the H2O molecule formed by the partial dissociation of the H2 molecule and the surface O atom, we found that the interaction between H2O and the (001) surface was weaker, thus, H2O was easier to separate from the surface to create an O vacancy. On the (001) surface, a supercell was constructed to accurately study the most stable adsorption site. The results from analyses of the charge population; electron localization function; and density of the states indicated that the dissociated H and O atoms form a typical covalent bond and that the interaction between the H2 molecule and surface is mainly due to the overlap-hybridization among the H 1s, O 2s, and O 2p states. Therefore, the conductivity of LaNiO3(001)/H2 is stronger after adsorption and furthermore, the conductivity of the LaNiO3 surface is better than that of the LaFeO3 surface. PMID:28772396

Sc-Decorated Porous Graphene for High-Capacity Hydrogen Storage: First-Principles Calculations.

PubMed

Chen, Yuhong; Wang, Jing; Yuan, Lihua; Zhang, Meiling; Zhang, Cairong

2017-08-02

The generalized gradient approximation (GGA) function based on density functional theory is adopted to investigate the optimized geometrical structure, electron structure and hydrogen storage performance of Sc modified porous graphene (PG). It is found that the carbon ring center is the most stable adsorbed position for a single Sc atom on PG, and the maximum number of adsorbed H₂ molecules is four with the average adsorption energy of -0.429 eV/H₂. By adding a second Sc atom on the other side of the system, the hydrogen storage capacity of the system can be improved effectively. Two Sc atoms located on opposite sides of the PG carbon ring center hole is the most suitable hydrogen storage structure, and the hydrogen storage capacity reach a maximum 9.09 wt % at the average adsorption energy of -0.296 eV/H₂. The adsorption of H₂ molecules in the PG system is mainly attributed to orbital hybridization among H, Sc, and C atoms, and Coulomb attraction between negatively charged H₂ molecules and positively charged Sc atoms.

Sc-Decorated Porous Graphene for High-Capacity Hydrogen Storage: First-Principles Calculations

PubMed Central

Chen, Yuhong; Wang, Jing; Yuan, Lihua; Zhang, Meiling

2017-01-01

The generalized gradient approximation (GGA) function based on density functional theory is adopted to investigate the optimized geometrical structure, electron structure and hydrogen storage performance of Sc modified porous graphene (PG). It is found that the carbon ring center is the most stable adsorbed position for a single Sc atom on PG, and the maximum number of adsorbed H2 molecules is four with the average adsorption energy of −0.429 eV/H2. By adding a second Sc atom on the other side of the system, the hydrogen storage capacity of the system can be improved effectively. Two Sc atoms located on opposite sides of the PG carbon ring center hole is the most suitable hydrogen storage structure, and the hydrogen storage capacity reach a maximum 9.09 wt % at the average adsorption energy of −0.296 eV/H2. The adsorption of H2 molecules in the PG system is mainly attributed to orbital hybridization among H, Sc, and C atoms, and Coulomb attraction between negatively charged H2 molecules and positively charged Sc atoms. PMID:28767084

Identification of B-K near edge x-ray absorption fine structure peaks of boron nitride thin films prepared by sputtering deposition

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

Niibe, Masahito; Miyamoto, Kazuyoshi; Mitamura, Tohru

2010-09-15

Four {pi}{sup *} resonance peaks were observed in the B-K near edge x-ray absorption fine structure spectra of boron nitride thin films prepared by magnetron sputtering. In the past, these peaks have been explained as the K-absorption of boron atoms, which are present in environment containing nitrogen vacancies, the number of which is 1-3 corresponding to the three peaks at higher photon energy. However, the authors found that there was a strong correlation between the intensities of these three peaks and that of O-K absorption after wide range scanning and simultaneous measurement of nitrogen and oxygen K-absorptions of the BNmore » films. Therefore, the authors conclude that these three peaks at the higher energy side correspond to boron atoms bound to one-to-three oxygen atoms instead of three nitrogen atoms surrounding the boron atom in the h-BN structure. The result of the first-principles calculation with a simple cluster model supported the validity of this explanation.« less

Multiscale molecular dynamics simulations of rotary motor proteins.

PubMed

Ekimoto, Toru; Ikeguchi, Mitsunori

2018-04-01

Protein functions require specific structures frequently coupled with conformational changes. The scale of the structural dynamics of proteins spans from the atomic to the molecular level. Theoretically, all-atom molecular dynamics (MD) simulation is a powerful tool to investigate protein dynamics because the MD simulation is capable of capturing conformational changes obeying the intrinsically structural features. However, to study long-timescale dynamics, efficient sampling techniques and coarse-grained (CG) approaches coupled with all-atom MD simulations, termed multiscale MD simulations, are required to overcome the timescale limitation in all-atom MD simulations. Here, we review two examples of rotary motor proteins examined using free energy landscape (FEL) analysis and CG-MD simulations. In the FEL analysis, FEL is calculated as a function of reaction coordinates, and the long-timescale dynamics corresponding to conformational changes is described as transitions on the FEL surface. Another approach is the utilization of the CG model, in which the CG parameters are tuned using the fluctuation matching methodology with all-atom MD simulations. The long-timespan dynamics is then elucidated straightforwardly by using CG-MD simulations.

Structural and electronic properties of boron-doped double-walled silicon carbide nanotubes

NASA Astrophysics Data System (ADS)

Behzad, Somayeh; Moradian, Rostam; Chegel, Raad

2010-12-01

The effects of boron doping on the structural and electronic properties of (6,0)@(14,0) double-walled silicon carbide nanotube (DWSiCNT) are investigated by using spin-polarized density functional theory. It is found that boron atom could be more easily doped in the inner tube. Our calculations indicate that a Si site is favorable for B under C-rich condition and a C site is favorable under Si-rich condition. Additionally, B-substitution at either single carbon or silicon atom site in DWSiCNT could induce spontaneous magnetization.

Mechanism for chelated sulfate formation from SO2 and bis (triphenylphosphine) platinum

NASA Technical Reports Server (NTRS)

Mehandru, S. P.; Anderson, A. B.

1985-01-01

Structure and energy surface calculations using the atom superposition and electron delocalization molecular orbital theory show that the first step in the reaction between SO2 and the dioxygen complex (PPh3)2PtO2 is the coordination of SO2 with one oxygen atom of the complex, followed by metal-oxygen bond breaking and reorientation, leading to a five-membered cyclic structure. This then rearranges to form the bidentate coordinated sulfate. Alternative pathways are considered and are found to be less favorable.

Tuning the electronic structure of graphene through alkali metal and halogen atom intercalation

NASA Astrophysics Data System (ADS)

Ahmad, Sohail; Miró, Pere; Audiffred, Martha; Heine, Thomas

2018-04-01

The deposition, intercalation and co-intercalation of heavy alkali metals and light halogens atoms in graphene mono- and bilayers have been studied using first principles density-functional calculations. Both the deposition and the intercalation of alkali metals gives rise to n-type doping due to the formation of M+-C- pairs. The co-intercalation of a 1:1 ratio of alkali metals and halogens derives into the formation of ionic pairs among the intercalated species, unaltering the electronic structure of the layered material.

Geometry-dependent atomic multipole models for the water molecule.

PubMed

Loboda, O; Millot, C

2017-10-28

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Geometry-dependent atomic multipole models for the water molecule

NASA Astrophysics Data System (ADS)

Loboda, O.; Millot, C.

2017-10-01

Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

Modeling of the Structure of Disordered Metallic Alloys and Its Transformation Under Thermal Forcing

NASA Astrophysics Data System (ADS)

Cress, Ryan Paul

The morphology of disordered binary metallic alloys is investigated. The structure of disordered binary metallic alloys is modeled as a randomly close packed (RCP) assembly of atoms. It was observed through a 2-D binary hard sphere experiment that RCP structure can be modeled as a mixture of nano-crystallites and glassy matter. We define the degree of crystallinity as the fraction of atoms contained in nano-crystallites in an RCP medium. Nano-crystallites by size in a crystallite size distribution were determined experimentally to define the morphology of the RCP medium. Both the degree of crystallinity and the crystallite size distribution have been found to be determined by the composition of a given binary mixture. A 2-D Monte Carlo simulation was developed in order to replicate the RCP structure observed in the experiment which is then extended to cases of arbitrary composition. Crystallites were assumed to be spherical with isotropic cross sections. The number of atoms in an individual crystallite in 2-D is simply transformed into the number of atoms in 3-D; we then obtain the crystallite size distribution in 3-D. This experiment accounts for the contribution from the repulsive core of the inter-atomic potential. The attractive part of the potential is recovered by constructing spherical nano-crystallites of a given radius from a crystalline specimen of each given alloy. A structural model of a disordered alloy is thus obtained. With the basic structure of the RCP medium defined, the response to heating would be in the form of changes to the crystallite size distribution. This was first investigated in a hard sphere mechanical oven experiment. The experimental setup consists of a 2-D cell which is driven by two independent stepper motors. The motors drive a binary RCP bed of spheres on a slightly tilted plane according to a chaotic algorithmm. The motors are driven at four different speed settings. The RCP medium was analyzed using a sequence of digital images taken of the beds. The bursts of images provide a Gaussian distribution of particle speeds in x and y directions thus giving rise to the notion of "temperature." This temperature scales with the motor speed settings. The measured average degree of crystallinity is found to decrease as the effective temperature was raised suggesting that nano-crystallites dissociate under thermal forcing. The evolution of a specimen's structure is calculated rigorously by means of the law of mass action formalism. A system of thermal dissociation reaction equations is written out for the set of nano-crystallites according to the 3-D crystallite size distribution. The equilibrium treatment is justified because the energy differences between metastable RCP structures fall within kT. Thermal dissociation of one surface atom at a time is assumed because the energy cost in dissociation of a surface atom on a nano-crystallite is significantly less than that of a multi atom cluster. The full set of reaction equations cover all possible dissociation steps, which may amount to several thousand for a disordered alloy specimen. The primary determining factor in each of these dissociation equations is the dissociation potential or the amount of attractive energy needed to remove a surface atom on a nano-crystallite of a given size. The attractive potential between atoms is calculated using a Lennard-Jones potential between a pair of atoms for which quantum chemistry calculations exist in the literature. All interactions impinged on the surface atom by all other atoms in a crystallite are summed. As the nano-crystallites dissociate due to heating, the structure of the alloy changes, and this leads to modifications of alloy's transport properties. The model is found to predict the melting temperature of various disordered binary alloys as well as refractory metals in good agreement with known data. The structure model for disordered binary alloys gives an excellent characterization of the alloy morphology. It therefore provides fruitful avenues for making predictions about how thermophysical properties of disordered binary alloys change as the alloy temperature is raised by heating.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

PubMed

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

Numerical calculations of energy, nucleus size and coulomb decay rate for ddμ* resonance states in the variational approach using new wavefunctions

NASA Astrophysics Data System (ADS)

Eskandari, M. R.; Gheisari, R.; Kashian, S.

2006-02-01

This paper provides a theoretical complement to the experimental measurement of the population of excited dμ(2s) and dμ(1s) atoms in a deuterium. The population of these atoms plays an important role in a muon catalyzed fusion cycle. Symmetric and non-symmetric muonic molecular ions have been predicted to form in excited states in collisions between excited muonic atoms and hydrogen molecules. One example is the ddμ*, which is a muonic deuterium-deuterium symmetric ion in excited state and is initially produced in the interaction of dμ(2s) atoms with deuterium nuclei. Our calculations interpret the experimental findings in terms of the so-called side-path model. This model essentially deals with the interaction mentioned above in which the ddμ* ion undergoes Coulomb de-excitation where the excitation energy is shared between a dμ(1s) atom and one deuterium. The structure of ddμ* is studied here using the numerical, variational method and the given wavefunctions. Few resonance energies for ddμ* molecular states are calculated below the 2s threshold. For more precise assessment of the reliability of the given wavefunctions, the nucleus sizes and Coulomb decay rates for the zeroth, first and second vibrational meta-stable states of the mentioned ion are also calculated. The obtained results are close to those previously reported. The advantage of the given method over previous methods is that the used wavefunction has only two terms, which simplifies the calculations with the same results as those from the complicated coupled rearrangement channel method with a Gaussian basis set. These energies are the base data required for size, formation and decay rate calculations of the ddμ* ion.

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

Structural, electronic and optical properties of CO adsorbed on the defective anatase TiO2 (101) surface; a DFT study

NASA Astrophysics Data System (ADS)

Rafique, Muhammad; Shuai, Yong; Hassan, Muhammad

2017-08-01

This paper illustrates the study of stable structural, electronic and optical properties of carbon mono oxide (CO) molecule adsorbed on pure anatase TiO2 (101) surface and CO molecule adsorbed on defective anatase TiO2 (101) surface containing oxygen (O) atom subsurface vacancy using first-principles study calculations based on density functional theory (DFT) method. A foreign molecule CO was added in the interstitial space of anatase TiO2 (101) surface. It was observed that, adsorption of CO molecule is not favorable on pure anatase TiO2 (101) surface, however adsorption process is improved when subsurface contains O atom vacancy defect. In case of anatase TiO2 (101) surface containing subsurface vacancy, adsorption process is exothermic, resulting in stable structures. The adsorption energies calculated for CO molecules adsorbed at O2c site, at defect site and at Ti5c site of anatase surface containing subsurface O vacancy are 0.16 eV (at O2c), 0.32 eV (at defect site) and 0.43 eV (at Ti5c) site. DOS and PDOS plots are calculated for all the structures. Results indicated that CO molecule adsorption introduces surface states at the Fermi energy level (EF) as shown in partial density of states (PDOS) plots. The dielectric matrix and absorption coefficient (α) for defective anatase TiO2 (101) surface, CO adsorbed at O2c site, at defect site and at Ti5C site of anatase TiO2 (101) surface containing O atom subsurface vacancy has been calculated within the random phase approximation (RPA) using VASP (Vienna ab-initio simulation package) code. It was observed that upon CO adsorption at defective anatase surface, real and imaginary dielectric function peaks were shifted towards lower energy level and a small absorption peak was observed at 1.1 eV energy level which is not present in case of defective anatase (101) surface. CO adsorption produces a red shift in the absorption spectrum of anatase TiO2 (101) surface containing subsurface O atom vacancy.

New determination of the fine structure constant from the electron value and QED.

PubMed

Gabrielse, G; Hanneke, D; Kinoshita, T; Nio, M; Odom, B

2006-07-21

Quantum electrodynamics (QED) predicts a relationship between the dimensionless magnetic moment of the electron (g) and the fine structure constant (alpha). A new measurement of g using a one-electron quantum cyclotron, together with a QED calculation involving 891 eighth-order Feynman diagrams, determine alpha(-1)=137.035 999 710 (96) [0.70 ppb]. The uncertainties are 10 times smaller than those of nearest rival methods that include atom-recoil measurements. Comparisons of measured and calculated g test QED most stringently, and set a limit on internal electron structure.

Mössbauer spectroscopy and the structure of interfaces on the atomic scale in metallic nanosystems

NASA Astrophysics Data System (ADS)

Uzdin, V. M.

2007-10-01

A microscopic model of the formation of an alloy on the interface has been constructed, which takes into account the exchange of atoms with the substrate atoms and the “floating up” of the latter into the upper layers in the process of epitaxial growth. The self-consistent calculations of atomic magnetic moments of spatially inhomogeneous structures obtained in this case are used for the interpretation of data of Mössbauer spectroscopy. The proposed scenario of mixing leads to the appearance of a preferred direction in the sample and the asymmetry of interfaces in the direction of epitaxial growth. In the multilayer M 1/ M 2 ( M 1,2 = Fe, Cr, V, Sn, or Ag) systems, this asymmetry makes it possible to understand the difference in the magnetic behavior of M 1-on M 2 and M 2-on- M 1 interfaces which has been observed experimentally. The correlation between the calculated distributions of magnetic moments and the measured distributions of hyperfine fields at iron atoms confirms the assumption about their proportionality for a broad class of metallic multilayer systems. However, a linear decrease of hyperfine fields at the 57Fe nuclei with increasing number of impurity atoms among the nearest and next-nearest neighbors is not confirmed for Fe/Cr systems, although is correct in Fe/V superlattices. In the Fe/Cr multilayer systems, the experimentally measured value of magnetoresistance grows with increasing fraction of the “floated up” atoms of 57Fe. Thus, it is the bulk scattering by impurity atoms that gives the basic contribution to the effect of giant magnetoresistance. The problem of the influence of mixing and adsorption of hydrogen in the vanadium layers on the state of the spin-density wave in V/Cr superlattices has been considered.

The π-Electron Delocalization in 2-Oxazolines Revisited: Quantification and Comparison with Its Analogue in Esters

PubMed Central

Fimberger, Martin; Luef, Klaus P.; Payerl, Claudia; Fischer, Roland C.; Stelzer, Franz; Kállay, Mihály; Wiesbrock, Frank

2015-01-01

The single crystal X-ray analysis of the ester-functionalized 2-oxazoline, methyl 3-(4,5-dihydrooxazol-2-yl)propanoate, revealed π-electron delocalization along the N–C–O segment in the 2-oxazoline pentacycle to significant extent, which is comparable to its counterpart along the O–C–O segment in the ester. Quantum chemical calculations based on the experimental X-ray geometry of the molecule supported the conjecture that the N–C–O segment has a delocalized electronic structure similar to an ester group. The calculated bond orders were 1.97 and 1.10 for the N=C and C–O bonds, and the computed partial charges for the nitrogen and oxygen atoms of −0.43 and −0.44 were almost identical. In the ester group, the bond orders were 1.94 and 1.18 for the C–O bonds, while the partial charges of the oxygen atom are −0.49 and −0.41, which demonstrates the similar electronic structure of the N–C–O and O–C–O segments. In 2-oxazolines, despite the higher electronegativity of the oxygen atom (compared to the nitrogen atom), the charges of the hetero atoms oxygen and nitrogen are equalized due to the delocalization, and it also means that a cationic attack on the nitrogen is possible, enabling regioselectivity during the initiation of the cationic ring-opening polymerization of 2-oxazoline monomers, which is a prerequisite for the synthesis of materials with well-defined structures. PMID:28184258

Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals.

PubMed

Sayfutyarova, Elvira R; Sun, Qiming; Chan, Garnet Kin-Lic; Knizia, Gerald

2017-09-12

We introduce the atomic valence active space (AVAS), a simple and well-defined automated technique for constructing active orbital spaces for use in multiconfiguration and multireference (MR) electronic structure calculations. Concretely, the technique constructs active molecular orbitals capable of describing all relevant electronic configurations emerging from a targeted set of atomic valence orbitals (e.g., the metal d orbitals in a coordination complex). This is achieved via a linear transformation of the occupied and unoccupied orbital spaces from an easily obtainable single-reference wave function (such as from a Hartree-Fock or Kohn-Sham calculations) based on projectors to targeted atomic valence orbitals. We discuss the premises, theory, and implementation of the idea, and several of its variations are tested. To investigate the performance and accuracy, we calculate the excitation energies for various transition-metal complexes in typical application scenarios. Additionally, we follow the homolytic bond breaking process of a Fenton reaction along its reaction coordinate. While the described AVAS technique is not a universal solution to the active space problem, its premises are fulfilled in many application scenarios of transition-metal chemistry and bond dissociation processes. In these cases the technique makes MR calculations easier to execute, easier to reproduce by any user, and simplifies the determination of the appropriate size of the active space required for accurate results.

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

McCurdy, C. W.; Rescigno, T. N.; Trevisan, C. S.

A dramatic symmetry breaking in K-shell photoionization of the CF 4 molecule in which a core-hole vacancy is created in one of four equivalent fluorine atoms is displayed in the molecular frame angular distribution of the photoelectrons. In observing the photoejected electron in coincidence with an F + atomic ion after Auger decay we see how selecting the dissociation path where the core hole was localized was almost exclusively on that atom. A combination of measurements and ab initio calculations of the photoelectron angular distribution in the frame of the recoiling CF 3 + and F + atoms elucidates themore » underlying physics that derives from the Ne-like valence structure of the F(1s -1) core-excited atom.« less

Synthesis of borophenes: Anisotropic, two-dimensional boron polymorphs.

PubMed

Mannix, Andrew J; Zhou, Xiang-Feng; Kiraly, Brian; Wood, Joshua D; Alducin, Diego; Myers, Benjamin D; Liu, Xiaolong; Fisher, Brandon L; Santiago, Ulises; Guest, Jeffrey R; Yacaman, Miguel Jose; Ponce, Arturo; Oganov, Artem R; Hersam, Mark C; Guisinger, Nathan P

2015-12-18

At the atomic-cluster scale, pure boron is markedly similar to carbon, forming simple planar molecules and cage-like fullerenes. Theoretical studies predict that two-dimensional (2D) boron sheets will adopt an atomic configuration similar to that of boron atomic clusters. We synthesized atomically thin, crystalline 2D boron sheets (i.e., borophene) on silver surfaces under ultrahigh-vacuum conditions. Atomic-scale characterization, supported by theoretical calculations, revealed structures reminiscent of fused boron clusters with multiple scales of anisotropic, out-of-plane buckling. Unlike bulk boron allotropes, borophene shows metallic characteristics that are consistent with predictions of a highly anisotropic, 2D metal. Copyright © 2015, American Association for the Advancement of Science.

Structural modifications of graphyne layers consisting of carbon atoms in the sp- and sp{sup 2}-hybridized states

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

Belenkov, E. A., E-mail: belenkov@csu.ru; Mavrinskii, V. V.; Belenkova, T. E.

2015-05-15

A model scheme is proposed for obtaining layered compounds consisting of carbon atoms in the sp- and (vnsp){sup 2}-hybridized states. This model is used to find the possibility of existing the following seven basic structural modifications of graphyne: α-, β1-, β2-, β3-, γ1-, γ2-, and γ3-graphyne. Polymorphic modifications β3 graphyne and γ3 graphyne are described. The basic structural modifications of graphyne contain diatomic polyyne chains and consist only of carbon atoms in two different crystallographically equivalent states. Other nonbasic structural modifications of graphyne can be formed via the elongation of the carbyne chains that connect three-coordinated carbon atoms and viamore » the formation of graphyne layers with a mixed structure consisting of basic layer fragments, such as α-β-graphyne, α-γ-graphyne, and β-γ-graphyne. The semiempirical quantum-mechanical MNDO, AM1, and PM3 methods and ab initio STO6-31G basis calculations are used to find geometrically optimized structures of the basic graphyne layers, their structural parameters, and energies of their sublimation. The energy of sublimation is found to be maximal for γ2-graphyne, which should be the most stable structural modification of graphyne.« less

Atomic partial charges on CH{sub 3}NH{sub 3}PbI{sub 3} from first-principles electronic structure calculations

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

Madjet, Mohamed E., E-mail: mmadjet@qf.org.qa; El-Mellouhi, Fedwa; Carignano, Marcelo A.

We calculated the partial charges in methylammonium (MA) lead-iodide perovskite CH{sub 3}NH{sub 3}PbI{sub 3} in its different crystalline phases using different first-principles electronic charge partitioning approaches, including the Bader, ChelpG, and density-derived electrostatic and chemical (DDEC) schemes. Among the three charge partitioning methods, the DDEC approach provides chemically intuitive and reliable atomic charges for this material, which consists of a mixture of transition metals, halide ions, and organic molecules. The DDEC charges are also found to be robust against the use of hybrid functionals and/or upon inclusion of spin–orbit coupling or dispersive interactions. We calculated explicitly the atomic charges withmore » a special focus on the dipole moment of the MA molecules within the perovskite structure. The value of the dipole moment of the MA is reduced with respect to the isolated molecule due to charge redistribution involving the inorganic cage. DDEC charges and dipole moment of the organic part remain nearly unchanged upon its rotation within the octahedral cavities. Our findings will be of both fundamental and practical importance, as the accurate and consistent determination of the atomic charges is important in order to understand the average equilibrium distribution of the electrons and to help in the development of force fields for larger scale atomistic simulations to describe static, dynamic, and thermodynamic properties of the material.« less

Direct quantitative identification of the “surface trans-effect”

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

Deimel, Peter S.; Bababrik, Reda M.; Wang, Bin

The strong parallels between coordination chemistry and adsorption on metal surfaces, with molecules and ligands forming local bonds to individual atoms within a metal surface, have been established over many years of study. The recently proposed “surface trans-effect” (STE) appears to be a further manifestation of this analogous behaviour, but so far the true nature of the modified molecule–metal surface bonding has been unclear. The STE could play an important role in determining the reactivities of surface-supported metal–organic complexes, influencing the design of systems for future applications. However, the current understanding of this effect is incomplete and lacks reliable structuralmore » parameters with which to benchmark theoretical calculations. Using X-ray standing waves, we demonstrate that ligation of ammonia and water to iron phthalocyanine (FePc) on Ag(111) increases the adsorption height of the central Fe atom; dispersion corrected density functional theory calculations accurately model this structural effect. The calculated charge redistribution in the FePc/H 2O electronic structure induced by adsorption shows an accumulation of charge along the σ-bonding direction between the surface, the Fe atom and the water molecule, similar to the redistribution caused by ammonia. Finally, this apparent σ-donor nature of the observed STE on Ag(111) is shown to involve bonding to the delocalised metal surface electrons rather than local bonding to one or more surface atoms, thus indicating that this is a true surface trans-effect.« less

Direct quantitative identification of the “surface trans-effect”

DOE PAGES

Deimel, Peter S.; Bababrik, Reda M.; Wang, Bin; ...

2016-06-09

The strong parallels between coordination chemistry and adsorption on metal surfaces, with molecules and ligands forming local bonds to individual atoms within a metal surface, have been established over many years of study. The recently proposed “surface trans-effect” (STE) appears to be a further manifestation of this analogous behaviour, but so far the true nature of the modified molecule–metal surface bonding has been unclear. The STE could play an important role in determining the reactivities of surface-supported metal–organic complexes, influencing the design of systems for future applications. However, the current understanding of this effect is incomplete and lacks reliable structuralmore » parameters with which to benchmark theoretical calculations. Using X-ray standing waves, we demonstrate that ligation of ammonia and water to iron phthalocyanine (FePc) on Ag(111) increases the adsorption height of the central Fe atom; dispersion corrected density functional theory calculations accurately model this structural effect. The calculated charge redistribution in the FePc/H 2O electronic structure induced by adsorption shows an accumulation of charge along the σ-bonding direction between the surface, the Fe atom and the water molecule, similar to the redistribution caused by ammonia. Finally, this apparent σ-donor nature of the observed STE on Ag(111) is shown to involve bonding to the delocalised metal surface electrons rather than local bonding to one or more surface atoms, thus indicating that this is a true surface trans-effect.« less

Thorium Copper Phosphides: More Diverse Metal-Phosphorus and Phosphorus-Phosphorus Interactions than U analogues

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

Jin, Geng Bang; Malliakas, Christos D.; Lin, Jian

To explore the chemical analogy between thorium and heavier actinides in soft anionic environments, three new thorium phosphides (ThCuP 2, beta-ThCu 2P 2, and ThCu 5P 3) have been prepared through solid-state reactions using CuI as a reaction promoter. The structure of ThCuP 2 can be described as a filled UTe 2-type with both dimeric P 2 4- and monomeric P 3- anions, in which Th is coordinated by eight P atoms in a bicapped trigonal prismatic arrangement and Cu is tetrahedrally coordinated by four P atoms. β-ThCu 2P 2 contains only P 3- anions and is isostructural with BaCumore » 2S 2. In this structure, Th is coordinated by seven P atoms in monocapped trigonal prismatic geometry and Cu is tetrahedrally coordinated by four P atoms. ThCu 5P 3 adopts the YCo 5P 3-type structure consisting of P 3- anions. This structure contains Th atoms coordinated by six P atoms in a trigonal prismatic arrangement and Cu atoms that are either tetrahedrally coordinated by four P atoms or square pyramidally coordinated by five P atoms. Electric resistivity measurements and electronic structure calculations on β-ThCu 2P 2 indicate a metal. These new compounds may be charge-balanced and formulated as Th 4+Cu +(P 2 4-) 1/2P 3-, Th 4+(Cu +) 2(P 3-) 2, and Th 4+(Cu +) 5(P 3-) 3, respectively. The structural, bonding, and property relationships between these Th compounds and related actinide and rare-earth phases are discussed. In conclusion, titled compounds display more diverse ion-ion interactions and different electronic structures from those in UCuP 2 and UCu 2P 2 that were synthesized under similar experimental conditions, suggesting divergence of thorium-phosphide chemistry from uranium-phosphide chemistry.« less

Thorium Copper Phosphides: More Diverse Metal-Phosphorus and Phosphorus-Phosphorus Interactions than U analogues

DOE PAGES

Jin, Geng Bang; Malliakas, Christos D.; Lin, Jian

2017-09-28

To explore the chemical analogy between thorium and heavier actinides in soft anionic environments, three new thorium phosphides (ThCuP 2, beta-ThCu 2P 2, and ThCu 5P 3) have been prepared through solid-state reactions using CuI as a reaction promoter. The structure of ThCuP 2 can be described as a filled UTe 2-type with both dimeric P 2 4- and monomeric P 3- anions, in which Th is coordinated by eight P atoms in a bicapped trigonal prismatic arrangement and Cu is tetrahedrally coordinated by four P atoms. β-ThCu 2P 2 contains only P 3- anions and is isostructural with BaCumore » 2S 2. In this structure, Th is coordinated by seven P atoms in monocapped trigonal prismatic geometry and Cu is tetrahedrally coordinated by four P atoms. ThCu 5P 3 adopts the YCo 5P 3-type structure consisting of P 3- anions. This structure contains Th atoms coordinated by six P atoms in a trigonal prismatic arrangement and Cu atoms that are either tetrahedrally coordinated by four P atoms or square pyramidally coordinated by five P atoms. Electric resistivity measurements and electronic structure calculations on β-ThCu 2P 2 indicate a metal. These new compounds may be charge-balanced and formulated as Th 4+Cu +(P 2 4-) 1/2P 3-, Th 4+(Cu +) 2(P 3-) 2, and Th 4+(Cu +) 5(P 3-) 3, respectively. The structural, bonding, and property relationships between these Th compounds and related actinide and rare-earth phases are discussed. In conclusion, titled compounds display more diverse ion-ion interactions and different electronic structures from those in UCuP 2 and UCu 2P 2 that were synthesized under similar experimental conditions, suggesting divergence of thorium-phosphide chemistry from uranium-phosphide chemistry.« less

Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface

PubMed Central

Sun, Ce; Paulauskas, Tadas; Sen, Fatih G.; Lian, Guoda; Wang, Jinguo; Buurma, Christopher; Chan, Maria K. Y.; Klie, Robert F.; Kim, Moon J.

2016-01-01

Extended defects are of considerable importance in determining the electronic properties of semiconductors, especially in photovoltaics (PVs), due to their effects on electron-hole recombination. We employ model systems to study the effects of dislocations in CdTe by constructing grain boundaries using wafer bonding. Atomic-resolution scanning transmission electron microscopy (STEM) of a [1–10]/(110) 4.8° tilt grain boundary reveals that the interface is composed of three distinct types of Lomer dislocations. Geometrical phase analysis is used to map strain fields, while STEM and density functional theory (DFT) modeling determine the atomic structure at the interface. The electronic structure of the dislocation cores calculated using DFT shows significant mid-gap states and different charge-channeling tendencies. Cl-doping is shown to reduce the midgap states, while maintaining the charge separation effects. This report offers novel avenues for exploring grain boundary effects in CdTe-based solar cells by fabricating controlled bicrystal interfaces and systematic atomic-scale analysis. PMID:27255415

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

DOE PAGES

Belianinov, Alex; Panchapakesan, G.; Lin, Wenzhi; ...

2014-12-02

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe0.55Se0.45 (Tc = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe1 x Sex structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified by their electronic signaturemore » and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Research Update: Spatially resolved mapping of electronic structure on atomic level by multivariate statistical analysis

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

Belianinov, Alex, E-mail: belianinova@ornl.gov; Ganesh, Panchapakesan; Lin, Wenzhi

2014-12-01

Atomic level spatial variability of electronic structure in Fe-based superconductor FeTe{sub 0.55}Se{sub 0.45} (T{sub c} = 15 K) is explored using current-imaging tunneling-spectroscopy. Multivariate statistical analysis of the data differentiates regions of dissimilar electronic behavior that can be identified with the segregation of chalcogen atoms, as well as boundaries between terminations and near neighbor interactions. Subsequent clustering analysis allows identification of the spatial localization of these dissimilar regions. Similar statistical analysis of modeled calculated density of states of chemically inhomogeneous FeTe{sub 1−x}Se{sub x} structures further confirms that the two types of chalcogens, i.e., Te and Se, can be identified bymore » their electronic signature and differentiated by their local chemical environment. This approach allows detailed chemical discrimination of the scanning tunneling microscopy data including separation of atomic identities, proximity, and local configuration effects and can be universally applicable to chemically and electronically inhomogeneous surfaces.« less

Atomic and electronic structure of Lomer dislocations at CdTe bicrystal interface

DOE PAGES

Sun, Ce; Paulauskas, Tadas; Sen, Fatih G.; ...

2016-06-03

Extended defects are of considerable importance in determining the electronic properties of semiconductors, especially in photovoltaics (PVs), due to their effects on electron-hole recombination. We employ model systems to study the effects of dislocations in CdTe by constructing grain boundaries using wafer bonding. Atomic-resolution scanning transmission electron microscopy (STEM) of a [1–10]/ (110) 4.8° tilt grain boundary reveals that the interface is composed of three distinct types of Lomer dislocations. Geometrical phase analysis is used to map strain fields, while STEM and density functional theory (DFT) modeling determine the atomic structure at the interface. The electronic structure of the dislocationmore » cores calculated using DFT shows significant mid-gap states and different charge-channeling tendencies. Cl-doping is shown to reduce the midgap states, while maintaining the charge separation effects. In conclusion, this report offers novel avenues for exploring grain boundary effects in CdTe-based solar cells by fabricating controlled bicrystal interfaces and systematic atomic-scale analysis.« less

First-principles calculations of phonons and Raman and infrared spectra in Cd-IV-N2 compounds

NASA Astrophysics Data System (ADS)

Lyu, Sai; Lambrecht, Walter R. L.

2018-05-01

A first-principles study of the phonons at the zone center in Cd-IV-N2 compounds is presented with IV = Si, Ge, Sn. The calculations are performed for the most likely Pbn21 crystal structure, after showing that it is indeed lower in total energy compared to the closely related Pmc21 structure. The normal mode frequencies are calculated using density functional perturbation theory and symmetry labeled. The longitudinal optical-transverse optical splittings are determined using the Born effective charges which are also reported. These are used to simulate polarized Raman spectra for different scattering configurations as well as the infrared absorption and reflection spectra. The mode frequencies are found to decrease from Si to Ge to Sn as group-IV cation. The spectra show a wide variety of number of prominent peaks and relative intensities in spite of the great similarities of these three materials. Phonon densities of states and their analysis in atom by atom contributions are also reported.

Edge-functionalization of armchair graphene nanoribbons with pentagonal-hexagonal edge structures.

PubMed

Ryou, Junga; Park, Jinwoo; Kim, Gunn; Hong, Suklyun

2017-06-21

Using density functional theory calculations, we have studied the edge-functionalization of armchair graphene nanoribbons (AGNRs) with pentagonal-hexagonal edge structures. While the AGNRs with pentagonal-hexagonal edge structures (labeled (5,6)-AGNRs) are metallic, the edge-functionalized (5,6)-AGNRs with substitutional atoms opens a band gap. We find that the band structures of edge-functionalized (5,6)-N-AGNRs by substitution resemble those of defect-free (N-1)-AGNR at the Γ point, whereas those at the X point show the original ones of the defect-free N-AGNR. The overall electronic structures of edge-functionalized (5,6)-AGNRs depend on the number of electrons, supplied by substitutional atoms, at the edges of functionalized (5,6)-AGNRs.

Ortho and para hydrogen dimers on G/SiC(0001): combined STM and DFT study.

PubMed

Merino, P; Švec, M; Martínez, J I; Mutombo, P; Gonzalez, C; Martín-Gago, J A; de Andres, P L; Jelinek, P

2015-01-01

The hydrogen (H) dimer structures formed upon room-temperature H adsorption on single layer graphene (SLG) grown on SiC(0001) are addressed using a combined theoretical-experimental approach. Our study includes density functional theory (DFT) calculations for the full (6√3 × 6√3)R30° unit cell of the SLG/SiC(0001) substrate and atomically resolved scanning tunneling microscopy images determining simultaneously the graphene lattice and the internal structure of the H adsorbates. We show that H atoms normally group in chemisorbed coupled structures of different sizes and orientations. We make an atomic scale determination of the most stable experimental geometries, the small dimers and ellipsoid-shaped features, and we assign them to hydrogen adsorbed in para dimers and ortho dimers configuration, respectively, through comparison with the theory.

Inelastic transport theory from first principles: Methodology and application to nanoscale devices

NASA Astrophysics Data System (ADS)

Frederiksen, Thomas; Paulsson, Magnus; Brandbyge, Mads; Jauho, Antti-Pekka

2007-05-01

We describe a first-principles method for calculating electronic structure, vibrational modes and frequencies, electron-phonon couplings, and inelastic electron transport properties of an atomic-scale device bridging two metallic contacts under nonequilibrium conditions. The method extends the density-functional codes SIESTA and TRANSIESTA that use atomic basis sets. The inelastic conductance characteristics are calculated using the nonequilibrium Green’s function formalism, and the electron-phonon interaction is addressed with perturbation theory up to the level of the self-consistent Born approximation. While these calculations often are computationally demanding, we show how they can be approximated by a simple and efficient lowest order expansion. Our method also addresses effects of energy dissipation and local heating of the junction via detailed calculations of the power flow. We demonstrate the developed procedures by considering inelastic transport through atomic gold wires of various lengths, thereby extending the results presented in Frederiksen [Phys. Rev. Lett. 93, 256601 (2004)]. To illustrate that the method applies more generally to molecular devices, we also calculate the inelastic current through different hydrocarbon molecules between gold electrodes. Both for the wires and the molecules our theory is in quantitative agreement with experiments, and characterizes the system-specific mode selectivity and local heating.

Characterization of Structural and Configurational Properties of DNA by Atomic Force Microscopy.

PubMed

Meroni, Alice; Lazzaro, Federico; Muzi-Falconi, Marco; Podestà, Alessandro

2018-01-01

We describe a method to extract quantitative information on DNA structural and configurational properties from high-resolution topographic maps recorded by atomic force microscopy (AFM). DNA molecules are deposited on mica surfaces from an aqueous solution, carefully dehydrated, and imaged in air in Tapping Mode. Upon extraction of the spatial coordinates of the DNA backbones from AFM images, several parameters characterizing DNA structure and configuration can be calculated. Here, we explain how to obtain the distribution of contour lengths, end-to-end distances, and gyration radii. This modular protocol can be also used to characterize other statistical parameters from AFM topographies.

XaNSoNS: GPU-accelerated simulator of diffraction patterns of nanoparticles

NASA Astrophysics Data System (ADS)

Neverov, V. S.

XaNSoNS is an open source software with GPU support, which simulates X-ray and neutron 1D (or 2D) diffraction patterns and pair-distribution functions (PDF) for amorphous or crystalline nanoparticles (up to ∼107 atoms) of heterogeneous structural content. Among the multiple parameters of the structure the user may specify atomic displacements, site occupancies, molecular displacements and molecular rotations. The software uses general equations nonspecific to crystalline structures to calculate the scattering intensity. It supports four major standards of parallel computing: MPI, OpenMP, Nvidia CUDA and OpenCL, enabling it to run on various architectures, from CPU-based HPCs to consumer-level GPUs.

Periodic Density Functional Theory Study of the Structure, Raman Spectrum, and Mechanical Properties of Schoepite Mineral.

PubMed

Colmenero, Francisco; Cobos, Joaquín; Timón, Vicente

2018-04-16

The structure and Raman spectrum of schoepite mineral, [(UO 2 ) 8 O 2 (OH) 12 ]·12H 2 O, was studied by means of theoretical calculations. The computations were carried out by using density functional theory with plane waves and pseudopotentials. A norm-conserving pseudopotential specific for the U atom developed in a previous work was employed. Because it was not possible to locate H atoms directly from X-ray diffraction (XRD) data by structure refinement in previous experimental studies, all of the positions of the H atoms in the full unit cell were determined theoretically. The structural results, including the lattice parameters, bond lengths, bond angles, and powder XRD pattern, were found to be in good agreement with their experimental counterparts. However, the calculations performed using the unit cell designed by Ostanin and Zeller in 2007, involving half of the atoms of the full unit cell, led to significant errors in the computed powder XRD pattern. Furthermore, Ostanin and Zeller's unit cell contains hydronium ions, H 3 O + , which are incompatible with the experimental information. Therefore, while the use of this schoepite model may be a very useful approximation requiring a much smaller amount of computational effort, the full unit cell should be used to study this mineral accurately. The Raman spectrum was also computed by means of density functional perturbation theory and compared with the experimental spectrum. The results were also in agreement with the experimental data. A normal-mode analysis of the theoretical spectra was performed to assign the main bands of the Raman spectrum. This assignment significantly improved the current empirical assignment of the bands of the Raman spectrum of schoepite mineral. In addition, the equation of state and elastic properties of this mineral were determined. The crystal structure of schoepite was found to be stable mechanically and dynamically. Schoepite can be described as a brittle material exhibiting small anisotropy and large compressibility in the direction perpendicular to the layers, which characterize its structure. The calculated bulk modulus, B, was ∼35 GPa.

Interplay of electronic, structural and magnetic properties as the driving feature of high-entropy CoCrFeNiPd alloys

NASA Astrophysics Data System (ADS)

Calvo-Dahlborg, M.; Cornide, J.; Tobola, J.; Nguyen-Manh, D.; Wróbel, J. S.; Juraszek, J.; Jouen, S.; Dahlborg, U.

2017-05-01

The structural and magnetic properties of CoCrFe y Ni and CoCrFeNi-Pd x alloys earlier investigated experimentally by x-ray and neutron diffraction techniques and magnetometry have been theoretically reproduced using two complementary approaches for electronic structure calculations, i.e. the Korringa-Kohn-Rostoker method with the coherent potential approximation (KKR-CPA) and implemented in the ab initio framework of density functional theory and the Vienna ab initio simulation package (VASP) for supercell models of high-entropy alloy (HEA) structures. The comparison between experimental results and calculations of the lattice constants by both calculation methods indicate that the structure of CoCrFe y Ni is well described by ordered fcc configurations. The values of local magnetic moments on Fe, Co, Cr, and Ni atoms depend not only on the Pd concentration but on chemical disordering. In the case of the CoCrFeNi-Pd x alloys, the KKR-CPA and the VASP calculations of disordered configurations reproduce the experimental values at 5 K up to equimolar composition and at 300 K above. The experimental values above the equimolar composition at 5 K are not satisfactorily reproduced by any of the calculations. The divergence between the experimental and calculated values is related to the variation of the ferromagnetic to paramagnetic transition temperature as a function of palladium content and to the existence of several phases, FeCoCr-rich above room temperature and FeCrPd-rich below, observed by diffraction and detected by microscopy and atom probe investigations. VASP calculations of a FeCrPd-rich phase effectively reproduced both the lattice constant and magnetization of the alloy above equimolar composition. An important conclusion of this work is that the combined analysis of the electronic, structural, and magnetic properties plays an important role in understanding the complexity of magnetic HEAs.

DGDFT: A massively parallel method for large scale density functional theory calculations.

PubMed

Hu, Wei; Lin, Lin; Yang, Chao

2015-09-28

We describe a massively parallel implementation of the recently developed discontinuous Galerkin density functional theory (DGDFT) method, for efficient large-scale Kohn-Sham DFT based electronic structure calculations. The DGDFT method uses adaptive local basis (ALB) functions generated on-the-fly during the self-consistent field iteration to represent the solution to the Kohn-Sham equations. The use of the ALB set provides a systematic way to improve the accuracy of the approximation. By using the pole expansion and selected inversion technique to compute electron density, energy, and atomic forces, we can make the computational complexity of DGDFT scale at most quadratically with respect to the number of electrons for both insulating and metallic systems. We show that for the two-dimensional (2D) phosphorene systems studied here, using 37 basis functions per atom allows us to reach an accuracy level of 1.3 × 10(-4) Hartree/atom in terms of the error of energy and 6.2 × 10(-4) Hartree/bohr in terms of the error of atomic force, respectively. DGDFT can achieve 80% parallel efficiency on 128,000 high performance computing cores when it is used to study the electronic structure of 2D phosphorene systems with 3500-14 000 atoms. This high parallel efficiency results from a two-level parallelization scheme that we will describe in detail.

Adsorption of alkali and alkaline earth metal atoms and dimers on monolayer germanium carbide

NASA Astrophysics Data System (ADS)

Gökçe, Aytaç Gürhan; Ersan, Fatih

2017-01-01

First-principles plane wave calculations have been performed to study the adsorption of alkali and alkaline earth metals on monolayer germanium carbide (GeC). We found that the favourable adsorption sites on GeC sheet for single alkali and alkaline earth adatoms are generally different from graphene or germanene. Among them, Mg, Na and their dimers have weakly bounded to GeC due to their closed valence electron shells, so they may have high mobility on GeC. Two different levels of adatom coverage (? and ?) have been investigated and we concluded that different electronic structures and magnetic moments for both coverages owing to alkali and alkaline earth atoms have long range electrostatic interactions. Lithium atom prefers to adsorbed on hollow site similar to other group-IV monolayers and the adsorption results in metallisation of GeC instead of semiconducting behaviour. Na and K adsorption can induce 1 ? total magnetic moment on GeC structures and they have shown semiconductor property which may have potential use in spintronic devices. We also showed that alkali or alkaline earth metal atoms can form dimer on GeC sheet. Calculated adsorption energies suggest that clustering of alkali and alkaline earth atoms is energetically favourable. All dimer adsorbed GeC systems have nonmagnetic semiconductor property with varying band gaps from 0.391 to 1.311 eV which are very suitable values for various device applications.

POLARIZED SCATTERING OF LIGHT FOR ARBITRARY MAGNETIC FIELDS WITH LEVEL-CROSSINGS FROM THE COMBINATION OF HYPERFINE AND FINE STRUCTURE SPLITTINGS

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

Sowmya, K.; Nagendra, K. N.; Sampoorna, M.

2015-12-01

Interference between magnetic substates of the hyperfine structure states belonging to different fine structure states of the same term influences the polarization for some of the diagnostically important lines of the Sun's spectrum, like the sodium and lithium doublets. The polarization signatures of this combined interference contain information on the properties of the solar magnetic fields. Motivated by this, in the present paper, we study the problem of polarized scattering on a two-term atom with hyperfine structure by accounting for the partial redistribution in the photon frequencies arising due to the Doppler motions of the atoms. We consider the scatteringmore » atoms to be under the influence of a magnetic field of arbitrary strength and develop a formalism based on the Kramers–Heisenberg approach to calculate the scattering cross section for this process. We explore the rich polarization effects that arise from various level-crossings in the Paschen–Back regime in a single scattering case using the lithium atomic system as a concrete example that is relevant to the Sun.« less

Self-consistent self-interaction corrected density functional theory calculations for atoms using Fermi-Löwdin orbitals: Optimized Fermi-orbital descriptors for Li-Kr

NASA Astrophysics Data System (ADS)

Kao, Der-you; Withanage, Kushantha; Hahn, Torsten; Batool, Javaria; Kortus, Jens; Jackson, Koblar

2017-10-01

In the Fermi-Löwdin orbital method for implementing self-interaction corrections (FLO-SIC) in density functional theory (DFT), the local orbitals used to make the corrections are generated in a unitary-invariant scheme via the choice of the Fermi orbital descriptors (FODs). These are M positions in 3-d space (for an M-electron system) that can be loosely thought of as classical electron positions. The orbitals that minimize the DFT energy including the SIC are obtained by finding optimal positions for the FODs. In this paper, we present optimized FODs for the atoms from Li-Kr obtained using an unbiased search method and self-consistent FLO-SIC calculations. The FOD arrangements display a clear shell structure that reflects the principal quantum numbers of the orbitals. We describe trends in the FOD arrangements as a function of atomic number. FLO-SIC total energies for the atoms are presented and are shown to be in close agreement with the results of previous SIC calculations that imposed explicit constraints to determine the optimal local orbitals, suggesting that FLO-SIC yields the same solutions for atoms as these computationally demanding earlier methods, without invoking the constraints.

Sizable band gap in organometallic topological insulator

NASA Astrophysics Data System (ADS)

Derakhshan, V.; Ketabi, S. A.

2017-01-01

Based on first principle calculation when Ceperley-Alder and Perdew-Burke-Ernzerh type exchange-correlation energy functional were adopted to LSDA and GGA calculation, electronic properties of organometallic honeycomb lattice as a two-dimensional topological insulator was calculated. In the presence of spin-orbit interaction bulk band gap of organometallic lattice with heavy metals such as Au, Hg, Pt and Tl atoms were investigated. Our results show that the organometallic topological insulator which is made of Mercury atom shows the wide bulk band gap of about ∼120 meV. Moreover, by fitting the conduction and valence bands to the band-structure which are produced by Density Functional Theory, spin-orbit interaction parameters were extracted. Based on calculated parameters, gapless edge states within bulk insulating gap are indeed found for finite width strip of two-dimensional organometallic topological insulators.

Magnetic ground state and electronic structure of CeRu(2)Al(10).

PubMed

Goraus, Jerzy; Ślebarski, Andrzej

2012-03-07

We present a combined theoretical and experimental study of the electronic structure for CeRu(2)Al(10) based on ab initio band structure calculations and x-ray photoemission spectroscopy (XPS) data. Our calculations were performed for the base unit cell and for the hypothetical unit cell which enables antiferromagnetic ordering. The stability of the magnetic phase was investigated within fixed spin moment calculations. When additional 4f correlations are not included in the LSDA C U approach, CeRu(2)Al(10) exhibits an unstable magnetic configuration with the difference in total energy per unit cell between the weakly magnetic state and the non-magnetic one of the order ~0.3 meV. We found that Coulomb correlations among 4f electrons, when they are included in the LSDA C U approach, stabilize the magnetic structure. In the weakly correlated system (small U) an antiferromagnetic (AFM) ground state with the lowest total energy is preferred. The situation is, however, the opposite when the 4f correlations are strong. In this case the ferromagnetic (FM) ground state is preferred. By comparing our calculations with the experimental data we conclude that the 4f correlations in CeRu(2)Al(10) are weak. We also carried out a structural relaxation of atomic positions within the Cmcm unit cell and we found that the Al atoms exhibit noticeable displacement from their positions known from x-ray diffraction (XRD) analysis.

Structure determination of Ba5AlF13 by coupling electron, synchrotron and neutron powder diffraction, solid-state NMR and ab initio calculations.

PubMed

Martineau, Charlotte; Allix, Mathieu; Suchomel, Matthew R; Porcher, Florence; Vivet, François; Legein, Christophe; Body, Monique; Massiot, Dominique; Taulelle, Francis; Fayon, Franck

2016-10-04

The room temperature structure of Ba 5 AlF 13 has been investigated by coupling electron, synchrotron and neutron powder diffraction, solid-state high-resolution NMR ( 19 F and 27 Al) and first principles calculations. An initial structural model has been obtained from electron and synchrotron powder diffraction data, and its main features have been confirmed by one- and two-dimensional NMR measurements. However, DFT GIPAW calculations of the 19 F isotropic shieldings revealed an inaccurate location of one fluorine site (F3, site 8a), which exhibited unusual long F-Ba distances. The atomic arrangement was reinvestigated using neutron powder diffraction data. Subsequent Fourier maps showed that this fluorine atom occupies a crystallographic site of lower symmetry (32e) with partial occupancy (25%). GIPAW computations of the NMR parameters validate the refined structural model, ruling out the presence of local static disorder and indicating that the partial occupancy of this F site reflects a local motional process. Visualisation of the dynamic process was then obtained from the Rietveld refinement of neutron diffraction data using an anharmonic description of the displacement parameters to account for the thermal motion of the mobile fluorine. The whole ensemble of powder diffraction and NMR data, coupled with first principles calculations, allowed drawing an accurate structural model of Ba 5 AlF 13 , including site-specific dynamical disorder in the fluorine sub-network.

Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

NASA Astrophysics Data System (ADS)

Nistor, Razvan A.

The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high-temperature superconducting materials in order to parameterize the apparently large nonlinear electron-phonon coupling. Thirdly, ab initio simulations are used to investigate the role of pressure-driven structural re-organization in the crystalline-to-amorphous (or, metallic-to-insulating) transition of a common binary phase-change material composed of Ge and Sb. Practical applications of each topic will be discussed. Keywords. Charge-equilibration methods, molecular dynamics, electronic structure calculations, ab initio simulations, high-temperature superconductors, phase-change materials.

The study on molecular structure and microbiological activity of alkali metal 3-hydroxyphenylycetates

NASA Astrophysics Data System (ADS)

Samsonowicz, M.; Regulska, E.; Kowczyk-Sadowy, M.; Butarewicz, A.; Lewandowski, W.

2017-10-01

The biological activity of chemical compounds depends on their molecular structure. In this paper molecular structure of 3-hydroxyphenylacetates in comparison to 3-hydroxyphenylacetic acid was studied. FT-IR, FT-Raman and NMR spectroscopy and density functional theory (DFT) calculations was used. The B3LYP/6-311++G(d,p) hybrid functional method was used to calculate optimized geometrical structures of studied compounds. The Mulliken, APT, MK, ChelpG and NBO atomic charges as well as dipole moment and energy values were calculated. Theoretical chemical shifts in NMR spectra and the wavenumbers and intensities of the bands in vibrational spectra were analyzed. Calculated parameters were compared to experimental characteristic of studied compounds. Microbiological analysis of studied compounds was performed relative to: Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli and Klebsiella oxytoca. The relationship between spectroscopic and structure parameters of studied compounds in regard to their activity was analyzed.

EON: software for long time simulations of atomic scale systems

NASA Astrophysics Data System (ADS)

Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

2014-07-01

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

Three-dimensional structure of interleukin 8 in solution.

PubMed

Clore, G M; Appella, E; Yamada, M; Matsushima, K; Gronenborn, A M

1990-02-20

The solution structure of the interleukin 8 (IL-8) dimer has been solved by nuclear magnetic resonance (NMR) spectroscopy and hybrid distance geometry-dynamical simulated annealing calculations. The structure determination is based on a total of 1880 experimental distance restraints (of which 82 are intersubunit) and 362 torsion angle restraints (comprising phi, psi, and chi 1 torsion angles). A total of 30 simulated annealing structures were calculated, and the atomic rms distribution about the mean coordinate positions (excluding residues 1-5 of each subunit) is 0.41 +/- 0.08 A for the backbone atoms and 0.90 +/- 0.08 A for all atoms. The three-dimensional solution structure of the IL-8 dimer reveals a structural motif in which two symmetry-related antiparallel alpha-helices, approximately 24 A long and separated by about 14 A, lie on top of a six-stranded antiparallel beta-sheet platform derived from two three-stranded Greek keys, one from each monomer unit. The general architecture is similar to that of the alpha 1/alpha 2 domains of the human class I histocompatibility antigen HLA-A2. It is suggested that the two alpha-helices form the binding site for the cellular receptor and that the specificity of IL-8, as well as that of a number of related proteins involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response, is achieved by the distinct distribution of charged and polar residues at the surface of the helices.

Pressure dependence of electron density distribution and d-p-π hybridization in titanate perovskite ferroelectrics

NASA Astrophysics Data System (ADS)

Yamanaka, Takamitsu; Nakamoto, Yuki; Ahart, Muhtar; Mao, Ho-kwang

2018-04-01

Electron density distributions of PbTi O3 , BaTi O3 , and SrTi O3 were determined by synchrotron x-ray powder diffraction up to 55 GPa at 300 K and ab initio quantum chemical molecular orbital (MO) calculations, together with a combination of maximum entropy method calculations. The intensity profiles of Bragg peaks reveal split atoms in both ferroelectric PbTi O3 and BaTi O3 , reflecting the two possible positions occupied by the Ti atom. The experimentally obtained atomic structure factor was used for the determination of the deformation in electron density and the d-p-π hybridization between dx z (and dy z) of Ti and px (and py) of O in the Ti-O bond. Ab initio MO calculations proved the change of the molecular orbital coupling and of Mulliken charges with a structure transformation. The Mulliken charge of Ti in the Ti O6 octahedron increased in the ionicity with increasing pressure in the cubic phase. The bonding nature is changed with a decrease in the hybridization of the Ti-O bond and the localization of the electron density with increasing pressure. The hybridization decreases with pressure and disappears in the cubic paraelectric phase, which has a much more localized electron density distribution.