Ab-initio phasing in protein crystallography
NASA Astrophysics Data System (ADS)
van der Plas, J. L.; Millane, Rick P.
2000-11-01
The central problem in the determination of protein structures form x-ray diffraction dada (x-ray crystallography) corresponds to a phase retrieval problem with undersampled amplitude data. Algorithms for this problem that have an increased radius of convergence have the potential for reducing the amount of experimental work, and cost, involved in determining protein structures. We describe such an algorithm. Application of the algorithm to a simulated crystallographic problem shows that it converges to the correct solution, with no initial phase information, where currently used algorithms fail. The results lend support to the possibility of ab initio phasing in protein crystallography.
Ab initio phase diagram of iridium
NASA Astrophysics Data System (ADS)
Burakovsky, L.; Burakovsky, N.; Cawkwell, M. J.; Preston, D. L.; Errandonea, D.; Simak, S. I.
2016-09-01
The phase diagram of iridium is investigated using the Z methodology. The Z methodology is a technique for phase diagram studies that combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. In the direct Z method, the solid phases along the melting curve are determined by comparing the solid-liquid equilibrium boundaries of candidate crystal structures. The inverse Z method involves quenching the liquid into the most stable solid phase at various temperatures and pressures to locate a solid-solid boundary. Although excellent agreement with the available experimental data (to ≲65 GPa) is found for the equation of state (EOS) of Ir, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes our ab initio data to higher pressure (P ) . Our results suggest the existence of a random-stacking hexagonal close-packed structure of iridium at high P . We offer an explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.
Ab Initio Study of Phase Equilibria in TiCx
NASA Astrophysics Data System (ADS)
Korzhavyi, P. A.; Pourovskii, L. V.; Hugosson, H. W.; Ruban, A. V.; Johansson, B.
2002-01-01
The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx ( x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies ( Ti2C, Ti3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures.
Uniaxial phase transition in Si: Ab initio calculations
NASA Astrophysics Data System (ADS)
Cheng, C.
2003-04-01
Based on a previously proposed thermodynamic analysis, [C. Cheng, W. H. Huang, and H. J. Li, Phys. Rev. B 63, 153202 (2001)] we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, βSn, simple-hexagonal (sh), simple-cubic, and hexagonal closed-packed structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different contributions to the relative phase stability, we identified the most important factors in reducing the phase-transition pressures at uniaxial compression. We also show that it is possible to have phase transitions occur only when the phases are under uniaxial compression, in spite of no phase transition when under hydrostatic compression. Taking all five phases into consideration, the phase diagram at uniaxial compression was constructed for pressures up to 20 GPa. The stable phases were found to be diamond, βSn, and sh structures, i.e., the same as those when under hydrostatic condition. According to the phase diagram, direct phase transition from the diamond to the sh phase is possible if the applied uniaxial pressures, on increasing, satisfy the condition Px>Pz. Similarly, the sh-to-βSn transition on increasing pressures is also possible if the applied uniaxial pressures are varied from the condition of Px>Pz, on which the phase of sh is stable to the condition Px
Volumic omit maps in ab initio dual-space phasing.
Oszlányi, Gábor; Sütő, András
2016-07-01
Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed.
2014-08-20
Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules The focus of this research was to apply efficient...methods for using ab initio potential energy surfaces (PESs) computed with high levels of quantum chemistry theory to predict chemical reaction properties...in non peer-reviewed journals: Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules Report
Ab initio molecular dynamics simulation of pressure-induced phase transformation in BeO
Xiao, Haiyan; Duan, G; Zu, X T; Weber, William J
2011-01-01
Ab initio molecular dynamics (MD) method has been used to study high pressure-induced phase transformation in BeO based on the local density approximation (LDA) and the generalized gradient approximation (GGA). Both methods show that the wurtzite (WZ) and zinc blende (ZB) BeO transforms to the rocksalt (RS) structure smoothly at high pressure. The transition pressures obtained from the LDA method are about 40 GPa larger than the GGA result for both WZ {yields} RS and ZB {yields} RS phase transformations, and the phase transformation mechanisms revealed by the LDA and GGA methods are different. For WZ {yields} RS phase transformations both mechanisms obtained from the LDA and GGA methods are not comparable to the previous ab initio MD simulations of WZ BeO at 700 GPa based on the GGA method. It is suggested that the phase transformation mechanisms of BeO revealed by the ab initio MD simulations are affected remarkably by the exchange-correlation functional employed and the way of applying pressure.
Ab initio simulations of phase stability and martensitic transitions in NiTi
NASA Astrophysics Data System (ADS)
Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.
2016-12-01
For NiTi-based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. We show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing phase transformation temperatures is discussed.
Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi
NASA Technical Reports Server (NTRS)
Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.
2016-01-01
For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.
Progress in low-resolution ab initio phasing with CrowdPhase
Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.
2016-01-01
Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data. PMID:26960132
Progress in low-resolution ab initio phasing with CrowdPhase.
Jorda, Julien; Sawaya, Michael R; Yeates, Todd O
2016-03-01
Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.
Progress in low-resolution ab initio phasing with CrowdPhase
Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.
2016-03-01
Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented.more » Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Lastly, performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.« less
Novel high-pressure phase of ZrO{sub 2}: An ab initio prediction
Durandurdu, Murat
2015-10-15
The high-pressure behavior of the orthorhombic cotunnite type ZrO{sub 2} is explored using an ab initio constant pressure technique. For the first time, a novel hexagonal phase (Ni{sub 2}In type) within P6{sub 3}/mmc symmetry is predicted through the simulation. The Ni{sub 2}In type crystal is the densest high-pressure phase of ZrO{sub 2} proposed so far and has not been observed in other metal dioxides at high pressure before. The phase transformation is accompanied by a small volume drop and likely to occur around 380 GPa in experiment. - Graphical abstract: Post-cotunnite Ni{sub 2}In type hexagonal phase forms in zirconia at high pressure. - Highlights: • A post-cotunnite phase is predicted for ZrO{sub 2} through an ab initio simulation. • Cotunnite ZrO{sub 2} adopts the Ni{sub 2}In type structure at high pressure. • The Ni{sub 2}In type structure is the densest high-pressure phase of ZrO{sub 2} proposed so far. • The preferred mechanism in ZrO{sub 2} differs from the other metal dioxides.
Superconductivity in an expanded phase of ZnO: an ab initio study
NASA Astrophysics Data System (ADS)
Hapiuk, D.; Marques, M. A. L.; Mélinon, P.; Botti, S.; Masenelli, B.; Flores-Livas, J. A.
2015-04-01
It is known that covalent semiconductors become superconducting if conveniently doped with large concentration of impurities. In this article we investigate, using ab initio methods, if the same situation is possible for an ionic, large-band gap semiconductor such as ZnO. We concentrate on the cage-like sodalite phase, with very similar electronic and phononic properties as wurtzite ZnO, but allow for endohedral doping of the cages. We find that sodalite ZnO becomes superconducting for a variety of dopants, reaching a maximum critical temperature of 7 K. This value is comparable to the transition temperatures of doped silicon clathrates, cubic silicon, and diamond.
Ab initio study of the anharmonic lattice dynamics of iron at the γ -δ phase transition
NASA Astrophysics Data System (ADS)
Lian, Chao-Sheng; Wang, Jian-Tao; Chen, Changfeng
2015-11-01
We report calculations of phonon dispersions of iron (Fe) at its γ -δ phase transition using a self-consistent ab initio lattice dynamical method in conjunction with an effective magnetic force approach via the antiferromagnetic approximation. Our results show that anharmonic phonon-phonon interactions play a crucial role in stabilizing the δ -Fe phase in the open bcc lattice. In contrast, the lattice dynamics of the close-packed fcc γ -Fe phase are dominated by magnetic interactions. Simultaneous considerations of the lattice anharmonic and magnetic interactions produced temperature-dependent phonon dispersions for δ -Fe and γ -Fe phases in excellent agreement with recent experimental measurements. The present results highlight the key role of lattice anharmonicity in determining the structural stability of iron at high temperatures, which has significant implications for other high-temperature paramagnetic metals like Ce and Pu.
Equation of state and phase diagram of ammonia at high pressures from ab initio simulations.
Bethkenhagen, Mandy; French, Martin; Redmer, Ronald
2013-06-21
We present an equation of state as well as a phase diagram of ammonia at high pressures and high temperatures derived from ab initio molecular dynamics simulations. The predicted phases of ammonia are characterized by analyzing diffusion coefficients and structural properties. Both the phase diagram and the subsequently computed Hugoniot curves are compared to experimental results. Furthermore, we discuss two methods that allow us to take into account nuclear quantum effects, which are of considerable importance in molecular fluids. Our data cover pressures up to 330 GPa and a temperature range from 500 K to 10,000 K. This regime is of great interest for interior models of the giant planets Uranus and Neptune, which contain, besides water and methane, significant amounts of ammonia.
Ab initio Prediction of Martensitic and Intermartensitic Phase Boundaries in Ni-Mn-Ga.
Dutta, B; Çakır, A; Giacobbe, C; Al-Zubi, A; Hickel, T; Acet, M; Neugebauer, J
2016-01-15
Despite the importance of martensitic transformations of Ni-Mn-Ga Heusler alloys for their magnetocaloric and shape-memory properties, the martensitic part of their phase diagrams is not well determined. Using an ab initio approach that includes the interplay of lattice and vibrational degrees of freedom we identify an intermartensitic transformation between a modulated and a nonmodulated phase as a function of excess Ni and Mn content. Based on an evaluation of the theoretical findings and experimental x-ray diffraction data for Mn-rich alloys, we are able to predict the phase diagram for Ni-rich alloys. In contrast to other mechanisms discussed for various material systems in the literature, we herewith show that the intermartensitic transformation can be understood solely using thermodynamic concepts.
Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.
Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R
2015-07-08
We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching.
Ab initio energetics for modeling phase stability of the Np-U system
NASA Astrophysics Data System (ADS)
Xie, Wei; Chang, Y. Austin; Morgan, Dane
2016-10-01
The Np-U system has been rarely studied despite this alloy being a key binary subsystem of metallic nuclear fuels. This study aims to further the understanding of the phase stability of the Np-U system through ab initio calculations. We first examined an existing CALPHAD model based on available experimental phase boundary data. We then focused on phases of which the CALPHAD model reproduces reasonably the experimental data and examined if values of the effective Hubbard U (i.e., Ueff) parameter for Np and U fitted previously in the Np-Zr and U-Zr systems are also applicable to the Np-U system, using CALPHAD predicted enthalpies as references. We found that in general DFT + U predicts improved or at least similarly accurate enthalpies compared to standard DFT when the Ueff's used are within the ranges of single-structure optimized Ueff's (0.65-0.9 eV for Np and 1-1.5 eV for U)-for example, the multi-structure optimized Ueff's (0.9 eV for Np and 1.24 eV for U)-determined in our previous U-Zr and Np-Zr studies. Finally, we focused on the intermediate phase ζ(Np,U), which at present is poorly characterized by experiments and unsatisfactorily described in the CALPHAD model. Based on ab initio calculated formation enthalpies for ordered end members and the compound energy formalism, we predicted its site occupations as functions of composition and temperature. Our study demonstrated that Ueff's fitted for U and Np determined in the U-Zr and Np-Zr systems may be transferable to the Np-U system and also provided new prediction of the site occupations for ζ(Np,U), which may serve as reference for future experimental and modeling study of the Np-U system.
NASA Astrophysics Data System (ADS)
Clementi, Enrico; Corongiu, Giorgina; Sciortino, Francesco
1993-08-01
Results are presented on the reliability of the ab initio, polarizable and flexible Nieser—Corongiu—Clementi potential at describing the structure and dynamics of the liquid and solid phases of water. For both structural and dynamic quantities the agreement between experimental and numerical results is good. A "substance" very similar to "real water" has indeed been created on the basis of ab initio quantum mechanical calculations. This gives confidence in the use of the simulations to examine features that are not directly measurable, but are of central importance in the understanding of water structure and dynamics.
High-pressure phase transitions of solid HF, HCl, and HBr: An ab initio evolutionary study
NASA Astrophysics Data System (ADS)
Zhang, Lijun; Wang, Yanchao; Zhang, Xinxin; Ma, Yanming
2010-07-01
Using ab initio evolutionary methodology for structure predictions, we investigated the high-pressure phase diagram for solid-state HF, HCl, and HBr at zero temperature. The ambient-pressure chain-type Cmc21 structure and sequent high-pressure symmetric hydrogen-bonded Cmcm structure were successfully reproduced by structural simulations with the only known information of chemical compositions. We have also presented insight into the underlying mechanism of hydrogen-bond symmetrization at the Cmc21→Cmcm transformation, by analysis of electron localization functions, potential wells, and zone-center phonons with pressure. At higher pressures, it was predicted that HF transforms from the Cmcm phase to another chain-type Pnma structure at ˜143GPa while the post- Cmcm phase of HCl and HBr adopts an intriguing triclinic P1¯ structure at above 108 GPa and 59 GPa, respectively, which consists of nearly planar squares resembling the ambient phase of HI. The newly predicted high-pressure phases of these halides all contain symmetric hydrogen bonds and satisfy lattice dynamical stability. As for the earlier proposed dissociation of HBr, we found that this can only occur at rather high pressures (above 120 GPa) with the formation of monatomic Br and solid H2 .
An ab initio molecular dynamics study of iron phases at high pressure and temperature
NASA Astrophysics Data System (ADS)
Belonoshko, A. B.; Arapan, S.; Rosengren, A.
2011-12-01
The crystal structure of iron, the major component of the Earth’s inner core (IC), is unknown for the IC high pressure (P; 3.3-3.6 Mbar) and temperature (T; 5000-7000 K). There is mounting evidence that the hexagonal close-packed (hcp) phase of iron, stable at the high P of the IC and a low T, might be unstable under the IC conditions due to the impact of high T and impurities. Experiments at the IC P and T are difficult and do not provide a conclusive answer as regards the iron stability at the pressure of the IC and temperatures close to the iron melting curve. Recent theory provides contradictory results regarding the nature of the stable Fe phase. We investigated the possibility of body-centered cubic (bcc) phase stabilization at the P and T in the vicinity of the Fe melting curve by using ab initio molecular dynamics. Thermodynamic calculations, relying on the model of uncorrelated harmonic oscillators, provide nearly identical free energies within the error bars of our calculations. However, direct simulation of iron crystallization demonstrates that liquid iron freezes in the bcc structure at the P of the IC and T = 6000 K. All attempts to grow the hcp phase from the liquid failed. The mechanism of bcc stabilization is explained. This resolves most of the earlier confusion.
The structure of the 1H-imidazol-3-ium lawsonate salt aided by ab initio gas-phase calculations.
Ribeiro, Marcos Antônio; Oliveira, Willian Xerxes Coelho; Stumpf, Humberto Osório; Pinheiro, Carlos Basílio
2013-04-01
For the new organic salt 1H-imidazol-3-ium 1,4-dioxo-1,4-dihydronaphthalen-2-olate, C3H5N2(+)·C10H5O3(-), ab initio calculations of the gas-phase structures of the lawsonate and imidazolium ions were performed to help in the interpretation of the structural features observed. Three different types of hydrogen bond are responsible for the three-dimensional packing of the salt.
NASA Astrophysics Data System (ADS)
Jameson, Cynthia J.; de Dios, Angel C.
1992-07-01
The chemical shifts observed in nuclear magnetic resonance experiments are the differences in shielding of the nuclear spin in different electronic environments. These are known to depend on intermolecular interactions as evidenced by density-dependent chemical shifts in the gas phase, gas-to-liquid shifts, and adsorption shifts on surfaces. We present the results of the first ab initio intermolecular chemical shielding function calculated for a pair of interacting atoms for a wide range of internuclear separations. We used the localized orbital local origin (LORG) approach of Hansen and Bouman and also investigated the second-order electron correlation contributions using second-order LORG (SOLO). The 39Ar shielding in Ar2 passes through zero at some very short distance, going through a minimum, and asymptotically approaches zero at larger separations. The 21Ne shielding function in Ne2 has a similar shape. The Drude model suggests a method of scaling that portion of the shielding function that is weighted most heavily by exp[-V(R)/kT]. The scaling factors, which have been verified in the comparison of 21Ne in Ne2 against 39Ar in Ar2 ab initio results, allows us to project out from the same 39Ar in Ar2 ab initio values the appropriate 129Xe shielding functions in the Xe-Ar, Xe-Kr, and Xe-Xe interacting pairs. These functions lead to temperature-dependent second virial coefficients of chemical shielding which agree with experiments in the gas phase. Ab initio calculations of 39Ar shielding in clusters of argon are used to model the observed 129Xe chemical shifts of Xe, Xe2,...,Xe8 trapped in the cages of zeolite NaA.
Velaga, Srinath C; Anderson, Brian J
2014-01-16
Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations.
NASA Astrophysics Data System (ADS)
Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.
2017-01-01
Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.
Ab initio protein phasing at 1.4 A resolution: the new phasing approach of SIR2003-N.
Burla, Maria C; Carrozzini, Benedetta; Caliandro, Rocco; Cascarano, Giovanni L; De Caro, Liberato; Giacovazzo, Carmelo; Polidori, Giampiero
2003-11-01
New algorithms for solving ab initio protein crystal structures have been identified and implemented in a modified version of the program SIR2002. They succeed in solving numerous protein structures diffracting at atomic resolution; the solution was also attained when data were cut at 1.4 A resolution. The direct-space refinement procedure of SIR2003-N takes advantage of using the envelope of the protein, calculated during the phasing process from the current phases. The electron-density map is modified by assuming different weights for pixels within the envelope or out of it, so tentatively depleting the intensities of the false peaks. The map is then inverted and the resulting phase sets may improve their values. The new phasing strategy is also based on an optimal use of some figures of merit, one of which may be successfully applied in the early stages of the phasing process: only the most promising trials are submitted to the complete phasing procedure, so saving computing time. SIR2003-N has been successfully applied also in solving some protein structures diffracting at 1.4-1.5 A resolution.
Progress in low-resolution ab initio phasing with CrowdPhase
Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.
2016-03-01
Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Lastly, performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.
Ab-initio atomic level stresses in Cu-Zr crystal, liquid and glass phases
NASA Astrophysics Data System (ADS)
Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi
2013-03-01
The Cu-Zr system provides interesting playground for the study of glass structure, stability, and formability and liquid dynamics. Glasses form over a wide range of concentrations while they compete against various intermetallic compounds. We have calculated from first-principles the atomic level stresses, a new tool to characterize materials, within the local approximation to Density Functional Theory (DFT) for Cu-Zr glasses and compounds from low temperature to 4500K. Comparisons between ordered crystalline compounds and liquids and glasses allow us to relate atomic level stress to relaxation of chemical short-range order and structural relaxation. The results are counter-intuitive at times; a smaller atom is under higher compressive pressure, whereas geometrically they should be under tension. Ab-initio calculations were done using Vienna Ab-initio Simulation Package (VASP) and Locally Self-consistent Multiple Scattering (LSMS) codes. The work at the University of Tennessee and Oak Ridge National laboratory was supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Science and Engineering Division.
Ab Initio Surface Phase Diagrams for Coadsorption of Aromatics and Hydrogen on the Pt(111) Surface
Ferguson, Glen Allen; Vorotnikov, Vassili; Wunder, Nicholas; ...
2016-11-02
Supported metal catalysts are commonly used for the hydrogenation and deoxygenation of biomass-derived aromatic compounds in catalytic fast pyrolysis. To date, the substrate-adsorbate interactions under reaction conditions crucial to these processes remain poorly understood, yet understanding this is critical to constructing detailed mechanistic models of the reactions important to catalytic fast pyrolysis. Density functional theory (DFT) has been used in identifying mechanistic details, but many of these works assume surface models that are not representative of realistic conditions, for example, under which the surface is covered with some concentration of hydrogen and aromatic compounds. In this study, we investigate hydrogen-guaiacolmore » coadsorption on Pt(111) using van der Waals-corrected DFT and ab initio thermodynamics over a range of temperatures and pressures relevant to bio-oil upgrading. We find that relative coverage of hydrogen and guaiacol is strongly dependent on the temperature and pressure of the system. Under conditions relevant to ex situ catalytic fast pyrolysis (CFP; 620-730 K, 1-10 bar), guaiacol and hydrogen chemisorb to the surface with a submonolayer hydrogen (~0.44 ML H), while under conditions relevant to hydrotreating (470-580 K, 10-200 bar), the surface exhibits a full-monolayer hydrogen coverage with guaiacol physisorbed to the surface. These results correlate with experimentally observed selectivities, which show ring saturation to methoxycyclohexanol at hydrotreating conditions and deoxygenation to phenol at CFP-relevant conditions. Additionally, the vibrational energy of the adsorbates on the surface significantly contributes to surface energy at higher coverage. Ignoring this contribution results in not only quantitatively, but also qualitatively incorrect interpretation of coadsorption, shifting the phase boundaries by more than 200 K and ~10-20 bar and predicting no guaiacol adsorption under CFP and hydrotreating conditions
Ab Initio Surface Phase Diagrams for Coadsorption of Aromatics and Hydrogen on the Pt(111) Surface
Ferguson, Glen Allen; Vorotnikov, Vassili; Wunder, Nicholas; Clark, Jared; Gruchalla, Kenny; Bartholomew, Timothy; Robichaud, David J.; Beckham, Gregg T.
2016-11-02
Supported metal catalysts are commonly used for the hydrogenation and deoxygenation of biomass-derived aromatic compounds in catalytic fast pyrolysis. To date, the substrate-adsorbate interactions under reaction conditions crucial to these processes remain poorly understood, yet understanding this is critical to constructing detailed mechanistic models of the reactions important to catalytic fast pyrolysis. Density functional theory (DFT) has been used in identifying mechanistic details, but many of these works assume surface models that are not representative of realistic conditions, for example, under which the surface is covered with some concentration of hydrogen and aromatic compounds. In this study, we investigate hydrogen-guaiacol coadsorption on Pt(111) using van der Waals-corrected DFT and ab initio thermodynamics over a range of temperatures and pressures relevant to bio-oil upgrading. We find that relative coverage of hydrogen and guaiacol is strongly dependent on the temperature and pressure of the system. Under conditions relevant to ex situ catalytic fast pyrolysis (CFP; 620-730 K, 1-10 bar), guaiacol and hydrogen chemisorb to the surface with a submonolayer hydrogen (~0.44 ML H), while under conditions relevant to hydrotreating (470-580 K, 10-200 bar), the surface exhibits a full-monolayer hydrogen coverage with guaiacol physisorbed to the surface. These results correlate with experimentally observed selectivities, which show ring saturation to methoxycyclohexanol at hydrotreating conditions and deoxygenation to phenol at CFP-relevant conditions. Additionally, the vibrational energy of the adsorbates on the surface significantly contributes to surface energy at higher coverage. Ignoring this contribution results in not only quantitatively, but also qualitatively incorrect interpretation of coadsorption, shifting the phase boundaries by more than 200 K and ~10-20 bar and predicting no guaiacol adsorption under CFP and hydrotreating conditions. We
Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung
2016-01-01
Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380
Ab initio phonon limited transport
NASA Astrophysics Data System (ADS)
Verstraete, Matthieu
We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)
Shrestha, Rojan; Simoncini, David; Zhang, Kam Y J
2012-11-01
Recent advancements in computational methods for protein-structure prediction have made it possible to generate the high-quality de novo models required for ab initio phasing of crystallographic diffraction data using molecular replacement. Despite those encouraging achievements in ab initio phasing using de novo models, its success is limited only to those targets for which high-quality de novo models can be generated. In order to increase the scope of targets to which ab initio phasing with de novo models can be successfully applied, it is necessary to reduce the errors in the de novo models that are used as templates for molecular replacement. Here, an approach is introduced that can identify and rebuild the residues with larger errors, which subsequently reduces the overall C(α) root-mean-square deviation (CA-RMSD) from the native protein structure. The error in a predicted model is estimated from the average pairwise geometric distance per residue computed among selected lowest energy coarse-grained models. This score is subsequently employed to guide a rebuilding process that focuses on more error-prone residues in the coarse-grained models. This rebuilding methodology has been tested on ten protein targets that were unsuccessful using previous methods. The average CA-RMSD of the coarse-grained models was improved from 4.93 to 4.06 Å. For those models with CA-RMSD less than 3.0 Å, the average CA-RMSD was improved from 3.38 to 2.60 Å. These rebuilt coarse-grained models were then converted into all-atom models and refined to produce improved de novo models for molecular replacement. Seven diffraction data sets were successfully phased using rebuilt de novo models, indicating the improved quality of these rebuilt de novo models and the effectiveness of the rebuilding process. Software implementing this method, called MORPHEUS, can be downloaded from http://www.riken.jp/zhangiru/software.html.
Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D.
2014-10-07
We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pair (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.
NASA Astrophysics Data System (ADS)
Chen, Jiangchao
Dissociative laser-driven photoreactions of open-shell lanthanide metal-organic complexes are analyzed from experimental and computational aspects. Experimental analysis, based on time-of-flight mass spectrometry suggests the most probable pathway for the photoreactions. A sequence of intermediates and the distribution of final products are identified. The computational analysis, based on excited-state ab initio molecular dynamics with surface hopping, is implemented at the DFT level of theory. Computational treatment prompts the mechanism of laser-driven photoreactions at time ranges from femtoseconds to picoseconds. The experimental and computational analyses agree on several key products of photoreactions. Branching between two reaction pathways, ligand ejection versus cracking, is observed and explained. The results obtained are of importance for basic studies of processes beyond the Born-Oppenheimer approximation and for nano-electronics application of laser-assisted chemical vapor deposition of insulators with super-high dielectric constant.
NASA Technical Reports Server (NTRS)
Jaffe, Richard L.; Pattengill, Merle D.; Schwenke, David W.
1989-01-01
Strategies for constructing global potential energy surfaces from a limited number of accurate ab initio electronic energy calculations are discussed. Generally, these data are concentrated in small regions of configuration space (e.g., in the vicinity of saddle points and energy minima) and difficulties arise in generating a potential function that is globally well-behaved. Efficient computer codes for carrying out classical trajectory calculations on vector and parallel processors are also described. Illustrations are given from recent work on the following chemical systems: Ca + HF yields CaF + H, H + H + H2 yields H2 + H2, N + O2 yields NO + O and O + N2 yields NO + N. The dynamics and kinetics of metathesis, dissociation, recombination, energy transfer and complex formation processes will be discussed.
Duan, Defang; Tian, Fubo; He, Zhi; Meng, Xing; Wang, Liancheng; Chen, Changbo; Zhao, Xiusong; Liu, Bingbing; Cui, Tian
2010-08-21
Ab initio calculations are performed to probe the hydrogen bonding, structural, and superconducting behaviors of HBr and HCl under high pressure. The calculated results show that the hydrogen bond symmetrization (Cmc2(1)-->Cmcm transition) of HBr and HCl occurs at 25 and 40 GPa, respectively, which can be attributed to the symmetry stretching A(1) mode softening. After hydrogen bond symmetrization, a pressure-induced soft transverse acoustic phonon mode of Cmcm phase is identified and a unique metallic phase with monoclinic structure of P2(1)/m (4 molecules/cell) for both compounds is revealed by ab initio phonon calculations. This phase preserves the symmetric hydrogen bond and is stable in the pressure range from 134 to 196 GPa for HBr and above 233 GPa for HCl, while HBr is predicted to decompose into Br(2)+H(2) above 196 GPa. Perturbative linear-response calculations predict that the phase P2(1)/m is a superconductor with T(c) of 27-34 K for HBr at 160 GPa and 9-14 K for HCl at 280 GPa.
NASA Astrophysics Data System (ADS)
Wang, Liancheng; Tian, Fubo; Feng, Wanxiang; Chen, Changbo; He, Zhi; Ma, Yanming; Cui, Tian; Liu, Bingbing; Zou, Guangtian
2010-04-01
The structural and dynamical properties of phase IV and V of hydrogen sulfide were investigated by means of extensive ab initio molecular dynamics simulations. Starting from an experimental proposal for the structure of phase IV, an Ibca symmetry with a stable hydrogen bonding network is found at 15 GPa and 100 K. Molecular dynamics simulations at increasing temperature and at the pressure of 15 GPa suggest that phase IV will transform to a proton disordered structure at 15 GPa and 350 K. The newfound structure has a hexagonal lattice of P63/mmc symmetry, which is believed to be the remaining crystalline structure of phase V. The high mobility of protons in phase V is believed to be the key point to the dissociation and decomposition of hydrogen sulfide.
Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.
2008-05-20
Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.
Enthalpy of the gas-phase CO2 + Mg reaction from ab initio total energies.
Lesar, Antonija; Prebil, Sasa; Hodoscek, Milan
2002-01-01
Various highly accurate ab initio composite methods of Gaussian-n (G1, G2, G3), their variations (G2(MP2), G3(MP2), G3//B3LYP, G3(MP2)//B3LYP), and complete basis set (CBS-Q, CBS-Q//B3LYP) series of models were applied to compute reaction enthalpies of the ground-state reaction of CO2 with Mg. All model chemistries predict highly endothermic reactions, with DeltaH(298) = 63.6-69.7 kcal x mol(-1). The difference between the calculated reaction enthalpies and the experimental value, evaluated with recommended experimental standard enthalpies of formation for products and reactants, is more than 20 kcal x mol(-1) for all methods. This difference originates in the incorrect experimental enthalpy of formation of gaseous MgO given in thermochemical databases. When the theoretical formation enthalpy for MgO calculated by a particular method is used, the deviation is reduced to 1.3 kcal x mol(-1). The performance of the methodologies used to calculate the heat of this particular reaction and the enthalpy of formation of MgO are discussed.
AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS
Turchi, P A
2004-04-14
Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.
Pigozzi, Giancarlo; Janczak-Rusch, Jolanta; Passerone, Daniele; Antonio Pignedoli, Carlo; Patscheider, Joerg; Jeurgens, Lars P. H.; Antusek, Andrej; Parlinska-Wojtan, Magdalena; Bissig, Vinzenz
2012-10-29
Nano-sized Ag-Cu{sub 8nm}/AlN{sub 10nm} multilayers were deposited by reactive DC sputtering on {alpha}-Al{sub 2}O{sub 3}(0001) substrates. Investigation of the phase constitution and interface structure of the multilayers evidences a phase separation of the alloy sublayers into nanosized grains of Ag and Cu. The interfaces between the Ag grains and the quasi-single-crystalline AlN sublayers are semi-coherent, whereas the corresponding Cu/AlN interfaces are incoherent. The orientation relationship between Ag and AlN is constant throughout the entire multilayer stack. These observations are consistent with atomistic models of the interfaces as obtained by ab initio calculations.
NASA Astrophysics Data System (ADS)
Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge
2014-07-01
The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.
Prediction of B1 to B10 phase transition in LuN under pressure: An ab-initio investigation
NASA Astrophysics Data System (ADS)
Sahoo, B. D.; Mukherjee, D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.
2016-05-01
Ab-initio total energy calculations have been performed in lutetium nitride (LuN) as a function of hydrostatic compression to understand the high pressure behavior of this compound. Our calculations predict a phase transition from ambient rocksalt type structure (B1 phase) to a tetragonal structure (B10 phase) at ~ 240 GPa. The phase transition has been identified as first order in nature with volume discontinuity of ~ 6%. The predicted high pressure phase has been found to be stable up to at least 400 GPa, the maximum pressure up to which calculations have been performed.Further, to substantiate the results of static lattice calculations analysis of lattice dynamic stability of B1 and B10 phase has been carried out at different pressures. Apart from this, we have analyzed the lattice dynamic stability CsCl type (B2) phase around the 240 GPa, the pressure reported for B1 to B2 transition in previous all-electron calculations by Gupta et al. 2013. We find that the B2 structure is lattice dynamically unstable at this pressure and remains unstable up to ~ 400 GPa, ruling out the possibility of B1 to B2 phase transition at least up to ~ 400 GPa. Further, the theoretically determined equation of state has been utilized to derive various physical quantities such as zero pressure equilibrium volume, bulk modulus, and pressure derivative of bulk modulus of B1 phase at ambient conditions.
Malbon, Christopher L; Zhu, Xiaolei; Guo, Hua; Yarkony, David R
2016-12-21
For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian H(d) (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the H(d) by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding H(d) determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.
NASA Astrophysics Data System (ADS)
Malbon, Christopher L.; Zhu, Xiaolei; Guo, Hua; Yarkony, David R.
2016-12-01
For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian Hd (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the Hd by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding Hd determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.
Kaminski, George A.; Stern, Harry A.; Berne, Bruce J.; Friesner, Richard A.; Cao, Yixiang; Murphy, Robert B.; Zhou, Ruhong; Halgren, Thomas A.
2002-12-01
We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.
KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.
2014-01-01
We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421
Ab initio dynamical vertex approximation
NASA Astrophysics Data System (ADS)
Galler, Anna; Thunström, Patrik; Gunacker, Patrik; Tomczak, Jan M.; Held, Karsten
2017-03-01
Diagrammatic extensions of dynamical mean-field theory (DMFT) such as the dynamical vertex approximation (DΓ A) allow us to include nonlocal correlations beyond DMFT on all length scales and proved their worth for model calculations. Here, we develop and implement an Ab initio DΓ A approach (AbinitioDΓ A ) for electronic structure calculations of materials. The starting point is the two-particle irreducible vertex in the two particle-hole channels which is approximated by the bare nonlocal Coulomb interaction and all local vertex corrections. From this, we calculate the full nonlocal vertex and the nonlocal self-energy through the Bethe-Salpeter equation. The AbinitioDΓ A approach naturally generates all local DMFT correlations and all nonlocal G W contributions, but also further nonlocal correlations beyond: mixed terms of the former two and nonlocal spin fluctuations. We apply this new methodology to the prototypical correlated metal SrVO3.
NASA Astrophysics Data System (ADS)
Scherrer, Arne; Vuilleumier, Rodolphe; Sebastiani, Daniel
2016-08-01
We report the first fully ab initio calculation of dynamical vibrational circular dichroism spectra in the liquid phase using nuclear velocity perturbation theory (NVPT) derived electronic currents. Our approach is rigorous and general and thus capable of treating weak interactions of chiral molecules as, e.g., chirality transfer from a chiral molecule to an achiral solvent. We use an implementation of the NVPT that is projected along the dynamics to obtain the current and magnetic dipole moments required for accurate intensities. The gauge problem in the liquid phase is resolved in a twofold approach. The electronic expectation values are evaluated in a distributed origin gauge, employing maximally localized Wannier orbitals. In a second step, the gauge invariant spectrum is obtained in terms of a scaled molecular moments, which allows to systematically include solvent effects while keeping a significant signal-to-noise ratio. We give a thorough analysis and discussion of this choice of gauge for the liquid phase. At low temperatures, we recover the established double harmonic approximation. The methodology is applied to chiral molecules ((S)-d2-oxirane and (R)-propylene-oxide) in the gas phase and in solution. We find an excellent agreement with the theoretical and experimental references, including the emergence of signals due to chirality transfer from the solute to the (achiral) solvent.
Scherrer, Arne; Vuilleumier, Rodolphe; Sebastiani, Daniel
2016-08-28
We report the first fully ab initio calculation of dynamical vibrational circular dichroism spectra in the liquid phase using nuclear velocity perturbation theory (NVPT) derived electronic currents. Our approach is rigorous and general and thus capable of treating weak interactions of chiral molecules as, e.g., chirality transfer from a chiral molecule to an achiral solvent. We use an implementation of the NVPT that is projected along the dynamics to obtain the current and magnetic dipole moments required for accurate intensities. The gauge problem in the liquid phase is resolved in a twofold approach. The electronic expectation values are evaluated in a distributed origin gauge, employing maximally localized Wannier orbitals. In a second step, the gauge invariant spectrum is obtained in terms of a scaled molecular moments, which allows to systematically include solvent effects while keeping a significant signal-to-noise ratio. We give a thorough analysis and discussion of this choice of gauge for the liquid phase. At low temperatures, we recover the established double harmonic approximation. The methodology is applied to chiral molecules ((S)-d2-oxirane and (R)-propylene-oxide) in the gas phase and in solution. We find an excellent agreement with the theoretical and experimental references, including the emergence of signals due to chirality transfer from the solute to the (achiral) solvent.
Ab initio quantum chemistry: Methodology and applications
Friesner, Richard A.
2005-01-01
This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212
Ab initio based polarizable force field parametrization
NASA Astrophysics Data System (ADS)
Masia, Marco
2008-05-01
Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by ˜30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.
Ab initio study of H and He migrations in β-phase Sc, Y, and Er hydrides
Chen, Ru-Cheng; Yang, Li; Dai, Yunya; Zhu, Zi Qiang; Peng, SM; Long, XG; Gao, Fei; Zu, Xiaotao
2012-05-01
Ab initio calculations based on the density functional theory have been performed to investigate the migrations of hydrogen (H) and helium (He) atoms in {beta}-phase scandium (Sc), yttrium (Y), and erbium (Er) hydrides with three different ratios of H to metal. The results show that the migration mechanisms of H and He atoms mainly depend on the crystal structures of hydrides, but their energy barriers are affected by the host-lattice in metal hydrides. The formation energies of octahedral-occupancy H (H{sub oct}) and tetrahedral vacancy (V{sub tet}) pairs are almost the same (about 1.2 eV). It is of interest to note that the migration barriers of H increase with increasing host-lattice atomic number. In addition, the results show that the favorable migration mechanism of He depends slightly on the V{sub tet} in the Sc hydride, but strongly on that in the Y and Er hydrides, which may account for different behaviours of initial He release from ScT{sub 2} and ErT{sub 2}.
Ab initio study of the phase stability in paramagnetic duplex steel alloys
NASA Astrophysics Data System (ADS)
Pitkänen, H.; Alatalo, M.; Puisto, A.; Ropo, M.; Kokko, K.; Punkkinen, M. P. J.; Olsson, P.; Johansson, B.; Hertzman, S.; Vitos, L.
2009-01-01
Duplex stainless steels have many superior properties compared to conventional steels, this being mainly due to their microstructure containing approximately equal amount of ferrite and austenite phases formed by iron, chromium (or Cr equivalent), and nickel (or Ni equivalent). Using computational methods based on first-principles theories, the phase stability of paramagnetic Fe1-c-nCrcNin alloys ( 0.12≤c≤0.32 and 0.04≤n≤0.32 ) at high temperatures (≳1000K) is addressed. It is shown that the stabilization of the ferrite-austenite two-phase field in duplex steels is a result of complex interplay of several competing phenomena. Taking into account only the formation energies yields a complete phase separation, strongly overestimating the two-phase region. The formation energies are calculated to be lower for the austenite than for the ferrite, meaning that the configurational entropy has a more significant impact on the stability field of the austenitic phase. The magnetic and vibrational free energies have opposite effects on the phase stability. Namely, the magnetic entropy favors the ferrite phase, whereas the vibrational free energy stabilizes the austenite phase. Combining the formation energies with the magnetic, vibrational, and configurational free energies, a region of coexistence between the two phases is obtained, in line with former thermodynamic assessments as well as with experimental observations.
Bharadwaj, Vivek S; Vyas, Shubham; Villano, Stephanie M; Maupin, C Mark; Dean, Anthony M
2015-02-14
The fumarate addition reaction mechanism is central to the anaerobic biodegradation pathway of various hydrocarbons, both aromatic (e.g., toluene, ethyl benzene) and aliphatic (e.g., n-hexane, dodecane). Succinate synthase enzymes, which belong to the glycyl radical enzyme family, are the main facilitators of these biochemical reactions. The overall catalytic mechanism that converts hydrocarbons to a succinate molecule involves three steps: (1) initial H-abstraction from the hydrocarbon by the radical enzyme, (2) addition of the resulting hydrocarbon radical to fumarate, and (3) hydrogen abstraction by the addition product to regenerate the radical enzyme. Since the biodegradation of hydrocarbon fuels via the fumarate addition mechanism is linked to bio-corrosion, an improved understanding of this reaction is imperative to our efforts of predicting the susceptibility of proposed alternative fuels to biodegradation. An improved understanding of the fuel biodegradation process also has the potential to benefit bioremediation. In this study, we consider model aromatic (toluene) and aliphatic (butane) compounds to evaluate the impact of hydrocarbon structure on the energetics and kinetics of the fumarate addition mechanism by means of high level ab initio gas-phase calculations. We predict that the rate of toluene degradation is ∼100 times faster than butane at 298 K, and that the first abstraction step is kinetically significant for both hydrocarbons, which is consistent with deuterium isotope effect studies on toluene degradation. The detailed computations also show that the predicted stereo-chemical preference of the succinate products for both toluene and butane are due to the differences in the radical addition rate constants for the various isomers. The computational and kinetic modeling work presented here demonstrates the importance of considering pre-reaction and product complexes in order to accurately treat gas phase systems that involve intra and inter
Joubert, J.-M.; Colinet, C.; Rodrigues, G.; Suzuki, P.A.; Nunes, C.A.; Coelho, G.C.; Tedenac, J.-C.
2012-06-15
The solid solution based on Nb{sub 5}Si{sub 3} (Cr{sub 5}B{sub 3} structure type, D8{sub l}, tI32, I4/mcm, No140, a=6.5767 A, c=11.8967 A) in the Nb-Si-B system was studied from the structural and thermodynamic point of view both experimentally and by ab initio calculations. Rietveld refinement of powder X-ray synchrotron data allowed to determine the boron to silicon substitution mechanism and the structural parameters. Ab initio calculations of different ordered compounds and selected disordered alloys allowed to obtain in addition to the enthalpy of formation of the solution, substitution mechanism and structural parameters which are in excellent agreement with the experimental data. The stability of the phase is discussed. - Graphial abstract: Valence-charge electron localization function in the z=0 plane of the D8{sub l} structure for the ordered compound Nb{sub 5}SiB{sub 2}. Highlights: Black-Right-Pointing-Pointer Coupling between ab initio data and experimental results from synchrotron powder diffraction. Black-Right-Pointing-Pointer Excellent agreement between the two techniques for the site occupancies and internal coordinates. Black-Right-Pointing-Pointer Explanation of the phase stability up to Nb{sub 5}SiB{sub 2}.
Pressure Induced Structural Phase Transition in Actinide Monophospides: Ab Initio Calculations
NASA Astrophysics Data System (ADS)
Makode, Chandrabhan; Sanyal, Sankar P.
2011-07-01
The structural and electronic properties of monophospides of Thorium, Uranium and Neptunium have been investigated using tight binding linear muffin-in-orbital (TB-LMTO) method within the local density approximation (LDA). From present study with the help of total energy calculations it is found that ThP, UP and NpP are stable in NaCl- type structure under ambient pressure. The structure stability of ThP, UP and NpP changes under the application of pressure. We predict a structural phase transition from NaCl-type (B1-phase) structure to CsCl-type (B2-phase) structure for these phospides in the pressure range of 37.0-24.0 GPa (ThP to NpP). The calculated equilibrium lattice parameters and bulk modulus are in good agreement with experimental and theoretical work.
Pressure induced structural phase transition in actinide mono-bismuthides: Ab initio calculations
NASA Astrophysics Data System (ADS)
Pataiya, J.; Makode, C.; Aynyas, M.; Sanyal, Sankar P.
2013-06-01
The structural and electronic properties of mono-bismuthides of Plutonium and Americium have been investigated using tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). From present study with the help of total energy calculations it is found that PuBi and AmBi are stable in NaCl - type structure under ambient pressure. The structure stability of PuBi and AmBi changes under the application of pressure. We predict a structural phase transition from NaCl-type (B1-phase) structure to CsCl-type (B2-phase) structure for these phospides in the pressure range of 45 - 4.5 GPa for PuBi and AmBi respectively. The calculated equilibrium lattice parameters and bulk modulus are in good agreement with experimental and theoretical work.
Phase behavior of metastable liquid silicon at negative pressure: Ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Zhao, G.; Yu, Y. J.; Yan, J. L.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.
2016-04-01
Extensive first-principle molecular dynamics simulations are performed to study the phase behavior of metastable liquid Si at negative pressure. Our results show that the high-density liquid (HDL) and HDL-vapor spinodals indeed form a continuous reentrant curve and the liquid-liquid critical point seems to just coincide with its minimum. The line of density maxima also has a strong tendency to pass through this minimum. The phase behaviour of metastable liquid Si therefore tends to be a critical-point-free scenario rather than a second-critical-point one based on SW potential.
NASA Astrophysics Data System (ADS)
Errandonea, D.; Manjón, F. J.; Garro, N.; Rodríguez-Hernández, P.; Radescu, S.; Mujica, A.; Muñoz, A.; Tu, C. Y.
2008-08-01
The room-temperature Raman scattering was measured in ZnWO4 up to 45 GPa. We report the pressure dependence of all the Raman-active phonons of the low-pressure wolframite phase. As pressure increases additional Raman peaks appear at 30.6 GPa due to the onset of a reversible structural phase transition to a distorted monoclinic β -fergusonite-type phase. The low-pressure and high-pressure phases coexist from 30.6 to 36.5 GPa. In addition to the Raman measurements we also report ab initio total-energy and lattice-dynamics calculations for the two phases. These calculations helped us to determine the crystalline structure of the high-pressure phase and to assign the observed Raman modes in both the wolframite and β -fergusonite phases. Based upon the ab initio calculations we propose the occurrence of a second phase transition at 57.6 GPa from the β -fergusonite phase to an orthorhombic Cmca phase. The pressure evolution of the lattice parameters and the atomic positions of wolframite ZnWO4 are also theoretically calculated, and an equation of state reported.
NASA Astrophysics Data System (ADS)
Janssen, W. B. J. M.; van der Avoird, A.
1990-07-01
Starting from an ab initio H2-H2 potential that contains anisotropic short-range and dispersion terms, in addition to the quadrupole-quadrupole interactions, we have performed lattice-dynamics calculations for the orientationally disordered hexagonal (hcp) and ordered cubic (Pa3) phases of solid (ortho and para) hydrogen and deuterium. The method used is the time-dependent Hartree (TDH) formalism, with the explicit inclusion of translation-rotation coupling. By an anharmonic expansion of the potential through sixth order in the molecular displacements and the use of wave functions for the translational vibrations that are sufficiently flexible to adapt to this strong anharmonicity, we could avoid the usual (effective) Jastrow correction to the potential. The calculated phonon and roton or libron frequencies are in fairly good agreement with infrared, Raman, and neutron-scattering data, significantly better in general than the results from earlier (separate) phonon calculations and roton or libron calculations that have used empirical potentials. The transition pressure for ordering para-H2 or ortho-D2 appears to be dominated by the classical quadrupole-quadrupole interactions. It is significantly affected by the increase of the rotational constant and, especially, by the reduction of the quadrupole moment, which follows from a shortening of the intramolecular bond. Translation-rotation coupling yields the observed mixing of phonons and rotons at high pressure, but its effect on the transition pressure is minute. The remaining discrepancy between the calculated and observed transition pressures must be caused by three-body interactions and by correlations between the molecular motions that are beyond the TDH approximation.
Gas-phase acidities of tetrahedral oxyacids from ab initio electronic structure theory
Rustad, J.R.; Dixon, D.A.; Kubicki, J.D.; Felmy, A.R.
2000-05-04
Density functional calculations have been performed on several protonation states of the oxyacids of Si, P, V, As, Cr, and S. Structures and vibrational frequencies are in good agreement with experimental values where these are available. A reasonably well-defined correlation between the calculated gas-phase acidities and the measured pK{sub a} in aqueous solution has been found. The pK{sub a}/gas-phase acidity slopes are consistent with those derived from previous molecular mechanics calculations on ferric hydrolysis and the first two acidity constants for orthosilicic acid. The successive deprotonation of other H{sub n}TO{sub 4} species, for a given tetrahedral anion T are roughly consistent with this slope, but not to the extent that there is a universal correlation among all species.
NASA Astrophysics Data System (ADS)
Makode, Chandrabhan; Sanyal, Sankar P.
2011-09-01
We have investigated the structural and electronic properties of monophospides of thorium, uranium and neptunium. The total energy as a function of volume is obtained by means of the self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). From the present study with the help of total energy calculations it is found that ThP, UP and NpP are stable in NaCl-type structure at ambient pressure. The structural stability of ThP, UP and NpP changes under the application of pressure. We predict a structural phase transition from NaCl-type (B 1-phase) structure to CsCl-type (B 2-phase) structure for these phospides in the pressure range of 37.0-24.0 GPa (ThP-NpP). We also calculate lattice parameter ( a0), bulk modulus ( B0), band structure and density of states. From energy band diagram it is observed that ThP, UP and NpP exhibit metallic behavior. The calculated equilibrium lattice parameters and bulk modulus are in good agreement with experimental and theoretical work.
Ab initio calculations of the thermodynamics and phase diagram of zirconium
NASA Astrophysics Data System (ADS)
Hao, Yan-Jun; Zhang, Lin; Chen, Xiang-Rong; Cai, Ling-Cang; Wu, Qiang; Alfè, Dario
2008-10-01
The finite-temperature density-functional theory and quasiharmonic lattice dynamics are used to calculate the Gibbs free energy and quasiharmonic phonons of the hexagonal-close-packed (hcp) and omega (ω) crystal structures for Zr. The hcp phonon dispersions agree with experiment; the ω phonon dispersions have not been measured yet. From the free energy, the volume thermal expansion coefficients of α-Zr are predicted. The calculated volume thermal expansion coefficients for α-Zr are in good agreement with the experiment data at T>100K . Our calculated results found that at zero-temperature the lowest-energy phase is not the ω but the hcp phase. This conclusion is in accordance with the result of Schnell and Albers, but in disagreement with those of Ahuja and Jona and Marcus. The predicted phase boundary of α→ω is in good agreement with the available experiment; however, other theoretical results are far from the experiment at high temperatures.
Ab initio theory of phase stability and structural selectivity in Fe-Pd alloys
NASA Astrophysics Data System (ADS)
Chepulskii, Roman V.; Barabash, Sergey V.; Zunger, Alex
2012-04-01
In Fe-Pd alloys, the competing geometric (fcc versus bcc) and magnetic tendencies result in rich phase stability and ordering physics. Here, we study these alloys via a first principles mixed-basis cluster expansion (CE) approach. Highly accurate fcc and bcc CEs are iteratively and self-consistently constructed using a genetic algorithm, based on the first principles results for ˜100 ordered structures. The structural and magnetic “filters” are introduced to determine whether a fully relaxed structure is of fcc/bcc and high-/low-spin types. All structures satisfying the Lifshitz condition for stability in extended phase diagram regions are included as inputs to our CEs. We find that in a wide composition range (with more than 1/3 atomic content of Fe), an fcc-constrained alloy has a single stable ordered compound, L10 FePd. However, L10 is higher in energy than the phase-separated mixture of bcc Fe and fcc-FePd2 (β2 structure) at low temperatures. In the Pd-rich composition range, we find several fcc β2-like ground states: FePd2 (β2), Fe3Pd9, Fe2Pd7, FePd5, Fe2Pd13, and FePd8, yet we do not find FePd3 with the the experimentally observed L12 structure. Fcc Monte Carlo simulations show a transformation from any of the attempted β2-like ground states directly into a disordered alloy. We suggest that the phonon and/or spin excitation contributions to the free energy are responsible for the observed stability of L12 at higher temperatures, and likely lead to a β2↔L12 transition. Finally, we present here a complete characterization of all the fcc and bcc Lifshitz structures, i.e., the structures with ordering vectors exclusively at high-symmetry k points.
Ab initio study of thiol aqueous phase ionization energies. Methyl mercaptan and cysteamine
Colson, A.O.; Sevilla, M.D. )
1994-10-13
The ionization energies of two thiol model compounds (methyl mercaptan and cysteamine) are calculated at the ROHF/6-31G* level to aid our understanding of the mechanisms involved in DNA radioprotection. Methyl mercaptan, the thiolate anion, and its trihydrated form are fully geometry optimized. The resulting gas-phase Koopmans ionization energies are 9.68, 1.67, and 3.63 eV, respectively. The ionization energy for the solvated methylthiolate anion, CH[sub 3]S[sup [minus
Ab initio studies of aspartic acid conformers in gas phase and in solution
NASA Astrophysics Data System (ADS)
Chen, Mingliang; Lin, Zijing
2007-10-01
Systematic and extensive conformational searches of aspartic acid in gas phase and in solution have been performed. For the gaseous aspartic acid, a total of 1296 trial canonical structures and 216 trial zwitterionic structures were generated by allowing for all combinations of internal single-bond rotamers. All the trial structures were optimized at the B3LYP /6-311G* level and then subjected to further optimization at the B3LYP /6-311++G** level. A total of 139 canonical conformers were found, but no stable zwitterionic structure was found. The rotational constants, dipole moments, zero-point vibrational energies, harmonic frequencies, and vertical ionization energies of the canonical conformers were determined. Single-point energies were also calculated at the MP2/6-311++G** and CCSD /6-311++G** levels. The equilibrium distributions of the gaseous conformers at various temperatures were calculated. The proton affinity and gas phase basicity were calculated and the results are in excellent agreement with the experiments. The conformations in the solution were studied with different solvation models. The 216 trial zwitterionic structures were first optimized at the B3LYP /6-311G* level using the Onsager self-consistent reaction field model (SCRF) and then optimized at the B3LYP /6-311++G** level using the conductorlike polarized continuum model (CPCM) SCRF theory. A total of 22 zwitterions conformers were found. The gaseous canonical conformers were combined with the CPCM model and optimized at the B3LYP /6-311++G** level. The solvated zwitterionic and canonical structures were further examined by the discrete/SCRF model with one and two water molecules. The incremental solvation of the canonical and zwitterionic structures with up to six water molecules in gas phase was systematically examined. The studies show that combining aspartic acid with at least six water molecules in the gas phase or two water molecules and a SCRF solution model is required to provide
Kafka, Graeme R; Masters, Sarah L; Rankin, David W H
2007-07-05
A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).
Evidence for plasma phase transition in high pressure hydrogen from ab-initio simulations
Morales, M; Pierleoni, C; Schwegler, E; Ceperley, D
2010-02-08
We have performed a detailed study of molecular dissociation in liquid hydrogen using both Born-Oppenheimer molecular dynamics with Density Functional Theory and Coupled Electron-Ion Monte Carlo simulations. We observe a range of densities where (dP/d{rho}){sub T} = 0 that coincides with sharp discontinuities in the electronic conductivity, which is clear evidence of the plasma phase transition for temperatures 600K {le} T {le} 1500K. Both levels of theory exhibit the transition, although Quantum Monte Carlo predicts higher transition pressures. Based on the temperature dependence of the discontinuity in the electronic conductivity, we estimate the critical point of the transition at temperatures slightly below 2000 K. We examine the influence of proton zero point motion by using Path Integral Molecular Dynamics with Density Functional Theory; the main effect is to shift the transition to lower pressures. Furthermore, we calculate the melting curve of molecular hydrogen up to pressures of 200 GPa, finding a reentrant melting line in good agreement with previous calculations. The melting line crosses the metalization line at 700 K and 220 GPa using density functional energetics and at 550 K and 290 GPa using Quantum Monte Carlo energetics.
Ab Initio Studies of Stratospheric Ozone Depletion Chemistry
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.
Ab initio alpha-alpha scattering.
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-12-03
Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Ab initio alpha-alpha scattering
NASA Astrophysics Data System (ADS)
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.
2015-12-01
Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
NASA Astrophysics Data System (ADS)
Chauhan, Mamta; Gupta, Dinesh C.
2015-12-01
The structural, electronic, mechanical, phase transition, and thermo-physical properties of refractory carbides, viz. VC, NbC, and TaC have been computed in stable B1 and high pressure B2 phases by means of two different ab initio calculations using pseudo- and full-potential schemes. These materials have mixed covalent-, metallic-, and ionic-type bonding. The calculations of elastic constants show the mechanical stability of these materials in B1 phase only. The brittle nature and anisotropy is observed in these materials in B1 phase. Non-central forces are present in both the phases. Elastic wave velocities and Debye temperature have also been calculated. The present results on structural, phase transition, elastic, and other properties are in reasonably good agreement with the available experimental and theoretical data. The calculations in high pressure phase need experimental verification.
NASA Astrophysics Data System (ADS)
Shimamura, Kohei; Hakamata, Tomoya; Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
2016-12-01
Rotation of methylammonium (CH3NH3 or MA) molecules is believed to govern the excellent transport properties of photocarriers in the MA lead iodide (MAPbI3) perovskite. Of particular interest is its cubic phase, which exists in industrially important films at room temperature. In order to investigate the rotational behaviors of the MA molecules, we have performed ab initio molecular dynamics simulations of cubic-MAPbI3 at room temperature. There are two types of rotational motions of MA molecules in a crystalline PbI3 cage: reorientation of a whole molecule and intramolecular rotation around the C-N bond within MA molecules. Using a cubic symmetry-assisted analysis (CSAA), we found that the prominent orientation of the C-N bond is the crystalline ⟨110 ⟩ directions, rather than the ⟨100 ⟩ and ⟨111 ⟩ directions. Rapid rotation around the C-N bond is also observed, which easily occurs when the rotational axis is parallel to the ⟨110 ⟩ directions according to the CSAA. To explain the atomistic mechanisms underlying these CSAA results, we have focused on the relation between H-I hydrogen bonds and the orientation of an MA molecule. Here, the hydrogen bonds were defined by population analysis, and it has been found that, while H atoms in the CH3 group (HC) hardly interacts with I atoms, those in the NH3 group (HN) form at least one hydrogen bond with I atoms and their interatomic distances are in a wide range, 2.2-3.7 Å. Based on these findings, we have given a possible explanation to why the ⟨110 ⟩ directions are preferred. Namely, the atomic arrangement and interatomic distance between MA and surrounding I atoms are most suitable for the formation of hydrogen bonds. In addition to films, these results are potentially applicable to the rotational behaviors in bulk MAPbI3 as well, considering that the atomistic structure and time constants regarding the rotation of MA molecules statistically agree with bulk experiments.
Ab initio study of cyanoguanidine isomers
NASA Astrophysics Data System (ADS)
Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.
1995-06-01
An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers ('cyanioime' and 'cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.
Ab initio study of cyanoguanidine isomers
NASA Astrophysics Data System (ADS)
Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.
1995-06-01
An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers (‘cyanioime' and ‘cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.
NASA Astrophysics Data System (ADS)
Dakkouri, Marwan; Typke, Volker
2010-08-01
The molecular structure of 1,1-dichlorosilacyclopentane (DCSCP) has been investigated by means of gas-phase electron diffraction and quantum mechanical calculation. We applied both a pseudorotation model to account for the dynamic and large amplitude motion in DCSCP, and a one-conformer model of C1 symmetry. Using the computational results we analyzed the dependency of the ring geometrical parameters and vibrational mean amplitudes on the phase angle φ. The joint electron diffraction and ab initio study has led to the following ra structural parameters of DCSCP ( C1 conformer): r(Si-Cl) = 2.047(2) Å, r(Si-C) = 1.867(4) Å, average r(C-C) ring = 1.548(4) Å, average r(C-H) = 1.103(7) Å, <(C-Si-C) = 97.4(6)°, <(Cl-Si-Cl) = 104.8(10)°, and effective phase angle φ = 74.8(58)°. The puckering amplitude for the five-membered ring was determined to be q = 0.480(24) Å. The quantum mechanical calculations were performed by utilizing the UHF, B3LYP, and MP2 methods in combination with basis sets 6-311++G(2df,2pd), 6-311++G(df,pd), 6-311++G(p,d), 6-311+G(d,p), 6-311G(d,p) and Dunning double and triple zeta (with and without augmentation). All these methods have consistently shown that the C2 conformer is more stable than the C s symmetric form. For all calculations we used the MOLPRO and Gaussian03 packages. NBO and AIM analyses were also carried out to explore the bond/anti-bond hyperconjugative interactions and the topological properties of the charge density distribution in DCSCP. NBO scheme including second-order perturbation analysis has shown that the major orbital stabilizing interactions are between the chlorine lone pair ( nπ) Cl and the low-lying σSi-C2∗ and σSi-C5∗ antibonding orbitals. It was found that remote σSi-C → σC-H∗ interactions are stabilized by 4.4 kcal mol -1 and contribute to the stabilization of the C2 conformer in DCSCP. Deletion analysis was performed using various deletion algorithms like NOSTAR, NOVIC, NOGEM (see text). The
NASA Astrophysics Data System (ADS)
Faria Junior, Paulo E.; Campos, Tiago; Bastos, Carlos M. O.; Gmitra, Martin; Fabian, Jaroslav; Sipahi, Guilherme M.
2016-06-01
Semiconductor nanowires based on non-nitride III-V compounds can be synthesized under certain growth conditions to favor the appearance of the wurtzite crystal phase. Despite reports in the literature of ab initio band structures for these wurtzite compounds, we still lack effective multiband models and parameter sets that can be simply used to investigate physical properties of such systems, for instance, under quantum confinement effects. In order to address this deficiency, in this study we calculate the ab initio band structure of bulk InAs and InP in the wurtzite phase and develop an 8 ×8 k .p Hamiltonian to describe the energy bands around the Γ point. We show that our k .p model is robust and can be fitted to describe the important features of the ab initio band structure. The correct description of the spin-splitting effects that arise due to the lack of inversion symmetry in wurtzite crystals is obtained with the k -dependent spin-orbit term in the Hamiltonian, often neglected in the literature. All the energy bands display a Rashba-like spin texture for the in-plane spin expectation value. We also provide the density of states and the carrier density as functions of the Fermi energy. Alternatively, we show an analytical description of the conduction band, valid close to the Γ point. The same fitting procedure is applied to the 6 ×6 valence band Hamiltonian. However, we find that the most reliable approach is the 8 ×8 k .p Hamiltonian for both compounds. The k .p Hamiltonians and parameter sets that we develop in this paper provide a reliable theoretical framework that can be easily applied to investigate electronic, transport, optical, and spin properties of InAs- and InP-based nanostructures.
Piñeiro, A; Pardo, V; Baldomir, D; Rodríguez, A; Cortés-Gil, R; Gómez, A; Arias, J E
2012-07-11
The chemical influence in the phase separation phenomenon that occurs in perovskite manganites is discussed by means of ab initio calculations. Supercells have been used to simulate a phase separated state, that occurs at Ca concentrations close to the localized itinerant crossover. We have first considered a model with two types of magnetic ordering coexisting within the same compound. This is not stable. However, a non-isotropic distribution of chemical dopants is found to be the ground state. This leads to regions in the system with different effective concentrations, that would always accompany the magnetic phase separation at the same nanometric scale, with hole-rich regions being more ferromagnetic in character and hole-poor regions being in the antiferromagnetic region of the phase diagram, as long as the system is close to a phase crossover.
Ab initio calculations of nitramine dimers
NASA Astrophysics Data System (ADS)
Koh-Fallet, Sharon; Schweigert, Igor
2015-06-01
Elevated temperatures and pressures are typically thought to have opposing effects on the reaction channels of nitramine decomposition. These high temperatures promote reactions with loose transition structures (positive activation entropies and volumes), such as N-N bond homolysis. Elevated pressures promote reactions with tight transition structures (negative activation entropies and volumes), such as intramolecular and intermolecular H transfer. However, no quantitative data exists regarding the range of temperatures and pressures at which these effects become pronounced. We are pursuing ab initio calculations of the corresponding unimolecular and bimolecular transition structures with the objective of estimating the relevant thermochemical parameters and quantifying the effects of elevated temperature and pressures on the corresponding rate constants. Here, we present density functional theory and complete active space calculations of gas-phase molecular dimers of nitramines as an intermediate step toward modeling transition structures directly in the condensed phase. This work was supported by the Naval Research Laboratory via the American Society for Engineering and Education and by the Office of Naval Research, both directly and through the Naval Research Laboratory.
Ab initio infrared and Raman spectra
NASA Astrophysics Data System (ADS)
Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.
1983-06-01
We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum
Ab initio Theory of Semiconductor Nanocrystals
NASA Astrophysics Data System (ADS)
Wang, Lin-Wang
2007-03-01
With blooming experimental synthesis of various nanostructures out of many semiconductor materials, there is an urgent need to calculate the electronic structures and optical properties of these nanosystems based on reliable ab initio methods. Unfortunately, due to the O(N^3) scaling of the conventional ab initio calculation methods based on the density functional theory (DFT), and the >1000 atom sizes of the most experimental nanosystems, the direct applications of these conventional ab intio methods are often difficult. Here we will present the calculated results using our O(N) scaling charge patching method (CPM) [1,2] to nanosystems up to 10,000 atoms. The CPM yields the charge density of a nanosystem by patching the charge motifs generated from small prototype systems. The CPM electron/hole eigen energies differ from the directly calculated results by only ˜10-20 meV. We will present the optical band gaps of quantum dots and wires, quantum rods, quantum dot/quantum well, and quantum dots doped with impurities. Besides good agreements with experimental measurements, we will demonstrate why it is important to perform ab initio calculations, in contrast with the continuum model k.p calculations. We will show the effects of surface polarization potentials and the internal electric fields. Finally, a linear scaling 3 dimensional fragment (LS3DF) method will be discussed. The LS3DF method can be used to calculate the total energy and atomic forces of a large nanosystem, with the results practically the same as the direct DFT method. Our work demonstrates that, with the help of supercomputers, it is now feasible to calculate the electronic structures and optical properties of >10,000 atom nanocrystals with ab initio accuracy. [1] L.W. Wang, Phys. Rev. Lett. 88, 256402 (2002). [2] J. Li, L.W. Wang, Phys. Rev. B 72, 125325 (2005).
Ab initio infrared and Raman spectra
NASA Technical Reports Server (NTRS)
Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.
1983-01-01
It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.
Ab-initio study of hexagonal apatites
NASA Astrophysics Data System (ADS)
Calderin, Lazaro; Stott, Malcom J.
2001-03-01
A silicon stabilized mixture of calcium phosphate phases has been recognized as playing an important role in actively resorbable coatings and in ceramics as bone materials. The nature of this material is being investigated using a variety of techniques including a combination of crystallographic analysis of measured x-ray diffraction spectra, and ab initio quantum mechanics simulations. We have used all-electron, density functional based calculations to investigate a group of hexagonal apatites. The fully relaxed crystallographic structures of hydroxyapatite, and related apatites have been obtained. We will present the results and discuss the nature of the bonding in these materials. The x-ray diffraction pattern and the infra-red spectra have also been obtained and will be compared with experiment. Acknowledgments:This work is part of a collaboration with the Applied Ceramics group of M.Sayer, and with Millenium Biologix Inc. Support of the NSERC of Canada through the award of a Co-operative R & D grant to the collaboration is acknowledged.
Ab Initio Crystal Field for Lanthanides.
Ungur, Liviu; Chibotaru, Liviu F
2017-03-13
An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc)2 ](-) (Pc=phthalocyanine) and Dy4 K2 ([Dy(4) K(2) O(OtBu)(12) ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides.
AB initio infrared and Raman spectra
NASA Astrophysics Data System (ADS)
Fredkin, D. R.; Komornicki, A.; White, S. R.; Wilson, K. R.
1982-08-01
We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schroedinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques, are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules.
Ab Initio and Ab Exitu No-Core Shell Model
Vary, J P; Navratil, P; Gueorguiev, V G; Ormand, W E; Nogga, A; Maris, P; Shirokov, A
2007-10-02
We outline two complementary approaches based on the no core shell model (NCSM) and present recent results. In the ab initio approach, nuclear properties are evaluated with two-nucleon (NN) and three-nucleon interactions (TNI) derived within effective field theory (EFT) based on chiral perturbation theory (ChPT). Fitting two available parameters of the TNI generates good descriptions of light nuclei. In a second effort, an ab exitu approach, results are obtained with a realistic NN interaction derived by inverse scattering theory with off-shell properties tuned to fit light nuclei. Both approaches produce good results for observables sensitive to spin-orbit properties.
NASA Astrophysics Data System (ADS)
Attaccalite, C.; Grüning, M.
2013-12-01
We present an ab initio real-time-based computational approach to study nonlinear optical properties in condensed matter systems that is especially suitable for crystalline solids and periodic nanostructures. The equations of motion and the coupling of the electrons with the external electric field are derived from the Berry-phase formulation of the dynamical polarization [Souza , Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.69.085106 69, 085106 (2004)]. Many-body effects are introduced by adding single-particle operators to the independent-particle Hamiltonian. We add a Hartree operator to account for crystal local effects and a scissor operator to correct the independent particle band structure for quasiparticle effects. We also discuss the possibility of accurately treating excitonic effects by adding a screened Hartree-Fock self-energy operator. The approach is validated by calculating the second-harmonic generation of SiC and AlAs bulk semiconductors: an excellent agreement is obtained with existing ab initio calculations from response theory in frequency domain [Luppi , Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.82.235201 82, 235201 (2010)]. We finally show applications to the second-harmonic generation of CdTe and the third-harmonic generation of Si.
Thermochemical data for CVD modeling from ab initio calculations
Ho, P.; Melius, C.F.
1993-12-31
Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.
Germacrene D Cyclization: An Ab Initio Investigation
Setzer, William N.
2008-01-01
Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G*) and post Hartree-Fock (MP2/6-31G* *) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils. PMID:19325722
Molecular associations from ab initio pair potentials
NASA Astrophysics Data System (ADS)
Iglesias, E.; Sordo, T. L.; Sordo, J. A.
1991-12-01
A method of building up stable molecular associations by using pair potentials from ab initio calculations is presented. The Matsuoka-Clementi-Yoshimine potential has been chosen to emulate the water-water interactions while 1-6-12 potentials are used to compute both solute-solvent and solute-solute interactions. Parameters for neutral-amino-acid-water and neutral- amino-acid-neutral-amino-acid interactions are provided by the program. Supermolecules are constructed by minimization of the interaction energy of the molecules involved. Both steepest-decent and Fletcher-Powell algorithms are available to carry out such a minimization.
Ab-initio Studies Of Lithium Oxide
NASA Astrophysics Data System (ADS)
Gupta, M. K.; Goel, Prabhatasree; Mittal, R.; Chaplot, S. L.
2010-12-01
Lithium oxide is an important material because of its high thermal conductivity and superionic behavior at high temperature. It behaves like a superionic conductor above 1200 K. Phonon frequencies have been calculated using ab-initio method. The calculations of phonon dispersion relation near unit cell volume corresponding to the superionic transition indicate softening of zone boundary transverse acoustic phonon mode along (110). The instability of phonon mode could lead to the dynamical disorder of lithium sub lattice. Thermal expansion and equation of states are also computed. The results compare well with our previous semi-empirical potential calculations.
Ab initio non-relativistic spin dynamics
Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong; Frisch, Michael J.
2014-12-07
Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.
NASA Astrophysics Data System (ADS)
Krosley, Kevin; Hagen, Kolbjørn; Hedberg, Kenneth
1995-06-01
Gas-phase electron diffraction data at 23°C together with molecular mechanics (MM3) and ab initio (HF/6-31G∗, gaussian 86) calculations have been used to determine the structure and conformations of 1,4-difluorobutane. The object was to ascertain whether effects similar to the gauche effect in 1,2-difluoroethane, which serves to stabilize the gauche form with the fluorine atoms in close proximity, could also operate in 1,4-difluorobutane. It was found both theoretically and experimentally that the proportion of those conformers having close fluorine atoms was small, implying the absence of effects similar to the gauche effect. The conformational composition estimated from the theoretical calculations is in good agreement with the experimental data. The experimental electron diffraction results constrained by assumptions drawn from the theoretical calculations, ED/MM3 [ED/ab initio], for the principal distances ( {r g}/{Å}) and angles ( {∠ α}/{deg}) with estimated 2σ uncertainties are as follows: r(CH) = 1.105(3) [1.106(3)], r(CF) = 1.398(2) [1.398(2)], r(C 1C 2) = 1.513(2) [1.516(2)], r(C 2C 3) = 1.537(2) [1.532(2)], ∠FCC = 110.9(3) [111.1(3)], ∠CCC = 112.9(4) [112.9(4)], and ∠HCH = 100(3) [100(3)].
Ab initio molecular dynamics using hybrid density functionals.
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; VandeVondele, Joost
2008-06-07
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Ab initio molecular dynamics using hybrid density functionals
NASA Astrophysics Data System (ADS)
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost
2008-06-01
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Towards Accurate Ab Initio Predictions of the Spectrum of Methane
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Kwak, Dochan (Technical Monitor)
2001-01-01
We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.
NASA Astrophysics Data System (ADS)
Singh, Baltej; Gupta, Mayanak Kumar; Mittal, Ranjan; Zbiri, Mohamed; Rols, Stephane; Patwe, Sadequa Jahedkhan; Achary, Srungarpu Nagabhusan; Schober, Helmut; Tyagi, Avesh Kumar; Chaplot, Samrath Lal
2017-02-01
β-Eucryptite (LiAlSiO4) shows anisotropic thermal expansion as well as one-dimensional super-ionic conductivity. We have performed the lattice dynamical calculations using ab-initio density functional theory along with inelastic neutron scattering measurements. The anisotropic stress dependence of the phonon spectrum is calculated to obtain the thermal expansion behavior along various axes. The calculations show that the Grüneisen parameters of the low-energy phonon modes around 10 meV have large negative values and govern the negative thermal expansion behavior at low temperatures along both the "a"- and "c"-axes. On the other hand, anisotropic elasticity along with anisotropic positive values of the Grüneisen parameters of the high-energy modes in the range 30-70 meV are responsible for the thermal expansion at high temperatures, which is positive in the a-b plane and negative along the c-axis. The analysis of the polarization vectors of the phonon modes sheds light on the mechanism of the anomalous thermal expansion behavior. The softening of a Γ-point mode at about 2 GPa may be related to the high-pressure phase transition.
Barrett, Bruce R.; Navrátil, Petr; Vary, James P.
2012-11-17
A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN
Ab initio calculations of the melting temperatures of refractory bcc metals.
Wang, L G; van de Walle, A
2012-01-28
We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental values. We compare the melting temperatures to those obtained from direct ab initio molecular dynamics simulations and see if they are in excellent agreement with each other. The small remaining discrepancies with experiment are thus likely due to inherent limitations associated with exchange-correlation energy approximations within density-functional theory.
2014-08-01
Technical Paper 3. DATES COVERED (From - To) December 2013- August 2014 4. TITLE AND SUBTITLE Ab initio Kinetics of Methylamine Radical Thermal...phase kinetics of H-abstraction reactions from CH3NHNH2 by H atoms was further investigated by ab initio second-order multireference perturbation...distribution unlimited Ab initio Kinetics of Methylamine Radical Thermal Decomposition and H-abstraction from Monomethylhydrazine by H Atom
NASA Astrophysics Data System (ADS)
Parisi, Filippo; Sciascia, Luciana; Princivalle, Francesco; Merli, Marcello
2012-02-01
In order to characterize the pressure-induced decomposition of ringwoodite (γ-Mg2SiO4), the topological analysis of the electron density ρ( r), based upon the theory of atoms in molecules (AIM) developed by Bader in the framework of the catastrophe theory, has been performed. Calculations have been carried out by means of the ab initio CRYSTAL09 code at the HF/DFT level, using Hamiltonians based on the Becke- LYP scheme containing hybrid Hartree-Fock/density functional exchange-correlation terms. The equation of state at 0 K has been constructed for the three phases involved in the post-spinel phase transition (ringwoodite → Mg-perovskite + periclase) occurring at the transition zone-lower mantel boundary. The topological results show that the decomposition of the ringwoodite at high pressures is caused by a conflict catastrophe. Furthermore, topological evidences of the central role played by the oxygen atoms to facilitate the pressure-induced ringwoodite decomposition and the subsequent phase transition have been noticed.
Ekholm, M.; Larsson, P.; Alling, B.; Helmersson, U.; Abrikosov, I. A.
2010-11-15
We perform a combined theoretical and experimental study of the phase stability and magnetism of the off-stoichiometric Ni{sub 1-x}Mn{sub 1+x}Sb in the half-Heusler crystal phase. Our work is motivated by the need for strategies to engineer the magnetism of potentially half-metallic materials, such as NiMnSb, for improved performance at elevated temperatures. By means of ab initio calculations we investigate Ni{sub 1-x}Mn{sub 1+x}Sb over the whole composition range 0{<=}x{<=}1 of Ni replacing Mn and show that at relevant temperatures, the half-Heusler phase should be thermodynamically stable up to at least x=0.20 with respect to the competing C38 structure of Mn{sub 2}Sb. Furthermore we find that half-Heusler Ni{sub 1-x}Mn{sub 1+x}Sb retains half-metallic band structure over the whole concentration range and that the magnetic moments of substitutional Mn{sub Ni} atoms display magnetic exchange interactions an order of magnitude larger than the Ni-Mn interaction in NiMnSb. We also demonstrate experimentally that the alloys indeed can be created by synthesizing off-stoichiometric Ni{sub 1-x}Mn{sub 1+x}Sb films on MgO substrates by means of magnetron sputtering.
NASA Astrophysics Data System (ADS)
Ko, Hsin-Yu; Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto
Hybrid functionals are known to alleviate the self-interaction error in density functional theory (DFT) and provide a more accurate description of the electronic structure of molecules and materials. However, hybrid DFT in the condensed-phase has a prohibitively high associated computational cost which limits their applicability to large systems of interest. In this work, we present a general-purpose order(N) implementation of hybrid DFT in the condensed-phase using Maximally localized Wannier function; this implementation is optimized for massively parallel computing architectures. This algorithm is used to perform large-scale ab initio molecular dynamics simulations of liquid water, ice, and aqueous ionic solutions. We have performed simulations in the isothermal-isobaric ensemble to quantify the effects of exact exchange on the equilibrium density properties of water at different thermodynamic conditions. We find that the anomalous density difference between ice I h and liquid water at ambient conditions as well as the enthalpy differences between ice I h, II, and III phases at the experimental triple point (238 K and 20 Kbar) are significantly improved using hybrid DFT over previous estimates using the lower rungs of DFT This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.
NASA Astrophysics Data System (ADS)
Karoui, K.; Ben Bechir, M.; Bulou, A.; Guidara, K.; Ben Rhaiem, A.
2016-06-01
The X-ray powder diffraction pattern shows that at room temperature, [N(CH3)3H]2CuCl4is crystallized in the monoclinic system with P21/c space group. The phase transitions at T1 ≈ 292/298 K, T2 ≈ 262/264 K and T3 ≈ 241 Khave been confirmed by the differential scanning calorimetry (DSC). Besides, the different phases have been studied by Raman scattering on single crystals, in the frequency range of 60-350 cm-1. The infrared and Raman spectra are attributed on the basis of ab initio calculations of the vibrational spectra. The optimized geometries, calculated vibrational frequencies, infrared intensities and Raman activities of [CuCl4]2- and [N(CH3)3H]+were calculated using the Hartree-Fock (HF) and density functional theory (B3LYP) with 3-21G, 6-31G(d) and 6-311G(d,p)basis sets. The temperature evolution of Raman spectra reveals the existence of phase transitions at T1, T2 and T3 and confirms their nature.
Ab Initio Modeling of Molecular Radiation
NASA Technical Reports Server (NTRS)
Jaffe, Richard; Schwenke, David
2014-01-01
Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.
Discovering chemistry with an ab initio nanoreactor
NASA Astrophysics Data System (ADS)
Martinez, Todd
Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.
Ab Initio Calculation of the Hoyle State
Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.
2011-05-13
The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.
Guiding ab initio calculations by alchemical derivatives
NASA Astrophysics Data System (ADS)
to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.
2016-03-01
We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-01-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less
Experimental and ab initio study of the mechanical properties of hydroxyapatite
NASA Astrophysics Data System (ADS)
Snyders, R.; Music, D.; Sigumonrong, D.; Schelnberger, B.; Jensen, J.; Schneider, J. M.
2007-05-01
The authors have studied the elastic properties of radio frequency sputtered phase pure, stoichiometric, and dense hydroxyapatite films by nanoindentation. The measured elastic modulus values have been compared to ab initio calculated data. The calculation technique was based on the determination of all elastic constants. The calculated and measured elastic modulus values differ by ˜10%. The good agreement indicates that the elasticity of hydroxyapatite can be described using ab initio calculations, establishing the elastic modulus thereof.
Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.
Li, Quan-Song; Zhang, Feng; Fang, Wei-Hai; Yu, Jian-Guo
2006-02-07
In the present work, the wavelength-dependent mechanistic photochemistry of glyoxal in the gas phase has been explored by ab initio calculations of potential-energy surfaces, surface crossing points, and adiabatic and nonadiabatic rates. The CHOCHO molecules in S1 by photoexcitation at 393-440 nm mainly decay to the ground state via internal conversion, which is followed by molecular eliminations to form CO, H2CO,H2, and HCOH. Upon photodissociation of CHOCHO at 350-390 nm, intersystem crossing to T1 followed by the C-C bond cleavage is the dominant process in this wavelength range, which is responsible for the formation of the CHO radicals. The C-C and C-H bond cleavages along the S1 pathway are energetically accessible upon photodissociation of CHOCHO at 290-310 nm, which can compete with the S1-->T1 intersystem crossing process. The present study predicts that the C-H bond cleavage on the S1 surface is probably a new photolysis pathway at high excitation energy, which has not been observed experimentally. In addition, the trans-cis isomerization is predicted to occur more easily in the ground state than in the excited states.
Carbonniere, Philippe; Pouchan, Claude; Improta, Roberto
2015-05-07
We report a study of intramolecular vibrational distribution (IVR) occurring in the electronic ground state of uracil (S0) in the gas phase, following photoexcitation in the lowest energy bright excited state (Sπ) and decay through the ethylene-like Sπ/S0 Conical Intersection (CI-0π). To this aim we have performed 20 independent ab initio molecular dynamics simulations starting from CI-0π (ten of them with 1 eV kinetic energy randomly distributed over the different molecular degrees of freedom) and 10 starting from the ground state minimum (Franck-Condon, FC, point), with the excess kinetic energy equal to the energy gap between CI-0π and the FC point. The simulations, exploiting PBE0/6-31G(d) calculations, were performed over an overall period of 10 ps. A thorough statistical analysis of the variation of the geometrical parameters of uracil during the simulation time and of the distribution of the kinetic energy among the different vibrational degrees of freedom provides a consistent picture of the IVR process. In the first 0-200 fs the structural dynamics involve mainly the recovery of the average planarity. In the 200-600 fs time range, a substantial activation of CO and NH degrees of freedom is observed. After 500-600 fs most of the geometrical parameters reach average values similar to those found after 10 ps, though the system cannot be considered to be in equilibrium yet.
Ab initio study of nontrivial topological phases in corundum-structured (M2O3)/ (Al2O3)5 multilayers
NASA Astrophysics Data System (ADS)
Afonso, Juan F.; Pardo, Victor
2015-12-01
Ab initio calculations have been performed on hexagonal layers of M2O3 (M being several transition metals of the 5 d series) sandwiched by a band insulator such as Al2O3 that provides the honeycomb lattice where the 5 d electrons reside. This corundum-structure-based superlattice is a way to design a honeycomb lattice with transition metal cations avoiding the use of largely polar surfaces. We find that this system supports the presence of Dirac cones at the Fermi level that open up with the introduction of spin-orbit coupling at various fillings of the 5 d band. The DFT calculations performed in this paper show that the 5 d5 situation is always a trivial insulator, whereas the 5 d8 filling presents topological insulating configurations which evolve into a trivial state with increasing tensile strain or on-site Coulomb potential U . However, LDA + U calculations show a stable antiferromagnetic solution for the 5 d8 case at every U value, which would break time reversal symmetry and could affect the topological properties of the system. We also discuss the similarities with the buckled honeycomb lattice obtained using perovskite (111) bilayers previously studied in literature, in particular for the 5 d5 and 5 d8 configurations. This paper provides some clues on the stability of topological phases using metal oxides in general.
The effects of Na on high pressure phases of CuIn(0.5)Ga(0.5)Se(2) from ab initio calculation.
Pluengphon, P; Bovornratanaraks, T; Vannarat, S; Pinsook, U
2012-03-07
The effects of Na atoms on high pressure structural phase transitions of CuIn(0.5)Ga(0.5)Se(2) (CIGS) were studied by an ab initio method using density functional theory. At ambient pressure, CIGS is known to have chalcopyrite (I42d) structure. The high pressure phase transitions of CIGS were proposed to be the same as the order in the CuInSe(2) phase transitions which are I42d → Fm3m → Cmcm structures. By using the mixture atoms method, the Na concentration in CIGS was studied at 0.1, 1.0 and 6.25%. The positive mixing enthalpy of Na at In/Ga sites (Na(InGa)) is higher than that of Na at Cu sites (Na(Cu)). It confirmed previous studies that Na preferably substitutes on the Cu sites more than the (In, Ga) sites. From the energy-volume curves, we found that the effect of the Na substitutes is to reduce the hardness of CIGS under high pressure. The most significant effects occur at 6.25% Na. We also found that the electronic density of states of CIGS near the valence band maximum is increased noticeably in the chalcopyrite phase. The band gap is close in the cubic and orthorhombic phases. Also, the Na(Cu)-Se bond length in the chalcopyrite phase is significantly reduced at 6.25% Na, compared with the pure Cu-Se bond length. Consequently, the energy band gap in this phase is wider than in pure CIGS, and the gap increased at the rate of 31 meV GPa(-1) under pressure. The Na has a small effect on the transition pressure. The path of transformation from the cubic to orthorhombic phase was derived. The Cu-Se plane in the cubic phase displaced relatively parallel to the (In, Ga)-Se plane by 18% in order to transform to the Cmcm phase. The enthalpy barrier is 0.020 eV/atom, which is equivalent to a thermal energy of 248 K. We predicted that Fm3m and Cmcm can coexist in some pressure range.
Havasi, Balázs; Pasinszki, Tibor; Westwood, Nicholas P C
2005-05-05
The unstable trifluoroacetonitrile N-oxide molecule, CF3CNO, has been generated in high yield in the gas phase from CF3BrC=NOH and studied for the first time by gas-phase mid-infrared spectroscopy. Cold trapping of this molecule followed by slow warming forms the stable ring dimer, bis(trifluoromethyl)furoxan, also investigated by gas-phase infrared spectroscopy. The spectroscopy provides an investigation into the vibrational character of the two molecules, the assignments supported by calculations of the harmonic vibrational frequencies using in the case of CF3CNO both ab initio (CCSD(T)) and density functional theory (B3LYP) and B3LYP for the ring dimer. The ground-state structures of both molecules were investigated at the B3LYP level of theory, with CF3CNO further investigated using coupled-cluster. The CCSD(T) method suggests a slightly bent (C(s)) structure for CF3CNO, while the B3LYP method (with basis sets ranging from 6-311G(d) to cc-pVTZ) suggests a close-to-linear or linear CCNO chain. The CCN bending potential in CF3CNO was explored at the CCSD(T)(fc)/cc-pVTZ level, with the results suggesting that CF3CNO exhibits strong quasi-symmetric top behavior with a barrier to linearity of 174 cm(-1). Since both isomerization and dimerization are feasible loss processes for this unstable molecule, the relative stability of CF3CNO with respect to the known cyanate (CF3OCN), isocyanate (CF3NCO), and fulminate (CF3ONC) isomers and the mechanism of the dimerization process to the ring furoxan and other isomers were studied with density functional theory.
Ab Initio: And a New Era of Airline Pilot Training.
ERIC Educational Resources Information Center
Gesell, Laurence E.
1995-01-01
Expansion of air transportation and decreasing numbers seeking pilot training point to a shortage of qualified pilots. Ab initio training, in which candidates with no flight time are trained to air transport proficiency, could resolve the problem. (SK)
Ab initio two-component Ehrenfest dynamics
Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong
2015-09-21
We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H{sub 2} and O{sub 2}. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.
Ab Initio Quantum Simulations of Liquid Water
NASA Astrophysics Data System (ADS)
Gergely, John; Ceperley, David; Gygi, Francois
2007-03-01
Some recent efforts at simulating liquid water have employed ``ab initio'' molecular dynamics (AIMD) methods with forces from a version of density functional theory (DFT) and, in some cases, imaginary-time path integrals (PI) to study quantum effects of the protons. Although AIMD methods have met with many successes, errors introduced by the approximations and choices of simulation parameters are not fully understood. We report on path integral Monte Carlo (PIMC) studies of liquid water using DFT energies that provide quantitative benchmarks for PI-AIMD work. Specifically, we present convergence studies of the path integrals and address whether the Trotter number can be reduced by improving the form of the (approximate) action. Also, we assess 1) whether typical AIMD simulations are sufficiently converged in simulation time, i.e., if there is reason to suspect that nonergodic behavior in PI-AIMD methods leads to poor convergence, and 2) the relative efficiency of the methods. E. Schwegler, J.C. Grossman, F. Gygi, G. Galli, J. Chem. Phys 121, 5400 (2004).
Theoretical calculations of high-pressure phases of NiF2: An ab initio constant-pressure study
NASA Astrophysics Data System (ADS)
Kürkçü, Cihan; Merdan, Ziya; Öztürk, Hülya
2016-12-01
We have studied the structural properties of the antiferromagnetic NiF2 tetragonal structure with P42/ mnm symmetry using density functional theory (DFT) under rapid hydrostatic pressure up to 400 GPa. For the exchange correlation energy we used the local density approximation (LDA) of Ceperley and Alder (CA). Two phase transformations are successfully observed through the simulations. The structures of XF2-type compounds crystallize in rutile-type structure. NiF2 undergoes phase transformations from the tetragonal rutile-type structure with space group P42/ mnm to orthorhombic CaCl2-type structure with space group Pnnm and from this orthorhombic phase to monoclinic structure with space group C2/ m at 152 GPa and 360 GPa, respectively. These phase changes are also studied by total energy and enthalpy calculations. According to these calculations, we perdict these phase transformations at about 1.85 and 30 GPa.
Ab initio construction of magnetic phase diagrams in alloys: The case of Fe1-xMnxPt
Pujari, B. S.; Larson, P.; Antropov, V. P.; ...
2015-07-28
A first-principles approach to the construction of concentration-temperature magnetic phase diagrams of metallic alloys is presented. The method employs self-consistent total energy calculations based on the coherent potential approximation for partially ordered and noncollinear magnetic states and is able to account for competing interactions and multiple magnetic phases. The application to the Fe1–xMnxPt “magnetic chameleon” system yields the sequence of magnetic phases at T = 0 and the c-T magnetic phase diagram in good agreement with experiment, and a new low-temperature phase is predicted at the Mn-rich end. The importance of non-Heisenberg interactions for the description of the magnetic phasemore » diagram is demonstrated.« less
Simple calculation of ab initio melting curves: Application to aluminum
NASA Astrophysics Data System (ADS)
Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean
2015-03-01
We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003), 10.1063/1.1624057] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013), 10.1103/PhysRevE.88.062145]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost.
Phase transitions in double perovskite Sr{sub 2}ScSbO{sub 6}: An Ab-initio study
Ray, Rajyavardhan; Kumar, Uday; Sinha, T. P.
2014-04-24
First Principles study of the electronic properties of recently synthesized double perovskite Sr{sub 2}ScSbO{sub 6} have been performed using density functional theory. With increasing temperature, the Sr compound undergoes three structural phase transitions at 400K, 550K and 650K approximately, leading to the following sequence of phases: P21/n → I2/m → I4/m → Fm-3m. Starting from the monoclinic phase P21/n at room temperature, resulting from the Sc/Sb ordering, the electronic structure for the tetragonal I4/m at 613K and cubic Fm-3m for T≥660K has been studied in terms of the density of states and band-structure. Presence of large band gap, both direct and indirect, has been reported and analyzed.
Skutterudites under pressure: An ab initio study
Ram, Swetarekha; Kanchana, V.; Valsakumar, M. C.
2014-03-07
Ab initio results on the band structure, density of states, and Fermi surface (FS) properties of LaRu{sub 4}X{sub 12} (X = P, As, Sb) are presented at ambient pressure as well as under compression. The analysis of density of states reveals the major contribution at the Fermi level to be mainly from the Ru-d and X-p states. We have a complicated Fermi surface with both electron and hole characters for all the three compounds which is derived mainly from the Ru-d and X-p states. There is also a simpler FS with hole character derived from the P-p{sub z} orbital for LaRu{sub 4}P{sub 12} and Ru-d{sub z{sup 2}} orbital in the case of As and Sb containing compounds. More interestingly, Fermi surface nesting feature is observed only in the case of the LaRu{sub 4}P{sub 12}. Under compression, we observe the topology of the complicated FS sheet of LaRu{sub 4}As{sub 12} to change around V/V{sub 0} = 0.85, leading to a behaviour similar to that of a multiband superconductor, and in addition, we have two more hole pockets centered around Γ at V/V{sub 0} = 0.8 for the same compound. Apart from this, we find the hole pocket to vanish at V/V{sub 0} = 0.8 in the case of LaRu{sub 4}Sb{sub 12} and the opening of the complicated FS sheet gets reduced. The de Haas van Alphen calculation shows the number of extremal orbits in the complicated sheet to change in As and Sb containing compounds under compression, where we also observe the FS topology to change.
Crystal structure of the pressure-induced metallic phase of SiH4 from ab initio theory.
Kim, D Y; Scheicher, R H; Lebègue, S; Prasongkit, J; Arnaud, B; Alouani, M; Ahuja, R
2008-10-28
Metallization of pure solid hydrogen is of great interest, not least because it could lead to high-temperature superconductivity, but it continues to be an elusive goal because of great experimental challenges. Hydrogen-rich materials, in particular, CH(4), SiH(4), and GeH(4), provide an opportunity to study related phenomena at experimentally achievable pressures, and they too are expected to be high-temperature superconductors. Recently, the emergence of a metallic phase has been observed in silane for pressures just above 60 GPa. However, some uncertainty exists about the crystal structure of the discovered metallic phase. Here, we show by way of elimination, that a single structure that possesses all of the required characteristics of the experimentally observed metallic phase of silane from a pool of plausible candidates can be identified. Our density functional theory and GW calculations show that a structure with space group P4/nbm is metallic at pressures >60 GPa. Based on phonon calculations, we furthermore demonstrate that the P4/nbm structure is dynamically stable at >43 GPa and becomes the ground state at 97 GPa when zero-point energy contributions are considered. These findings could lead the way for further theoretical analysis of metallic phases of hydrogen-rich materials and stimulate experimental studies.
Ab initio study of helium behavior in titanium tritides
Liang, J. H.; Dai, Yunya; Yang, Li; Peng, SM; Fan, K. M.; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei
2013-03-01
Ab initio calculations based on density functional theory have been performed to investigate the relative stability of titanium tritides and the helium behavior in stable titanium tritides. The results show that the β-phase TiT1.5 without two tritium along the [100] direction (TiT1.5[100]) is more stable than other possible structures. The stability of titanium tritides decrease with the increased generation of helium in TiT1.5[100]. In addition, helium generated by tritium decay prefers locating at a tetrahedral site, and favorably migrates between two neighbor vacant tetrahedral sites through an intermediate octahedral site in titanium tritides, with a migration energy of 0.23 eV. Furthermore, helium is easily accumulated on a (100) plane in β-phase TiT1.5[100].
Ab Initio Calculations of the N-N Bond Dissociation for the Gas-phase RDX and HMX
NASA Astrophysics Data System (ADS)
Liu, Lin-Lin; Liu, Pei-Jin; Hu, Song-Qi; He, Guo-Qiang
2017-01-01
NO2 fission is a vital factor for 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) decomposition. In this study, the geometry of the gas-phase RDX and HMX molecules was optimized, and the bond order and the bond dissociation energy of the N-N bonds were examined. Moreover, the rate constants of the gas-phase RDX and HMX conformers, concerning the N-N bond dissociation, were evaluated using the microcanonical variational transition state theory (μVT). The calculation results have shown that HMX is more stable than RDX in terms of the N-N bond dissociation, and the conformers stability parameters were as follows: RDXaaa < RDXaae < HMX I < HMX II. In addition, for the RDX conformers, the N-N bond of the pseudo-equatorial positioning of the nitro group was more stable than the N-N bond of the axial positioning of the nitro group, while the results were opposite in the case of the HMX conformers. Moreover, it has been shown that the dissociation rate constant of the N-N bond is influenced by the temperature significantly, thus the rate constants were much lower (<10‑10 s‑1) when the temperature was less than 1000 K.
Thermal conductivity of wurtzite and zinc blende cubic phases of BeO from ab initio calculations
NASA Astrophysics Data System (ADS)
Malakkal, Linu; Szpunar, Barbara; Siripurapu, Ravi Kiran; Zuniga, Juan Carlos; Szpunar, Jerzy A.
2017-03-01
The structural, mechanical, thermal and thermodynamic properties of Beryllium oxide (BeO) in the zinc blende (ZB) and wurtzite (WZ) form have been calculated using the density functional theory (DFT) in the general gradient approximation (GGA). The ground state structural and elastic properties of wurtzite BeO (w-BeO) is calculated using the new GGA ultrasoft pseudopotentials for solids (pbesol); the simulated results have shown excellent agreement with the experiments. The thermodynamic properties are studied using quasi-harmonic approximation (QHA), and the predicted properties agree well for the WZ phase for which the experimental data are available, while for ZB phase it remains to be validated with future experiments. Both Boltzmann transport equation (BTE) and Slack model were used to calculate the lattice thermal conductivity of wurtzite BeO (w-BeO). Furthermore, the thermal conductivity along the crystallographic 'a' and 'c' axis of wurtzite BeO is investigated using BTE. Our calculation of w-BeO agrees well with the available experimental measurements. Apart from these studies on w-BeO, we have also compared the mechanical, structural and phonon dispersions of z-BeO with previously reported theoretical studies. Additionally we report the volume thermal expansion and the heat capacity at constant pressure of z-BeO for the first time and the bulk thermal conductivity of zinc blende BeO (z-BeO) using BTE.
Ab Initio Calculations of the N-N Bond Dissociation for the Gas-phase RDX and HMX
Liu, Lin-lin; Liu, Pei-jin; Hu, Song-qi; He, Guo-qiang
2017-01-01
NO2 fission is a vital factor for 1,3,5-Trinitroperhydro-1,3,5-triazine (RDX) and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) decomposition. In this study, the geometry of the gas-phase RDX and HMX molecules was optimized, and the bond order and the bond dissociation energy of the N-N bonds were examined. Moreover, the rate constants of the gas-phase RDX and HMX conformers, concerning the N-N bond dissociation, were evaluated using the microcanonical variational transition state theory (μVT). The calculation results have shown that HMX is more stable than RDX in terms of the N-N bond dissociation, and the conformers stability parameters were as follows: RDXaaa < RDXaae < HMX I < HMX II. In addition, for the RDX conformers, the N-N bond of the pseudo-equatorial positioning of the nitro group was more stable than the N-N bond of the axial positioning of the nitro group, while the results were opposite in the case of the HMX conformers. Moreover, it has been shown that the dissociation rate constant of the N-N bond is influenced by the temperature significantly, thus the rate constants were much lower (<10−10 s−1) when the temperature was less than 1000 K. PMID:28094774
Phase diagram, chemical bonds, and gap bowing of cubic InxAl1-xN alloys: Ab initio calculations
NASA Astrophysics Data System (ADS)
Teles, L. K.; Scolfaro, L. M. R.; Leite, J. R.; Furthmüller, J.; Bechstedt, F.
2002-12-01
Thermodynamic, structural, and electronic properties of cubic InxAl1-xN alloys are studied by combining first-principles total energy calculations and the generalized quasichemical approach. Results for bond-lengths, second-nearest-neighbors distances, and bond angles in the alloy are presented. The calculated phase diagram of the alloy shows a broad and asymmetric miscibility gap. The gap fluctuations in the alloy allow for the definition of a minimum gap and an average gap with different bowing parameters, that can provide an explanation for the discrepancies found in the experimental values for the bowing parameter. It is also found that lattice matched In0.2Al0.8N with GaN is suitable to form a barrier material for electronic and optoelectronic nitride based devices.
THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY
Turchi, P A
2004-09-24
Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics '{acute a} la CALPHAD'. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys. Finally, comments will be made on challenges and future prospects.
Ab initio study of II-(VI)2 dichalcogenides
NASA Astrophysics Data System (ADS)
Olsson, P.; Vidal, J.; Lincot, D.
2011-10-01
The structural stabilities of the (Zn,Cd)(S,Se,Te)2 dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe2 pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications.
Ab initio quantum transport in atomic carbon chains
NASA Astrophysics Data System (ADS)
Botello-Méndez, Andrés R.; Charlier, Jean-Christophe; Banhart, Florian; NAPS Team; Carbyne Collaboration
2015-03-01
Carbyne, the sp-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. Recently, detailed electrical measurements and first-principles electronic transport calculations have been performed on monoatomic carbon chains. When the 1D system is under strain, the current-voltage curves exhibit a semiconducting behavior, which corresponds to the polyyne structure of the atomic chain with alternating single and triple bonds. Conversely, when the chain is unstrained, the ohmic behavior is observed in agreement with the metallic cumulene structure with double bonds, confirming recent theoretical predictions, namely that a metal-insulator transition can be induced by adjusting the strain. The key role of the contacting leads is also scrutinized by ab initio quantum conductance calculations, explaining the rectifying behavior measured in monoatomic carbon chains in a non-symmetric contact configuration.
Ab-initio theory of spin fluctuations in magnets
NASA Astrophysics Data System (ADS)
Antropov, Vladimir; Ke, Liqin; van Schilfgaarde, Mark; Katsnelson, Mikhael
2011-03-01
We propose a framework for a true ab initio theory of magnetism, based on many-body perturbation theory (MPBT). It fits in naturally with methods based MPBT such as the GW approximation; but the approach can be implemented as an extension to any existing static method for electronic structure such as the local spin density approximation to density functional theory, to include spin fluctuations. Initially we calculated the spin fluctuation contributions using random phase approximation. The self consistency procedure similar to the one used in Moryia-Kawabata theory can be naturally implemented. The fluctuation dissipation theorem is used to calculate the reduction of the mean field magnetic moment in itinerant magnets. The applications of the technique includes traditional 3d ferromagnetic metals, their alloys and compounds and 5f systems.
Ab initio computations of photodissociation products of CFC alternatives
Tai, S.; Illinger, K.H.; Kenny, J.E.
1995-12-31
Ab initio computations, have already been used to examine the energetics of the photodissociation of stratospheric chlorofluorocarbons. Our awn research has investigated the ab initio computation of vibrational frequencies and infrared intensities of CF{sub 3}CH{sub 2}F, CF{sub 3}CF{sub 2}H, and CF{sub 3}CH{sub 3}; continuing research will attempt to expand these computations to the energetics of the photodissociation of these molecules, since sane of the most common types of chlorofluorocarbon substitutes are hydrofluoroethanes.
Global exploration of the energy landscape of solids on the ab initio level.
Doll, K; Schön, J C; Jansen, M
2007-12-14
Predicting which crystalline modifications can be present in a chemical system requires the global exploration of its energy landscape. Due to the large computational effort involved, in the past this search for sufficiently stable minima has been performed employing a variety of empirical potentials and cost functions followed by a local optimization on the ab initio level. However, this entails the risk of overlooking important modifications that are not modeled accurately using empirical potentials. In order to overcome this critical limitation, we develop an approach to employ ab initio energy functions during the global optimization phase of the structure prediction. As an example, we perform a global exploration of the landscape of LiF on the ab initio level and show that the relevant crystalline modifications are found during the search.
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions.
Changlani, Hitesh J; Zheng, Huihuo; Wagner, Lucas K
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U(∗)/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
NASA Astrophysics Data System (ADS)
Lucas, J. M.; de Andrés, J.; López, E.; Albertí, M.; Bofill, J. M.; Bassi, D.; Ascenzi, D.; Tosi, P.; Aguilar, A.
2009-08-01
The association reactions between Li+, K+, and Rb+ (M) and butanone and cyclohexanone molecules under single collision conditions have been studied using a radiofrequency-guided ion-beam apparatus, characterizing the adducts by mass spectrometry. The excitation function for the [M-(molecule)]+ adducts (in arbitrary units) has been obtained at low collision energies in the 0.10 eV up to a few eV range in the center of mass frame. The measured relative cross sections decrease when collision energy increases, showing the expected energy dependence for adduct formation. The energetics and structure of the different adducts have been calculated ab initio at the MP2(full) level, showing that the M+-molecule interaction takes place through the carbonyl oxygen atom, as an example of a nontypical covalent chemical bond. The cross-section energy dependence and the role of radiative cooling rates allowing the stabilization of the collision complexes are also discussed.
Ab-Initio Study of Incongruent Melting in Silicates
NASA Astrophysics Data System (ADS)
Pinilla, C.; Stixrude, L. P.
2014-12-01
Knowledge of the multi-component thermodynamics and phase equilibria of silicate melts at Earth's interior conditions are key to understand the chemical and thermal evolution of the planet. Yet they remain poorly constrained with a wide uncertainty on the eutectic composition and temperature. In this work we present results from ab-initio molecular dynamics in combination with the two-phase coexistance method to study properties of a system of MgSiO3 liquid coexisting with crystalline MgO at conditions of the deep lower mantle. During incongruent melting the crystal may either grow via partial freezing of the liquid or shrink via partial melting at a given temperature and pressure. The melting process can be studied using the two-phases method where liquid and solid are in contact at a given temperature and pressure and so under thermodynamic equilibrium. We characterise the composition and densities of the resultant solid and liquid phases, provide chemical potentials of the liquid phase and study the structural and dynamical properties of the melt. In addition, we discuss the performance of alternative computational methods applied to the study of incongruent melting in silicate systems where long simulation times and a large number of atoms are usually needed. Finally, we discuss the implication of our findings for the evolution of the Earth's interior.
Ab Initio Infrared and Raman Spectra.
1982-08-01
tions. For parameters not depending on momenta, a parallel ab fhti Monte Carlo approach would use electronic energies and other parameters of... Monte Carlo approach. Specifically, as one of us has suggested,t I classical molecular dynamics may be integrated with ab iniHo quan- tum force...alternative approach, for phenomena which are not explicitly time dependent, is a Monte Carlo procedure in which at each trial nuclear configuration
Multiple time step integrators in ab initio molecular dynamics
Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.
2014-02-28
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.
Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures
Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan
2006-04-05
A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.
Towards SiC Surface Functionalization: An Ab Initio Study
Cicero, G; Catellani, A
2005-01-28
We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.
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.
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.
Computer simulation of acetonitrile and methanol with ab initio-based pair potentials
NASA Astrophysics Data System (ADS)
Hloucha, M.; Sum, A. K.; Sandler, S. I.
2000-10-01
This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.
Lead-Chalcogenides Under Pressure: Ab-Initio Study
NASA Astrophysics Data System (ADS)
Gupta, Dinesh C.; Hamid, Idris
ab-initio calculations using fully relativistic pseudo-potential have been performed to investigate the high pressure phase transition, elastic and electronic properties of lead-chalcogenides including the less known lead polonium. The calculated ground state parameters, for the rock-salt structure show good agreement with the experimental data. The enthalpy calculations show that these materials undergo a first-order phase transition from rock-salt to CsCl structure at 19.4, 15.5, 11.5 and 7.3 GPa for PbS, PbSe, PbTe and PbPo, respectively. Present calculations successfully predicted the location of the band gap at L-point of Brillouin zone as well as the value of the band gap in every case at ambient pressure. It is observed that unlike other lead-chalcogenides, PbPo is semi-metal at ambient pressure. The pressure variation of the energy gap indicates that these materials metalized under high pressures. For this purpose, the electronic structure of these materials has also been computed in parent as well as in high pressure phase.
Ab initio Raman spectroscopy of water under extreme conditions
NASA Astrophysics Data System (ADS)
Rozsa, Viktor; Pan, Ding; Wan, Quan; Galli, Giulia
Water exhibits one of the most complex phase diagrams of any binary compound. Despite extensive studies, the melting lines of high-pressure ice phases remain very controversial, with reports differing by hundreds of Kelvin. The boundary between ice VII and liquid phase is particularly disputed, with recent work exploring plasticity and amorphization mediating the transition. Raman measurements are often used to fingerprint melting, yet their interpretation is difficult without atomistic modeling. Here, we report a study of high P/T water where we computed Raman spectra using a method combining ab initio molecular dynamics and density functional perturbation theory, as implemented in the Qbox code. Spectra were computed for the liquid at 10 and 20 GPa, both at 1000 K, and for solid ice VII (20 GPa, 500 K). Decomposing the spectra into inter and intra molecular contributions provided insight into the dynamics of the hydrogen-bonded network at extreme conditions. The relevance of our simulation results for models of water in Earth, Uranus, and Neptune will be discussed, and an interpretation of existing experiments at high pressure will be presented.
Ab initio studies of niobium defects in uranium
Xiang, S; Huang, H; Hsiung, L
2007-06-01
Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.
Exploring the free energy surface using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-01
Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.
Yamaji, Youhei
2015-12-31
Recently, condensed-matter ab initio approaches to strongly correlated electrons confined in crystalline solids have been developed and applied to transition-metal oxides and molecular conductors. In this paper, an ab initio scheme based on constrained random phase approximations and localized Wannier orbitals is applied to a spin liquid candidate Na{sub 2}IrO{sub 3} and is shown to reproduce experimentally observed specific heat.
The Pu-U-Am system: An ab initio informed CALPHAD thermodynamic study
NASA Astrophysics Data System (ADS)
Perron, A.; Turchi, P. E. A.; Landa, A.; Söderlind, P.; Ravat, B.; Oudot, B.; Delaunay, F.
2015-03-01
Phase diagram and thermodynamic properties of the Am-U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu-U and Am-Pu thermodynamic assessments are combined to build a Pu-U-Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies.
Protons in polar media: An ab initio molecular dynamics study
NASA Astrophysics Data System (ADS)
von Rosenvinge, Tycho
1998-10-01
The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations
Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S. E-mail: hochlaf@univ-mlv.fr; Linguerri, Roberto; Hochlaf, Majdi E-mail: hochlaf@univ-mlv.fr
2013-11-07
Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.
Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung
2014-09-01
A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ{sub 1} and ϕ{sub 2}) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ{sub DS} list as a criterion to select optimized phases ϕ{sub am} from ϕ{sub 1} or ϕ{sub 2} of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ{sub SAD} has been developed. Based on this work, reflections with an angle θ{sub DS} in the range 35–145° are selected for an optimized improvement, where θ{sub DS} is the angle between the initial phase ϕ{sub SAD} and a preliminary density-modification (DM) phase ϕ{sub DM}{sup NHL}. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.
Separable metamaterials: analytical ab-initio homogenization and chirality
NASA Astrophysics Data System (ADS)
Ciattoni, Alessandro; Rago, Domenico; Rizza, Carlo
2016-11-01
We investigate the ab-initio homogenization of separable metamaterials with factorized dielectric permittivity profiles, which can be achieved through suitable grey-scale permittivity design techniques. Separability allows such metamaterials to be physically regarded as the superposition of three fictitious 1D generating media. We prove that, in the long-wavelength limit, separable metamaterials admit a simple and analytical description of their electromagnetic bi-anisotropic response, which can be reconstructed from the properties of the 1D generating media. Our approach provides a strategy that allows the full ab-initio and flexible design of a complex bianisotropic response by using the simple and well-known properties of 1D metamaterials.
High Level Ab Initio Kinetics as a Tool for Astrochemistry
NASA Astrophysics Data System (ADS)
Klippenstein, Stephen
2015-05-01
We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.
Ab Initio Calculations Of Light-Ion Reactions
Navratil, P; Quaglioni, S; Roth, R; Horiuchi, W
2012-03-12
The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.
Ab initio theories for light nuclei and neutron stars
NASA Astrophysics Data System (ADS)
Gezerlis, Alexandros
2016-09-01
In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).
Spin-orbit decomposition of ab initio nuclear wave functions
NASA Astrophysics Data System (ADS)
Johnson, Calvin W.
2015-03-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.
Ab initio study of MoS2 nanotube bundles
NASA Astrophysics Data System (ADS)
Verstraete, Matthieu; Charlier, Jean-Christophe
2003-07-01
Recently, the synthesis of a new phase of MoS2I1/3 stoichiometry was reported [M. Remskar, A. Mrzel, Z. Skraba, A. Jesih, M. Ceh, J. Demšar, P. Stadelmann, F. Lévy, and D. Mihailovic, Science 292, 479 (2001)]. Electron microscope images and diffraction data were interpreted to indicate bundles of sub-nanometer-diameter single-wall MoS2 nanotubes. After experimental characterization, the structure was attributed to an assembly of “armchair” nanotubes with interstitial iodine. Using first-principles total-energy calculations, bundles of MoS2 nanotubes with different topologies and stoichiometries are investigated. All of the systems are strongly metallic. Configurations with “zigzag” structures are found to be more stable energetically than the “armchair” ones, though all of the structures have similar stabilities. After relaxation, there remain several candidates which give a lattice parameter in relative agreement with experiment. Further, spin-polarized calculations indicate that a structure with armchair tubes iodine atoms in their center acquires a very large spontaneous magnetic moment of 12μB, while the other structures are nonmagnetic. Our ab initio calculations show that in most of the other structures, the tubes are very strongly bound together, and that the compounds should be considered as a crystal, rather than as a bundle of tubes in the habitual sense.
Challenges for large scale ab initio Quantum Monte Carlo
NASA Astrophysics Data System (ADS)
Kent, Paul
2015-03-01
Ab initio Quantum Monte Carlo is an electronic structure method that is highly accurate, well suited to large scale computation, and potentially systematically improvable in accuracy. Due to increases in computer power, the method has been applied to systems where established electronic structure methods have difficulty reaching the accuracies desired to inform experiment without empiricism, a necessary step in the design of materials and a helpful step in the improvement of cheaper and less accurate methods. Recent applications include accurate phase diagrams of simple materials through to phenomena in transition metal oxides. Nevertheless there remain significant challenges to achieving a methodology that is robust and systematically improvable in practice, as well as capable of exploiting the latest generation of high-performance computers. In this talk I will describe the current state of the art, recent applications, and several significant challenges for continued improvement. Supported through the Predictive Theory and Modeling for Materials and Chemical Science program by the Office of Basic Energy Sciences (BES), Department of Energy (DOE).
Predicting lattice thermal conductivity with help from ab initio methods
NASA Astrophysics Data System (ADS)
Broido, David
2015-03-01
The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. This research was supported primarily by the NSF under Grant CBET-1402949, and by the S3TEC, an Energy Frontier Research Center funded by the US DOE, office of Basic Energy Sciences under Award No. DE-SC0001299.
Ab Initio Atomistic Thermodynamics for Surfaces: A Primer
2006-02-01
Ab Initio Atomistic Thermodynamics for Surfaces: A Primer Jutta Rogal and Karsten Reuter Fritz - Haber -Institut der Max-Planck-Gesellschaft... Fritz - Haber -Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING...of the Fritz - Haber -Institut, in particular Wei-Xue Li, Cathy Stampfl and Mira Todorova. Particular thanks go to Matthias Scheffler for his continued
The study of molecular spectroscopy by ab initio methods
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.
1991-01-01
This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.
GAUSSIAN 76: An ab initio Molecular Orbital Program
DOE R&D Accomplishments Database
Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.
1978-01-01
Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.
Ab initio calculations for industrial materials engineering: successes and challenges.
Wimmer, Erich; Najafabadi, Reza; Young, George A; Ballard, Jake D; Angeliu, Thomas M; Vollmer, James; Chambers, James J; Niimi, Hiroaki; Shaw, Judy B; Freeman, Clive; Christensen, Mikael; Wolf, Walter; Saxe, Paul
2010-09-29
Computational materials science based on ab initio calculations has become an important partner to experiment. This is demonstrated here for the effect of impurities and alloying elements on the strength of a Zr twist grain boundary, the dissociative adsorption and diffusion of iodine on a zirconium surface, the diffusion of oxygen atoms in a Ni twist grain boundary and in bulk Ni, and the dependence of the work function of a TiN-HfO(2) junction on the replacement of N by O atoms. In all of these cases, computations provide atomic-scale understanding as well as quantitative materials property data of value to industrial research and development. There are two key challenges in applying ab initio calculations, namely a higher accuracy in the electronic energy and the efficient exploration of large parts of the configurational space. While progress in these areas is fueled by advances in computer hardware, innovative theoretical concepts combined with systematic large-scale computations will be needed to realize the full potential of ab initio calculations for industrial applications.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.
Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Draayer, Jerry P.
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Diffusion in liquid Germanium using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.
1996-03-01
We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.
A highly accurate ab initio potential energy surface for methane
NASA Astrophysics Data System (ADS)
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2016-09-01
A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of 12CH4 reproduced with a root-mean-square error of 0.70 cm-1. The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.
Ab initio rotation-vibration spectra of HCN and HNC
NASA Astrophysics Data System (ADS)
Harris, Gregory J.; Polyansky, Oleg L.; Tennyson, Jonathan
2002-03-01
We have calculated an ab initio HCN/HNC linelist for all transitions up to J=25 and 18 000 cm -1 above the zero point energy. This linelist contains more than 200 million lines each with frequencies and transition dipoles. The linelist has been calculated using our semi-global HCN/HNC VQZANO+PES and dipole moment surface, which were reported in van Mourik et al. (J. Chem. Phys. 115 (2001) 3706). With this linelist we synthesise absorption spectra of HCN and HNC at 298 K and we present the band centre and band transition dipoles for the bands which are major features in these spectra. Several of the HCN bands and many of the HNC bands have not been previously studied. Our line intensities reproduce via fully ab initio methods the unusual intensity structure of the HCN CN stretch fundamental (00 01) for the first time and also the forbidden (02 20) HCN bending overtone. We also compare the J=1→0 pure rotational transition dipole in the HCN/HNC ground and vibrationally excited states with experimental and existing ab initio results.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
NASA Astrophysics Data System (ADS)
Kolobov, A. V.; Fons, P.; Krbal, M.; Mitrofanov, K.; Tominaga, J.; Uruga, T.
2017-02-01
Phase-change memories are usually associated with GeTe-Sb2Te3 quasibinary alloys, where the large optical contrast between the crystalline and amorphous phases is attributed to the formation of resonant bonds in the crystalline phase, which has a rocksalt-like structure. The recent findings that tetrahedrally bonded Ga2Te3 possesses a similarly large property contrast and very low thermal conductivity in the crystalline phase and undergoes low-energy switching [H. Zhu et al., Appl. Phys. Lett. 97, 083504 (2010), 10.1063/1.3483762; K. Kurosaki et al., Appl. Phys. Lett. 93, 012101 (2008), 10.1063/1.2940591] challenge the existing paradigm. In this work we report on the local structure of the crystalline and amorphous phases of Ga2Te3 obtained from x-ray absorption measurements and ab initio simulations. Based on the obtained results, a model of phase change in Ga2Te3 is proposed. We argue that efficient switching in Ga2Te3 is due to the presence of primary and secondary bonding in the crystalline phase originating from the high concentration of Ga vacancies, whereas the structural stability of both phases is ensured by polyvalency of Te atoms due to the presence of lone-pair electrons and the formation of like-atom bonds in the amorphous phase.
NASA Astrophysics Data System (ADS)
Li, Xia; Zhang, Xiaomei; Yan, Bing
2015-05-01
Ab initio calculations have been performed on the low-lying excited and ground states of PH+. The potential energy curves (PECs) of the Λ-S states were calculated with multi-reference configuration interaction (MRCI) method along with the basis sets at 5-ξ level. In order to improve the PECs, the Davidson(+Q) correction and the Scalar relativistic effect are included. The corresponding spectroscopic constants were determined and good agreements with the available measurement were found. The interactions of the A2Δ-4Π and 12Σ+-4Π by the spin-orbit coupling (SOC) effect were well described by the spin-orbit matrix elements. The SOC effect makes the original 8 Λ-S states split into 15 Ω states. The Ω = 1/2 state generated from the X2Π state is confirmed to the ground Ω state. And the SOC splitting for the X2Π is calculated to be 294 cm-1. The SOC effect has large effect on the PECs of the A2Δ and 12Σ+ states, leading to much more shallow potential wells as well as potential barriers. The analysis of the wavefunction for the Ω states shows that the strong spin-orbit interaction exists near the crossing points of the PECs for the Λ-S states. The transition dipole moments (TDMs) of transitions A2Δ-X2Π and 12Σ--X2Π are evaluated with the MRCI wavefunction. Based on the TDMs along with the calculated Franck-Condon factors, the radiative lifetimes for the selected vibrational levels of A2Δ and 12Σ- states are predicted at the microseconds (μs). Good agreement with the measurement shows that the lowest vibrational level for A2Δ state is almost uninfluenced by the perturbation via the SOC effect.
NASA Astrophysics Data System (ADS)
Wei, Yong-Kai; Ge, Ni-Na; Chen, Xiang-Rong; Ji, Guang-Fu; Cai, Ling-Cang; Gu, Zhuo-Wei
2014-03-01
The phase transition, thermoelastic, lattice dynamic, and thermodynamic properties of the cubic metallic phase AlH3 were obtained within the density-function perturbation theory. The calculated elastic modulus and phonon dispersion curves under various pressures at 0 K indicate the cubic phase is both mechanically and dynamically stable above 73 GPa. The superconducting transition temperature Tc was calculated using the Allen-Dynes modification of the McMillan formula based on BCS theory. The calculations show that Tc for the cubic phase AlH3 is 8.5 K (μ*=0.1) at the onset of this phase (73 GPa), while decreases to 5.7 K at 80 GPa and almost disappears at 110 GPa, consisting with experimental phenomenon that there was no superconducting transition observed down to 4 K over a wide pressure range 110-164 GPa. It is found that the soft phonon mode for branch 1, namely, the lowest acoustic mode, plays a crucial role in elevating the total EPC parameter λ of cubic AlH3. And the evolution of Tc with pressure follows the corresponding change of this soft mode, i.e. this mode is responsible for the disappearance of Tc in experiments. Meanwhile, the softening of this lowest acoustic mode originates from the electronic momentum transfer from M to R point. This phenomenon provides an important insight into why drastic changes in the diffraction pattern were observed in the pressure range of 63-73 GPa in Goncharenko's experiments. Specifically, once finite electronic temperature effects are included, we find that dynamical instabilities can be removed in the phonon dispersion for P ≥63 GPa, rendering the metastability of this phase in the range of 63-73 GPa, and Tc (15.4 K) becomes remarkably high under the lowest possible pressure (63 GPa) compared with that of under 73 GPa (8.5 K). Our calculations open the possibility that finite temperature may allow cubic AlH3 to be dynamically stabilized even for pressures below 73 GPa. It is reasonable to deduced that if special
Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective
NASA Astrophysics Data System (ADS)
Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge
2013-03-01
Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at < 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ~300 K across the entire pressure range considered.
Optical and other material properties of SiO2 from ab initio studies
NASA Astrophysics Data System (ADS)
Warmbier, Robert; Mohammed, Faris; Quandt, Alexander
2014-07-01
The optical properties of photonic devices largely depend on the dielectric properties of the underlying materials. We apply modern ab initio methods to study crystalline SiO2 phases, which serve as toy models for amorphous glass. We discuss the dielectric response from the infrared to the VIS/UV, which is crucial for glass based photonic applications. Low density silica, like cristobalite, may provide a good basis for high transmission optical devices.
Ab initio molecular dynamics of liquid hydrogen chloride
NASA Astrophysics Data System (ADS)
Dubois, Vincent; Pasquarello, Alfredo
2005-03-01
We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (ℓ-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)2 dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in ℓ-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.
Ab initio molecular simulations with numeric atom-centered orbitals
NASA Astrophysics Data System (ADS)
Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias
2009-11-01
We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.
Ab initio Study of He Stability in hcp-Ti
Dai, Yunya; Yang, Li; Peng, SM; Long, XG; Gao, Fei; Zu, Xiaotao T.
2010-12-20
The stability of He in hcp-Ti was studied using ab initio method based on density functional theory. The results indicate that a single He atom prefers to occupy the tetrahedral site rather than the octahedral site. The interaction of He defects with Ti atoms has been used to explain the relative stabilities of He point defects in hcp-Ti. The relative stability of He defects in hcp-Ti is useful for He clustering and bubble nucleation in metal tritides, which provides the basis for development of improved atomistic models.
Pseudorotation motion in tetrahydrofuran: an ab initio study.
Rayón, Víctor M; Sordo, Jose A
2005-05-22
The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.
Accelerating ab initio molecular dynamics simulations by linear prediction methods
NASA Astrophysics Data System (ADS)
Herr, Jonathan D.; Steele, Ryan P.
2016-09-01
Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.
Morphing ab initio potential energy curve of beryllium monohydride
NASA Astrophysics Data System (ADS)
Špirko, Vladimír
2016-12-01
Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.
Ab initio evidence for nonthermal characteristics in ultrafast laser melting
NASA Astrophysics Data System (ADS)
Lian, Chao; Zhang, S. B.; Meng, Sheng
2016-11-01
Laser melting of semiconductors has been observed for almost 40 years; surprisingly, it is not well understood where most theoretical simulations show a laser-induced thermal process. Ab initio nonadiabatic simulations based on real-time time-dependent density functional theory reveal intrinsic nonthermal melting of silicon, at a temperature far below the thermal melting temperature of 1680 K. Both excitation threshold and time evolution of diffraction intensity agree well with experiment. Nonthermal melting is attributed to excitation-induced drastic changes in bonding electron density, and the subsequent decrease in the melting barrier, rather than lattice heating as previously assumed in the two-temperature models.
Communication: Ab initio Joule-Thomson inversion data for argon
NASA Astrophysics Data System (ADS)
Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter
2013-02-01
The Joule-Thomson coefficient μH(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.
Ab initio quantum chemical study of electron transfer in carboranes
NASA Astrophysics Data System (ADS)
Pati, Ranjit; Pineda, Andrew C.; Pandey, Ravindra; Karna, Shashi P.
2005-05-01
The electron transfer (ET) properties of 10- and 12-vertex carboranes are investigated by the ab initio Hartree-Fock method within the Marcus-Hush (MH) two-state model and the Koopman theorem (KT) approach. The calculated value of the ET coupling matrix element, VAB, is consistently higher in the KT approach than in the MH two-state model. For the carborane molecules functionalized by -CH 2 groups at C-vertices, VAB strongly depends on the relative orientation of the planes containing the terminal -CH 2 groups. The predicted conformation dependence of VAB offers a molecular mechanism to control ET between two active centers in molecular systems.
Ab-Initio Shell Model with a Core
Lisetskiy, A F; Barrett, B R; Kruse, M; Navratil, P; Stetcu, I; Vary, J P
2008-06-04
We construct effective 2- and 3-body Hamiltonians for the p-shell by performing 12{h_bar}{Omega} ab initio no-core shell model (NCSM) calculations for A=6 and 7 nuclei and explicitly projecting the many-body Hamiltonians onto the 0{h_bar}{Omega} space. We then separate these effective Hamiltonians into 0-, 1- and 2-body contributions (also 3-body for A=7) and analyze the systematic behavior of these different parts as a function of the mass number A and size of the NCSM basis space. The role of effective 3- and higher-body interactions for A > 6 is investigated and discussed.
Ab-initio study of transition metal hydrides
Sharma, Ramesh; Shukla, Seema Dwivedi, Shalini Sharma, Yamini
2014-04-24
We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.
Ab Initio Calculations Applied to Problems in Metal Ion Chemistry
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)
1994-01-01
Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.
Electric field response in bilayer graphene: Ab initio investigation
NASA Astrophysics Data System (ADS)
Mori, Yutaro; Minamitani, Emi; Ando, Yasunobu; Kasamatsu, Shusuke; Watanabe, Satoshi
2016-11-01
Stimulated by quantum capacitance measurements, we have investigated the electric properties of bilayer graphene (BLG) with carrier doping under an external electric field using ab initio calculations. We found that the relative permittivity of BLG depends weakly on the applied electric field, and that the BLG can be regarded as a dielectric material rather than a pair of metallic films. We also found that carrier doping affects the band gap of BLG under electric fields, although carrier doping has a much smaller effect on the band gap and density of states than the application of electric fields.
Communication: Ab initio Joule-Thomson inversion data for argon.
Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter
2013-02-21
The Joule-Thomson coefficient μ(H)(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.
Ab initio study of AlxMoNbTiV high-entropy alloys.
Cao, Peiyu; Ni, Xiaodong; Tian, Fuyang; Varga, Lajos K; Vitos, Levente
2015-02-25
The Al(x)MoNbTiV (x = 0-1.5) high-entropy alloys (HEAs) adopt a single solid-solution phase, having the body centered cubic (bcc) crystal structure. Here we employ the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to investigate the equilibrium volume, elastic constants, and polycrystalline elastic moduli of Al(x)MoNbTiV HEAs. A comparison between the ab initio and experimental equilibrium volumes demonstrates the validity and accuracy of the present approach. Our results indicate that Al addition decreases the thermodynamic stability of the bcc structure with respect to face-centered cubic and hexagonal close packed lattices. For the elastically isotropic Al(0.4)MoNbTiV HEAs, the valence electron concentration (VEC) is about 4.82, which is slightly different from VEC ∼ 4.72 obtained for the isotropic Gum metals and refractory--HEAs.
NASA Astrophysics Data System (ADS)
Whitfield, T. W.; Crain, J.; Martyna, G. J.
2006-03-01
In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.
Geng, Hua Y.
2015-02-15
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.
NASA Astrophysics Data System (ADS)
Geng, Hua Y.
2015-02-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.
Three-cluster dynamics within an ab initio framework
Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr
2013-09-26
In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to amore » 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core (4He) polarization effects.« less
Ab initio study of hot electrons in GaAs.
Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B; Louie, Steven G
2015-04-28
Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron-phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron-phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron-phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials.
Emission Spectroscopy and Ab Initio Calculations for TaN
NASA Astrophysics Data System (ADS)
Ram, R. S.; Liévin, J.; Bernath, P. F.
2002-10-01
The emission spectra of TaN have been investigated in the region 3000-35 000 cm -1 using a Fourier transform spectrometer. The spectra were observed in a tantalum hollow-cathode lamp by discharging a mixture of 1.5 Torr of Ne and about 6 mTorr of N 2. In addition to previously known bands, numerous additional bands were observed and assigned to a number of new transitions. The spectroscopic properties of the low-lying electronic states of TaN were also predicted by ab initio calculations. A 1Σ + state, with equilibrium constants of Be=0.457 852 1(48) cm -1, α e=0.002 235 9(67) cm -1, and Re=1.683 099 9(88) Å, has been identified as the ground state of TaN based on our experimental observations supported by the ab initio results. The first excited state has been identified as the a3Δ 1 spin component at 2827 cm -1 above the ground state. To higher energies, the states become difficult to assign because of their Hund's case (c) behavior and extensive interactions between the spin components of the electronic terms.
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-01-01
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906
Ab initio thermodynamic model for magnesium carbonates and hydrates.
Chaka, Anne M; Felmy, Andrew R
2014-09-04
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.
Unified ab initio approaches to nuclear structure and reactions
Navratil, Petr; Quaglioni, Sofia; Hupin, Guillaume; ...
2016-04-13
The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Bemore » $${({\\rm{p}},\\gamma )}^{8}{\\rm{B}}$$ radiative capture. Lastly, we highlight our efforts to describe transfer reactions including the 3H$${({\\rm{d}},{\\rm{n}})}^{4}$$He fusion.« less
Implementation of renormalized excitonic method at ab initio level.
Zhang, Hongjiang; Malrieu, Jean-Paul; Ma, Haibo; Ma, Jing
2012-01-05
The renormalized excitonic method [Hajj et al., Phys Rev B 2005, 72, 224412], in which the excited state of the whole system may be described as a linear combination of local excitations, has been implemented at ab initio level. Its performance is tested on the ionization potential and the energy gap between singlet ground state and lowest triplet for linear molecular hydrogen chains and more realistic systems, such as polyenes and polysilenes, using full configuration interaction (FCI) wave functions with a minimal basis set. The influence of different block sizes and the extent of interblock interactions are investigated. It has been demonstrated that satisfactory results can be obtained if the near degeneracies between the model space and the outer space are avoided and if interactions between the next-nearest neighbor blocks are considered. The method can be used with larger basis sets and other accurate enough ab initio evaluations (instead of FCI) of local excited states, from blocks, or from dimers or trimers of blocks. It provides a new possibility to accurately and economically describe the low-lying delocalized excited states of large systems, even inhomogeneous ones.
AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT
French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes
2012-09-15
We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.
Ab initio study of hot electrons in GaAs
Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B.; Louie, Steven G.
2015-01-01
Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron–phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron–phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron–phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials. PMID:25870287
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-02-14
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates
Chaka, Anne M.; Felmy, Andrew R.
2014-03-28
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.
NASA Astrophysics Data System (ADS)
Deng, L.; Liu, X.; Liu, H.; Dong, J.
2010-12-01
The high pressure physical-chemical behaviors of feldspar in subducted slab are very important to the geodynamic process in the deep interior of the Earth. Albite (NaAlSi3O8;Ab) is one of the few end members in the feldspar family, and its high-P behavior is obviously a prerequisite to the full understanding of the physical-chemical properties of feldspar at high pressures. So far it has been well accepted that Ab breaks down to the phase assemblage of Jadeite+Stishovite(NaAlSi2O6; Jd, SiO2; St,JS hereafter) at ~9-10 GPa. The JS phase assemblage might be stable up to ~23 GPa, and eventually directly change into the phase assemblage of calcium-ferrite type NaAlSiO4 (Cf) +2St (CS hereafter). However, some independent researches suggest there is an intermediate phase Na-hollandite (Na-Hall; a phase with the composition of NaAlSi3O8 and the structure of hollandite) between JS phase assemblage transition into CS phase assemblage (Liu 1978; Tutti 2007; Sekine and Ahrens, 1992; Beck et al., 2004). Whether Na-Hall is a thermodynamic stable phase under high P-T conditions remains unknown. In this work, phase relations in the composition of albite NaAlSi3O8 at pressures up to 40 GPa were constrained by a theoretical method that combines the ab initio calculation and quasi-harmonic Debyemodel. First, the P-T dependence of the thermodynamic potentials of the individual phase, St, Cf, Jd and the hypothetical Na-Holl were derived. Our results are generally in consistent agreement with available experimental data and previous theoretical predictions. Second, the Gibbs free energy of the hypothetical Na-Holl phase was compared with that of the phase assemblages JS and CS. Our results show that the Na-Holl phase is not a thermodynamically stable phase over the studied P-T conditions of 0-40 GPa and 100-600 K, which rules it out as a possible intermediate phase along the transition path from the JS phase assemblage to CS phase assemblage. Our calculations have predicted that the JS
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions
Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations
NASA Technical Reports Server (NTRS)
Good, Brian S.
2003-01-01
We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.
NASA Astrophysics Data System (ADS)
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Interatomic Coulombic decay widths of helium trimer: Ab initio calculations
Kolorenč, Přemysl; Sisourat, Nicolas
2015-12-14
We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.
Ab initio electronic and lattice dynamical properties of cerium dihydride
NASA Astrophysics Data System (ADS)
Gurel, Tanju; Eryigit, Resul
2007-03-01
The rare-earth metal hydrides are interesting systems because of the dramatic structural and electronic changes due to the hydrogen absorption and desorption. Among them, cerium dihydride (CeH2) is one of the less studied rare-earth metal-hydride. To have a better understanding, we have performed an ab initio study of electronic and lattice dynamical properties of CeH2 by using pseudopotential density functional theory within local density approximation (LDA) and a plane-wave basis. Electronic band structure of CeH2 have been obtained within LDA and as well as GW approximation. Lattice dynamical properties are calculated using density functional perturbation theory. The phonon spectrum is found to contain a set of high-frequency (˜ 850-1000 cm-1) optical bands, mostly hydrogen related, and low frequency cerium related acoustic modes climbing to 160 cm^ -1 at the zone boundary.
Approximate ab initio calculations of electronic structure of amorphous silicon
NASA Astrophysics Data System (ADS)
Durandurdu, M.; Drabold, D. A.; Mousseau, N.
2000-12-01
We report on ab initio calculations of electronic states of two large and realistic models of amorphous silicon generated using a modified version of the Wooten-Winer-Weaire algorithm and relaxed, in both cases, with a Keating and a modified Stillinger-Weber potentials. The models have no coordination defects and a very narrow bond-angle distribution. We compute the electronic density-of-states and pay particular attention to the nature of the band-tail states around the electronic gap. All models show a large and perfectly clean optical gap and realistic Urbach tails. Based on these results and the extended quasi-one-dimensional stringlike structures observed for certain eigenvalues in the band tails, we postulate that the generation of model a-Si without localized states might be achievable under certain circumstances.
The ab-initio density matrix renormalization group in practice
Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic; Nakatani, Naoki
2015-01-21
The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.
Ab initio engineering of materials with stacked hexagonal tin frameworks
Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.
2016-01-01
The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140
Efficient Ab initio Modeling of Random Multicomponent Alloys.
Jiang, Chao; Uberuaga, Blas P
2016-03-11
We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches.
Quantum plasmonics: from jellium models to ab initio calculations
NASA Astrophysics Data System (ADS)
Varas, Alejandro; García-González, Pablo; Feist, Johannes; García-Vidal, F. J.; Rubio, Angel
2016-08-01
Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT) calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.
Ab initio electronic stopping power of protons in bulk materials
NASA Astrophysics Data System (ADS)
Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia
2016-01-01
The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.
Reactive Monte Carlo sampling with an ab initio potential
Leiding, Jeff; Coe, Joshua D.
2016-05-04
Here, we present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We also discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH3 to those of ab initio molecular dynamics (AIMD). Furthermore, we find that there are regions of state space formore » which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.« less
Ab initio engineering of materials with stacked hexagonal tin frameworks
NASA Astrophysics Data System (ADS)
Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.
2016-07-01
The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator.
Ab initio water pair potential with flexible monomers.
Jankowski, Piotr; Murdachaew, Garold; Bukowski, Robert; Akin-Ojo, Omololu; Leforestier, Claude; Szalewicz, Krzysztof
2015-03-26
A potential energy surface for the water dimer with explicit dependence on monomer coordinates is presented. The surface was fitted to a set of previously published interaction energies computed on a grid of over a quarter million points in the 12-dimensional configurational space using symmetry-adapted perturbation theory and coupled-cluster methods. The present fit removes small errors in published fits, and its accuracy is critically evaluated. The minimum and saddle-point structures of the potential surface were found to be very close to predictions from direct ab initio optimizations. The computed second virial coefficients agreed well with experimental values. At low temperatures, the effects of monomer flexibility in the virial coefficients were found to be much smaller than the quantum effects.
Ab initio electron propagator theory of molecular wires. I. Formalism.
Dahnovsky, Yu; Zakrzewski, V G; Kletsov, A; Ortiz, J V
2005-11-08
Ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical approach is developed for the calculation of the retarded and advanced Green functions in terms of the electron propagator matrix for the bridge molecule. The calculation of the current requires integration in a complex half plane for a trace that involves terminal and Green's-function matrices. Because the Green's-function matrices have complex poles represented by matrices, a special scheme is developed to express these "matrix poles" in terms of ordinary poles. An expression for the current is derived for a terminal matrix of arbitrary rank. For a single terminal orbital, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator. It is shown that Dyson orbitals with high pole strengths and overlaps with terminal orbitals are most responsible for the conduction of electrical current.
Ab initio simulations of liquid carbon monoxide at high pressure
NASA Astrophysics Data System (ADS)
Leonhardi, Tanis C.; Militzer, Burkhard
2017-03-01
Carbon monoxide occurs as a volatile species in the interiors of terrestrial planets, and as a disequilibrium atmospheric constituent in the giant planets. It plays an important role during the accretionary stages of planet formation reacting with gases to form compounds such as CH4 and H2O. The structure of carbon monoxide is unknown over the majority of the temperature and pressure regime in giant planet interiors. Here we perform ab initio molecular dynamics simulations to characterize CO to 140 GPa and 5,000 K. We find that CO is stable as a molecular liquid at lower P-T conditions, as a polymeric liquid at higher P-T conditions found in ice giant interiors, and as a plasma at high-T.
Ab initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
An ab initio study on anionic aerogen bonds
NASA Astrophysics Data System (ADS)
Esrafili, Mehdi D.; Mohammadian-Sabet, Fariba
2017-01-01
An ab initio study is carried out to investigate the anionic aerogen bonds in complexes of KrO3, XeO3 and XeOF2 with F-, Cl-, Br-, CN-, NC-, N3-, SH-, SCN-, NCS-, OH- and OCH3- anions. All of the anionic aerogen bonds analyzed here have a partial covalent character. Charge transfer from the anion to the Kr-O or Xe-O σ∗ orbital stabilizes these complexes and leads to a sizable redshift in the corresponding stretching frequencies. The J(Kr-O) or J(Xe-O) spin-spin coupling constants can be regarded as a useful tool for the characterization of strength of the anionic aerogen-bonded complexes.
Ab Initio Study of KCl and NaCl Clusters
NASA Astrophysics Data System (ADS)
Brownrigg, Clifton; Hira, Ajit; Pacheco, Jose; Salazar, Justin
2013-03-01
We continue our interest in the theoretical study of molecular clusters to examine the chemical properties of small KnCln and NanCln clusters (n = 2 - 15). The potentially important role of these molecular species in biochemical and medicinal processes is well known. This work applies the hybrid ab initio methods of quantum chemistry to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations have been performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. The potential for design of new medicinal drugs is explored.
High-throughput ab-initio dilute solute diffusion database
NASA Astrophysics Data System (ADS)
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-07-01
We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.
An Ab Initio Study of Alkali-C60 Complexes
NASA Astrophysics Data System (ADS)
Frick, Nathan; Hira, A. S.; Ray, A. K.
2003-03-01
We extend our previous work on fullerene-alkali complexes1-2 by presenting the results of an ab initio theoretical study of the alkali LiC60+, LiC60, NaC60+, NaC60, KC60+, and KC60 complexes. In the endohedral complexes for Li and Na, there is displacement of the adatom from the center. Of the ions, exohedral Li+ will sit closest to the cage, and among the neutrals, exohedral K remains closest. Bond lengths are consistently longer for the fivefold and threefold approaches. Adsorbates inside the fullerene donate negative charge to the carbons, but ions outside obtain a small amount, resulting in a polarization of the molecule. In the ion complexes, there is lowering of the orbital energy levels by 3 to 4 eV, resulting in an increase in the number of bound, but unoccupied, electronic orbitals. The HOMO-LUMO gap, of interest in superconductivity studies, is reduced by about 50 1. A.S. Hira and A.K. Ray, Phys. Rev. A 52, 141(1995); A 54, 2205(1996). 2. Ajit Hira and A. K. Ray, "An Initio Modeling of the Endohedral and Exohedral Complexes of C60Na2+ Complexes", Bull. Am. Phys. Soc. 47 (March 2002).
NASA Astrophysics Data System (ADS)
Cao, Jun; Liu, Li-Hong; Fang, Wei-Hai; Xie, Zhi-Zhong; Zhang, Yong
2013-04-01
Azobenzene is one of the most widely used photoactive units and recently an ethylene-bridged azobenzene (BAB) was reported to have greatly enhanced conversion efficiency, quantum yield, and other favorable properties. As the first step towards exploring its photo-switchable character in real systems, we report here a systematic study on the photoisomerization dynamics between trans (E) and cis (Z) isomers in the gas phase and the CH3OH solution, using ab initio based surface hopping and molecular dynamics, which is the first report of dynamics simulation to reveal the environmental effects on BAB photoreactions. Results show that while the relatively faster S1 relaxation of the photo-induced E → Z process is only mildly affected by the solvent effect, the relatively slower S1 relaxation of the reverse reaction becomes even slower in the solution compared to the gas phase. The subsequent S0 dynamics from the conical intersection between S1 and S0 (CI_E) to Z is accelerated in solution compared to the gas phase because of avoided re-crossing to the S1 state, while the S0 dynamics from the conical intersection between S1 and S0 (CI_Z) to E are basically the same in both phases. Overall, the solvent effect was found to enhance the back-and-forth photo-switch efficiency between the Z and E isomers compared to the gas phase, while the quantum yields are reduced. But the solution yields of both the forward and backward photoreactions are still around 0.4. Therefore, BAB may have good photo-responsive properties if used as a photoactive unit in real systems. These results will facilitate future experimental and theoretical studies in this area to help design new azobenzene derivatives as photoactive units in biological processes, nanoscale devices, and photo-responsive materials.
Ab initio MCDHF calculations of electron-nucleus interactions
NASA Astrophysics Data System (ADS)
Bieroń, Jacek; Froese Fischer, Charlotte; Fritzsche, Stephan; Gaigalas, Gediminas; Grant, Ian P.; Indelicato, Paul; Jönsson, Per; Pyykkö, Pekka
2015-05-01
We present recent advances in the development of atomic ab initio multiconfiguration Dirac-Hartree-Fock theory, implemented in the GRASP relativistic atomic structure code. For neutral atoms, the deviations of properties calculated within the Dirac-Hartree-Fock (DHF) method (based on independent particle model of an atomic cloud) are usually dominated by electron correlation effects, i.e. the non-central interactions of individual electrons. We present the recent advances in accurate calculations of electron correlation effects in small, medium, and heavy neutral atoms. We describe methods of systematic development of multiconfiguration expansions leading to systematic, controlled improvement of the accuracy of the ab initio calculations. These methods originate from the concept of the complete active space (CAS) model within the DHF theory, which, at least in principle, permits fully relativistic calculations with full account of electron correlation effects. The calculations within the CAS model on currently available computer systems are feasible only for very light systems. For heavier atoms or ions with more than a few electrons, restrictions have to be imposed on the multiconfiguration expansions. We present methods and tools, which are designed to extend the numerical calculations in a controlled manner, where multiconfiguration expansions account for all leading electron correlation effects. We show examples of applications of the GRASP code to calculations of hyperfine structure constants, but the code may be used for calculations of arbitrary bound-state atomic properties. In recent years it has been applied to calculations of atomic and ionic spectra (transition energies and rates), to determinations of nuclear electromagnetic moments, as well as to calculations related to interactions of bound electrons with nuclear electromagnetic moments leading to violations of discrete symmetries.
Ashcraft, Robert W; Raman, Sumathy; Green, William H
2007-10-18
Ab initio molecular orbital calculations were performed and thermochemical parameters estimated for 46 species involved in the oxidation of hydroxylamine in aqueous nitric acid solution. Solution-phase properties were estimated using the several levels of theory in Gaussian03 and using COSMOtherm. The use of computational chemistry calculations for the estimation of physical properties and constants in solution is addressed. The connection between the pseudochemical potential of Ben-Naim and the traditional standard state-based thermochemistry is shown, and the connection of these ideas to computational chemistry results is established. This theoretical framework provides a basis for the practical use of the solution-phase computational chemistry estimates for real systems, without the implicit assumptions that often hide the nuances of solution-phase thermochemistry. The effect of nonidealities and a method to account for them is also discussed. A method is presented for estimating the solvation enthalpy and entropy for dilute aqueous solutions based on the solvation free energy from the ab initio calculations. The accuracy of the estimated thermochemical parameters was determined through comparison with (i) enthalpies of formation in the gas phase and in solution, (ii) Henry's law data for aqueous solutions, and (iii) various reaction equilibria in aqueous solution. Typical mean absolute deviations (MAD) for the solvation free energy in room-temperature water appear to be ~1.5 kcal/mol for most methods investigated. The MAD for computed enthalpies of formation in solution was 1.5-3 kcal/mol, depending on the methodology employed and the type of species (ion, radical, closed-shell) being computed. This work provides a relatively simple and unambiguous approach that can be used to estimate the thermochemical parameters needed to build detailed ab initio kinetic models of systems in aqueous solution. Technical challenges that limit the accuracy of the estimates are
Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate
Yu, Hongyu; Duan, Defang; Liu, Hanyu; Yang, Ting; Tian, Fubo; Bao, Kuo; Li, Da; Zhao, Zhonglong; Liu, Bingbing; Cui, Tian
2016-01-01
High-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5–60 GPa and temperature range of 250–400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation. PMID:26754622
Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate
NASA Astrophysics Data System (ADS)
Yu, Hongyu; Duan, Defang; Liu, Hanyu; Yang, Ting; Tian, Fubo; Bao, Kuo; Li, Da; Zhao, Zhonglong; Liu, Bingbing; Cui, Tian
2016-01-01
High-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5–60 GPa and temperature range of 250–400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation.
Lindenmaier, Rodica; Tipton, Nicole; Sams, Robert L.; Brauer, Carolyn S.; Blake, Thomas A.; Williams, Stephen D.; Johnson, Timothy J.
2016-08-04
Hydroxyacetone (acetol) is a simple organic molecule of interest in both the astrophysical and atmospheric communities, having recently been observed in biomass burning events, as well as a known degradation product of isoprene oxidation. However, its vibrational assignment has never been fully completed, and few quantitative data are available for its detection via infrared spectroscopy. Our recent acquisition of both the pressure-broadened gas-phase data and the far-IR spectra now allow for unambiguous assignment of several (new) bands. In particular, the observed C-type bands of several fundamentals (particularly in the far-infrared) and a few combination bands demonstrate that the monomer is in a planar (Cs) conformation, at least a majority of the time. As suggested by other researchers, the monomer is a cis-cis conformer stabilized by an intramolecular O—H···O=C hydrogen bond forming a five-membered planar ring structure. Band assignments in the Cs point group are justified (at least for a good fraction of the molecules in the ensemble) by the presence of the C-type bands. The results and band assignments are well confirmed by both ab initio MP2-ccpvtz calculations as well as GAMESS (B3LYP) theoretical calculations. In addition, using vetted methods for quantitative measurements, we report the first IR absorption band strengths of acetol (also in electronic format) that can be used for atmospheric monitoring and other applications.
Experimental and ab initio infrared study of chi-, kappa- and alpha-aluminas formed from gibbsite
Favaro, L.; Boumaza, A.; Roy, P.; Ledion, J.; Sattonnay, G.; Brubach, J.B.; Huntz, A.M.; Tetot, R.
2010-04-15
chi-, kappa- and alpha-alumina phases formed by dehydration of micro-grained gibbsite between 773 and 1573 K are studied using infrared spectroscopy (IR). The structural transitions evidenced by X-ray diffraction (XRD) were interpreted by comparing IR measurements with ab initio simulations (except for the chi form whose complexity does not allow a reliable simulation). For each phase, IR spectrum presents specific bands corresponding to transverse optical (TO) modes of Al-O stretching and bending under 900 cm{sup -1}. The very complex chi phase, obtained at 773 K, provides a distinctive XRD pattern in contrast with the IR absorbance appearing as a broad structure extending between 200 and 900 cm{sup -1} resembling the equivalent spectra for gamma-alumina phase. kappa-alumina is forming at 1173 K and its rich IR spectrum is in good qualitative agreement with ab initio simulations. This complexity reflects the large number of atoms in the kappa-alumina unit cell and the wide range of internuclear distances as well as the various coordinances of both Al and O atoms. Ab initio simulations suggest that this form of transition alumina demonstrates a strong departure from the simple pattern observed for other transition alumina. At 1573 K, the stable alpha-ALPHAl{sub 2}OMICRON{sub 3} develops. Its IR spectra extends in a narrower energy range as compared to transition alumina and presents characteristics features similar to model alpha-ALPHAl{sub 2}OMICRON{sub 3}. Ab initio calculations show again a very good general agreement with the observed IR spectra for this phase. In addition, for both kappa- and alpha-ALPHAl{sub 2}OMICRON{sub 3}, extra modes, measured at high energy (above 790 cm{sup -1} for kappa and above 650 cm{sup -1} for alpha), can originate from either remnant chi-alumina or from surface modes. - Graphical abstract: Infrared spectra of the sequence Gibbsite ->chi->kappa->alpha-Al{sub 2}O{sub 3} obtained from 24 h calcinations of Gibbsite at 773 K, 1173 K
Accurate calculation of the p Ka of trifluoroacetic acid using high-level ab initio calculations
NASA Astrophysics Data System (ADS)
Namazian, Mansoor; Zakery, Maryam; Noorbala, Mohammad R.; Coote, Michelle L.
2008-01-01
The p Ka value of trifluoroacetic acid has been successfully calculated using high-level ab initio methods such as G3 and CBS-QB3. Solvation energies have been calculated using CPCM continuum model of solvation at the HF and B3-LYP levels of theory with various basis sets. Excellent agreement with experiment (to within 0.4 p Ka units) was obtained using CPCM solvation energies at the B3-LYP/6-31+G(d) level (or larger) in conjunction with CBS-QB3 or G3 gas-phase energies of trifluoroacetic acid and its anion.
Ab initio study of the elastic anomalies in Pd-Ag alloys
NASA Astrophysics Data System (ADS)
Delczeg-Czirjak, E. K.; Delczeg, L.; Ropo, M.; Kokko, K.; Punkkinen, M. P. J.; Johansson, B.; Vitos, L.
2009-02-01
Ab initio total-energy calculations, based on the exact muffin-tin orbital method, are used to determine the elastic properties of Pd1-xAgx random alloys in the face-centered-cubic crystallographic phase. The compositional disorder is treated within the coherent-potential approximation. The single crystal and polycrystalline elastic constants and the Debye temperature are calculated for the whole range of concentration, 0≤x≤1 . It is shown that the variation in the elastic parameters of Pd-Ag alloys with chemical composition strongly deviates from a simple linear or parabolic trend. The complex electronic origin of these anomalies is demonstrated.
Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.
2013-12-12
Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.
Ab initio study of structural and magnetic properties of Si-doped Fe2P
NASA Astrophysics Data System (ADS)
Delczeg-Czirjak, E. K.; Delczeg, L.; Punkkinen, M. P. J.; Johansson, B.; Eriksson, O.; Vitos, L.
2010-08-01
Ab initio electronic-structure methods are used to study the properties of Fe2P1-xSix in ferromagnetic and paramagnetic states. The site preference and lattice relaxation are calculated with the projector augmented wave method as implemented in the Vienna ab initio simulation package. The paramagnetic state is modeled by the disordered local magnetic moment scheme, and the chemical and magnetic disorder is treated using the coherent potential approximation in combination with the exact muffin-tin orbital formalism. The calculated lattice parameters, atomic positions, and magnetic properties are in good agreement with the experimental and other theoretical results. In contrast to the observation, for the ferromagnetic state the body centered orthorhombic structure (bco, space group Imm2&barbelow; ) is predicted to have lower energy than the hexagonal structure (hex, space group P6¯2m ). The zero-point spin fluctuation energy difference is found to be large enough to stabilize the hex phase. For the paramagnetic state, the hex structure is calculated to be the stable phase and the computed total energy versus composition indicates a hex to bco crystallographic phase transition with increasing Si content. The phonon vibrational free energy, estimated from the theoretical equation of state, turns out to stabilize the hexagonal phase, whereas the electronic and magnetic entropies favor the low symmetry orthorhombic structure.
Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations
NASA Technical Reports Server (NTRS)
Good, Brian S.
2004-01-01
We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.
Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules
NASA Astrophysics Data System (ADS)
Shiga, Motoyuki; Nakayama, Akira
2008-01-01
The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.
Ab initio calculation of the potential bubble nucleus 34Si
NASA Astrophysics Data System (ADS)
Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.
2017-03-01
Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to
Ab initio construction of magnetic phase diagrams in alloys: The case of Fe_{1-x}Mn_{x}Pt
Pujari, B. S.; Larson, P.; Antropov, V. P.; Belashchenko, K. D.
2015-07-28
A first-principles approach to the construction of concentration-temperature magnetic phase diagrams of metallic alloys is presented. The method employs self-consistent total energy calculations based on the coherent potential approximation for partially ordered and noncollinear magnetic states and is able to account for competing interactions and multiple magnetic phases. The application to the Fe_{1–x}Mn_{x}Pt “magnetic chameleon” system yields the sequence of magnetic phases at T = 0 and the c-T magnetic phase diagram in good agreement with experiment, and a new low-temperature phase is predicted at the Mn-rich end. The importance of non-Heisenberg interactions for the description of the magnetic phase diagram is demonstrated.
Ab initio many-body calculations of nucleon-nucleus scattering
NASA Astrophysics Data System (ADS)
Quaglioni, Sofia; Navrátil, Petr
2009-04-01
We develop a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach preserves translational symmetry and the Pauli principle. We outline technical details and present phase-shift results for neutron scattering on H3, He4, and Be10 and proton scattering on He3,4, using realistic nucleon-nucleon (NN) potentials. Our A=4 scattering results are compared to earlier ab initio calculations. We find that the CD-Bonn NN potential in particular provides an excellent description of nucleon-He4S-wave phase shifts. In contrast, the experimental nucleon-He4P-wave phase shifts are not well reproduced by any NN potential we use. We demonstrate that a proper treatment of the coupling to the n-Be10 continuum is successful in explaining the parity-inverted ground state in Be11.
Longo, R C; Kong, F T; KC, Santosh; Park, M S; Yoon, J; Yeon, D-H; Park, J-H; Doo, S-G; Cho, K
2014-06-21
In this work, we present a density-functional theory (DFT) investigation of the phase stability, electrochemical stability and phase transformation mechanisms of the layered and over-lithiated Mn oxides. This study includes the thermodynamic stability of Li and oxygen vacancies, to examine the electrochemical activation mechanisms of these cathode materials. The DFT calculations provide phase diagrams of the Li-Mn-O system in both physical and chemical potential spaces, including the crystals containing vacancies as independent phases. The results show the ranges of electrochemical activity for both layered LiMnO2 and over-lithiated Li2MnO3. By using a thermodynamic model analysis, we found that the required temperature for oxygen evolution and Li vacancy formation is too high to be compatible with any practical synthesis temperature. Using solid-state transition calculations, we have identified the key steps in the phase transition mechanism of the layered LiMnO2 into the spinel phase. The calculated effects of pH on the Li-Mn-O phase stability elucidated the mechanism of Mn(2+) formation from the spinel phase under acidic conditions.
Javadian, Soheila; Taghavi, Fariba; Yari, Faramarz; Hashemianzadeh, Seyed Majid
2012-09-01
In this study, the mechanism of the temperature-dependent phase transition of confined water inside a (9,9) single-walled carbon nanotube (SWCNT) was studied using the hierarchical multi-scale modeling techniques of molecular dynamics (MD) and density functional theory (DFT). The MD calculations verify the formation of hexagonal ice nanotubes at the phase transition temperature T(c)=275K by a sharp change in the location of the oxygen atoms inside the SWCNT. Natural bond orbital (NBO) analysis provides evidence of considerable intermolecular charge transfer during the phase transition and verifies that the ice nanotube contains two different forms of hydrogen bonding due to confinement. Nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) analyses were used to demonstrate the fundamental influence of intermolecular hydrogen bonding interactions on the formation and electronic structure of ice nanotubes. In addition, the NQR analysis revealed that the rearrangement of nano-confined water molecules during the phase transition could be detected directly by the orientation of ¹⁷O atom EFG tensor components related to the molecular frame axes. The effects of nanoscale confinements in ice nanotubes and water clusters were analyzed by experimentally observable NMR and NQR parameters. These findings showed a close relationship between the phase behavior and orientation of the electronic structure in nanoscale structures and demonstrate the usefulness of NBO and NQR parameters for detecting phase transition phenomena in nanoscale confining environments.
Ab initio calculation of structural stability, electronic and optical properties of Ag2Se
NASA Astrophysics Data System (ADS)
Rameshkumar, S.; Jaiganesh, G.; Jayalakshmi, V.; Palanivel, B.
2015-06-01
The structural stability, electronic and optical properties of Ag2Se compound is studied using ab initio packages. Ag2Se is found to crystallize in orthorhombic structure with two different space groups i.e. P212121 (No. 19) and P2221 (No. 17). For this compound in these two space groups, the total energy has been computed as a function of volume. Our calculated results suggest that the P212121-phase is more stable than that of the P2221-phase. The band structure calculation show that Ag2Se is semimetallic with an overlap of about 0.014 eV in P212121-phase whereas is metallic in nature in P2221-phase. Moreover, the optical properties including the dielectric fuction, energy loss spectrum are obtained and analysed.
Arghavani Nia, Borhan; Sedighi, Matin; Shahrokhi, Masoud; Moradian, Rostam
2013-11-15
A density functional theory study of structural, electronical and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. In the exchange–correlation potential, generalized gradient approximation (PBE-GGA) has been used to calculate lattice parameters, bulk modulus, cohesive energy, dielectric function and energy loss spectra. The electronic band structure of this compound has been calculated using the above two approximations as well as another form of PBE-GGA, proposed by Engle and Vosko (EV-GGA). It is found that the hexagonal phase of Ca{sub 3}Sb{sub 2} has an indirect gap in the Γ→N direction; while in the cubic phase there is a direct-gap at the Γ point in the PBE-GGA and EV-GGA. Effects of applying pressure on the band structure of the system studied and optical properties of these systems were calculated. - Graphical abstract: A density functional theory study of structural, electronic and optical properties of Ca{sub 3}Sb{sub 2} compound in hexagonal and cubic phases is presented. Display Omitted - Highlights: • Physical properties of Ca{sub 3}Sb{sub 2} in hexagonal and cubic phases are investigated. • It is found that the hexagonal phase is an indirect gap semiconductor. • Ca{sub 3}Sb{sub 2} is a direct-gap semiconductor at the Γ point in the cubic phase. • By increasing pressure the semiconducting band gap and anti-symmetry gap are decreased.
Ab initio solution of macromolecular crystal structures without direct methods.
McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J
2017-04-04
The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.
Ab initio electronic structure and optical conductivity of bismuth tellurohalides
NASA Astrophysics Data System (ADS)
Schwalbe, Sebastian; Wirnata, René; Starke, Ronald; Schober, Giulio A. H.; Kortus, Jens
2016-11-01
We investigate the electronic structure, dielectric, and optical properties of bismuth tellurohalides BiTe X (X =I , Cl, Br) by means of all-electron density functional theory. In particular, we present the ab initio conductivities and dielectric tensors calculated over a wide frequency range, and compare our results with the recent measurements by Akrap et al. [Phys. Rev. B 90, 035201 (2014), 10.1103/PhysRevB.90.035201], Makhnev et al. [Opt. Spectrosc. 117, 764 (2014), 10.1134/S0030400X14110125], and Rusinov et al. [JETP Lett. 101, 507 (2015), 10.1134/S0021364015080147]. We show how the low-frequency branch of the optical conductivity can be used to identify characteristic intra- and interband transitions between the Rashba spin-split bands in all three bismuth tellurohalides. We further calculate the refractive indices and dielectric constants, which in turn are systematically compared to previous predictions and measurements. We expect that our quantitative analysis will contribute to the general assessment of bulk Rashba materials for their potential use in spintronics devices.
Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures
NASA Astrophysics Data System (ADS)
Debernardi, Alberto; Marchetti, Luigi
2016-06-01
Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.
Melting curves of metals by ab initio calculations
NASA Astrophysics Data System (ADS)
Minakov, Dmitry; Levashov, Pavel
2015-06-01
In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).
Ab initio description of the exotic unbound 7He nucleus
Baroni, Simone; Navratil, Petr; Quaglioni, Sofia
2013-01-11
In this study, the neutron-rich unbound 7He nucleus has been the subject of many experimental investigations. While the ground-state 3/2– resonance is well established, there is a controversy concerning the excited 1/2– resonance reported in some experiments as low lying and narrow (ER~1 MeV, Γ≤1 MeV) while in others as very broad and located at a higher energy. This issue cannot be addressed by ab initio theoretical calculations based on traditional bound-state methods. We introduce a new unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model, a bound-state technique, with the no-coremore » shell model combined with the resonating-group method, a nuclear scattering technique. Our calculations describe the ground-state resonance in agreement with experiment and, at the same time, predict a broad 1/2– resonance above 2 MeV.« less
Ab Initio Study of Covalently Functionalized Graphene and Carbon Nanotubes
NASA Astrophysics Data System (ADS)
Jha, Sanjiv; Hammouri, Mahmoud; Vasiliev, Igor; Magedov, Igor; Frolova, Liliya; Kalugin, Nikolai
2014-03-01
The electronic and structural properties of carbon nanomaterials can be affected by chemical functionalization. We apply ab initio computational methods based on density functional theory to study the properties of graphene and single-walled carbon nanotubes functionalized with benzyne. Our calculations are carried out using the SIESTA electronic structure code combined with the generalized gradient approximation for the exchange correlation functional. The calculated binding energies, densities of states, and band structures of functionalized graphene and carbon nanotubes are analyzed in comparison with the available experimental data. The surfaces of carbon nanotubes are found to be significantly more reactive toward benzyne molecules than the surface of graphene. The strength of interaction between benzyne and carbon nanotubes is affected by the curvature of the nanotube sidewall. The binding energies of benzyne molecules attached to both semiconducting zigzag and metallic armchair nanotubes increase with decreasing the nanotube diameter. Supported by NSF CHE-1112388, NMSU GREG Award, NSF ECCS-0925988, NIH-5P20RR016480-12, and NIH- P20 GM103451.
Accurate ab initio vibrational energies of methyl chloride
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2015-06-28
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup HL}, and CBS-37{sup HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup HL} and CBS-37{sup HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.
Ab initio liquid water from PBE0 hybrid functional simulations
NASA Astrophysics Data System (ADS)
Li, Zhaofeng; Wu, Xifan; Car, Roberto
2010-03-01
For reasons of computational efficiency, so far most ab initio molecular dynamics simulations of liquid water have been based on semi-local density functional approximations, such as PBE and BLYP. These approaches yield a liquid structure that, albeit qualitatively correct, is overstructured compared to experiment, even after nuclear quantum effects have been taken into account.footnotetextJ. A. Morrone and R. Car, Phys. Rev. Lett. 101, 017801(2008) A major cause of this inaccuracy is the delocalization error associated to semi-local density functional approximations, which, as a consequence, overestimate slightly the hydrogen bond strength in the liquid. In this work we adopt the PBE0 hybrid functional approximation, which, by mixing a fraction of exact (Hartree-Fock) exchange, reduces significantly the delocalization error of semi-local functionals. Our approach is based on a numerically efficient order-N implementation of exact exchange.footnotetextX. Wu, A. Selloni, and R. Car, Phys. Rev. B 79, 085102(2009) We find that PBE0 systematically improves the agreement of the simulated liquid with experiment. Our conclusion is substantiated by the calculated radial distribution functions, H-bond statistics, and molecular dipole distribution.
Ab initio predictions of the symmetry energy and recent constraints
NASA Astrophysics Data System (ADS)
Sammarruca, Francesca
2017-01-01
The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.
An efficient approach to ab initio Monte Carlo simulation.
Leiding, Jeff; Coe, Joshua D
2014-01-21
We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β(0)), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where-depending on the quality of the reference system potential-acceptance probabilities were enhanced by factors of 1.2-28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.
Ab initio studies of phosphorene island single electron transistor
NASA Astrophysics Data System (ADS)
Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.
2016-05-01
Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.
Ab-Initio Molecular Dynamics Simulation of Graphene Sheet
NASA Astrophysics Data System (ADS)
Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.
2017-01-01
The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.
Perovskite transparent conducting oxides: an ab initio study.
Dabaghmanesh, S; Saniz, R; Amini, M N; Lamoen, D; Partoens, B
2013-10-16
We present an ab initio study of the electronic structure and of the formation energies of various point defects in BaSnO3 and SrGeO3. We show that La and Y impurities substituting Ba or Sr are shallow donors with a preferred 1 + charge state. These defects have a low formation energy within all the suitable equilibrium growth conditions considered. Oxygen vacancies behave as shallow donors as well, preferring the 2 + charge state. Their formation energies, however, are higher in most growth conditions, indicating a limited contribution to conductivity. The calculated electron effective mass in BaSnO3, with a value of 0.21 m(e), and the very high mobility reported recently in La-doped BaSnO3 single-crystals, suggest that remarkably low scattering rates can be achieved in the latter. In the case of SrGeO3, our results point to carrier density and mobility values in the low range for typical polycrystalline TCOs, in line with experiment.
Ab initio calculations of nuclear reactions important for astrophysics
NASA Astrophysics Data System (ADS)
Navratil, Petr; Dohet-Eraly, Jeremy; Calci, Angelo; Horiuchi, Wataru; Hupin, Guillaume; Quaglioni, Sofia
2016-09-01
In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. One of the newly developed approaches is the No-Core Shell Model with Continuum (NCSMC), capable of describing both bound and scattering states in light nuclei simultaneously. We will present NCSMC results for reactions important for astrophysics that are difficult to measure at relevant low energies, such as 3He(α,γ)7Be and 3H(α,γ)7Li and 11C(p,γ)12N radiative capture, as well as the 3H(d,n)4He fusion. We will also address prospects of calculating the 2H(α,γ)6Li capture reaction within the NCSMC formalism. Prepared in part by LLNL under Contract DE-AC52-07NA27344. Supported by the U.S. DOE, OS, NP, under Work Proposal No. SCW1158, and by the NSERC Grant No. SAPIN-2016-00033. TRIUMF receives funding from the NRC Canada.
Ab Initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
An Ab Initio Based Potential Energy Surface for Water
NASA Technical Reports Server (NTRS)
Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)
1996-01-01
We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.
Electronic structure and conductivity of ferroelectric hexaferrite: Ab initio calculations
NASA Astrophysics Data System (ADS)
Knížek, K.; Novák, P.; Küpferling, M.
2006-04-01
Ba0.5Sr1.5Zn2Fe12O22 is a promising multiferroic compound in which the electric polarization is intimately connected to the magnetic state. In principle, ferroelectrity might exist above the room temperature, but the electrical conductivity that increases with increasing temperature limits it to temperatures below ≈130K . We present results of an ab initio electronic structure calculation of the (BaSr)Zn2Fe12O22 system. To improve the description of strongly correlated 3d electrons of iron, the GGA+U method is used. The results show that the electrical conductivity strongly depends on relative fractions of iron and zinc in the tetrahedral sublattice that belongs to the spinel block of the hexaferrite structure. If this sublattice is fully occupied by zinc, the system is an insulator with a gap of ≈1.5eV . If it is occupied equally by Fe and Zn the gap decreases by a factor of 2, and the system is metallic when this sublattice is filled by iron only.
Ab initio modeling of decomposition in iron based alloys
NASA Astrophysics Data System (ADS)
Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.
2016-12-01
This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.
Ab initio calculation of infrared intensities for hydrogen peroxide
NASA Technical Reports Server (NTRS)
Rogers, J. D.; Hillman, J. J.
1982-01-01
Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.
Ab initio calculations of correlated electron dynamics in ultrashort pulses
NASA Astrophysics Data System (ADS)
Feist, Johannes
2010-03-01
The availability of ultrashort and intense light pulses on the femtosecond and attosecond timescale promises to allow to directly probe and control electron dynamics on their natural timescale. A crucial ingredient to understanding the dynamics in many-electron systems is the influence of electron correlation, induced by the interelectronic repulsion. In order to study electron correlation in ultrafast processes, we have implemented an ab initio simulation of the two-electron dynamics in helium atoms. We solve the time-dependent Schr"odinger equation in its full dimensionality, with one temporal and five spatial degrees of freedom in linearly polarized laser fields. In our computational approach, the wave function is represented through a combination of time-dependent close coupling with the finite element discrete variable representation, while time propagation is performed using an Arnoldi-Lanczos approximation with adaptive step size. This approach is optimized to allow for efficient parallelization of the program and has been shown to scale linearly using up to 1800 processor cores for typical problem sizes. This has allowed us to perform highly accurate and well- converged computations for the interaction of ultrashort laser pulses with He. I will present some recent results on using attosecond and femtosecond pulses to probe and control the temporal structure of the ionization process. This work was performed in collaboration with Stefan Nagele, Renate Pazourek, Andreas Kaltenb"ack, Emil Persson, Barry I. Schneider, Lee A. Collins, and Joachim Burgd"orfer.
Ab initio molecular dynamics calculations of ion hydration free energies.
Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
Ab initio prediction of the critical thickness of a precipitate.
Sampath, S; Janisch, R
2013-09-04
Segregation and precipitation of second phases in metals and metallic alloys is an important phenomenon that has a strong influence on the mechanical properties of the material. Models exist that describe the growth of coherent, semi-coherent and incoherent precipitates. One important parameter of these models is the energy of the interface between matrix and precipitate. In this work we apply ab initio density functional theory calculations to obtain this parameter and to understand how it depends on chemical composition and mechanical strain at the interface.Our example is a metastable Mo-C phase, the body-centred tetragonal structure, which exists as a semi-coherent precipitate in body-centred cubic molybdenum. The interface of this precipitate is supposed to change from coherent to semi-coherent during the growth of the precipitate. We predict the critical thickness of the precipitate by calculating the different contributions to a semi-coherent interface energy by means of ab initio density functional theory calculations. The parameters in our model include the elastic strain energy stored in the precipitate, as well as a misfit dislocation energy that depends on the dislocation core width and the dislocation spacing. Our predicted critical thickness agrees well with experimental observations.
2015-06-28
Charts 3. DATES COVERED (From - To) June 2015-June 2015 4. TITLE AND SUBTITLE AB INITIO QUANTUM CHEMICAL REACTION KINETICS: RECENT APPLICATIONS IN...Unlimited. 13. SUPPLEMENTARY NOTES Briefing Charts presented at 9th Int. Conf. Chemical Kinetics; Ghent, Belgium; 28 Jun 2015. PA#15351. 14. ABSTRACT...ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry Ghanshyam L. Vaghjiani* DISTRIBUTION A
Paraguassu, W.; Saraiva, G.D.; Guerini, S.; Freire, P.T.C.; Abagaro, B.T.O.; Mendes Filho, J.
2012-12-15
This work reports high pressure Raman scattering results on dipotassium molybdate (K{sub 2}MoO{sub 4}). The effects of hydrostatic pressure on the vibrational properties of K{sub 2}MoO{sub 4} has been investigated in the pressure range from 0.5 to 7.3 GPa. This study also indicates that K{sub 2}MoO{sub 4} crystals exhibit a pressure-induced first-order phase transition at about 2.2 GPa from monoclinic to an unknown symmetry. Calculaions based on density-functional theory (DFT) unveiled the structural changes undergone by the K{sub 2}MoO{sub 4} system under hydrostatic pressure. The phase transition is connected with the increase of the polyhedral KO{sub 6} distortion due to an increased anionic interaction as volume decrease, therefore leading to tiltings and/or rotations of the MoO{sub 4} tetrahedra. The consequence of such tiltings and/or rotations of the MoO{sub 4} tetrahedra is to increase the disorder of these units. The high-pressure phase transforms directly into the ambient-pressure phase as pressure is released. - Graphical Abstract: Dipotassium molybdate (K{sub 2}MoO{sub 4}) belongs to the class of single molybdates and tungstates with a general composition of the A{sub 2}MO{sub 4} (A=Li, Na, K, Rb, Cs; {Mu}=Mo, W). At room temperature and ambient pressure, the crystal of K{sub 2}MoO{sub 4} is monoclinic and it belongs to the C2/m (C{sub 2h}{sup 3}) space group. This material is attracting a considerable attention due to its interesting structural and thermodynamic properties. This work reports a high pressure study on this system. Highlights: Black-Right-Pointing-Pointer We reports high pressure Raman scattering results on dipotassium molybdate. Black-Right-Pointing-Pointer Our study indicates a pressure-induced first-order phase transition at around 2.16 GPa. Black-Right-Pointing-Pointer DFT calculations indicate that phase transition is connected with the increase of KO{sub 6} distortion. Black-Right-Pointing-Pointer Tiltings and/or rotations of the Mo
Vitos, L.; Kollar, J.; Skriver, H.L.
1997-02-01
We have used a full charge-density technique based on the linear muffin-tin orbitals method in first-principles calculations of the atomic volumes of the light actinides including Fr, Ra, and Ac in their low-temperature crystallographic phases. The good agreement between the theoretical and experimental values along the series support the picture of itinerant 5f electronic states in Th to Pu. The increased deviation between theory and experiment found in Np and Pu may be an indication of correlation effects not included in the local density approximation. {copyright} {ital 1997} {ital The American Physical Society}
Bisti, F.; Stroppa, A.; Picozzi, S.; Ottaviano, L.
2011-05-07
The electronic structure of Croconic Acid in the condensed phase has been studied by comparing core level and valence band x-ray photoelectron spectroscopy experiments and first principles density functional theory calculations using the Heyd-Scuseria-Ernzerhof screened hybrid functional and the GW approximation. By exploring the photoemission spectra for different deposition thicknesses, we show how the formation of the hydrogen bond network modifies the O 1s core level lineshape. Moreover, the valence band can be explained only if the intermolecular interactions are taken into account in the theoretical approach.
NASA Astrophysics Data System (ADS)
Chun, Hye Jin; Ocola, Esther J.; Laane, Jaan
2016-11-01
The vapor-phase infrared and Raman spectra of cyclohexane-d11 in the C-H stretching region show two bands at 2891 and 2921 cm-1 corresponding to the axial and equatorial C-H stretching modes respectively. Similarly, cyclohexane-d1 has two C-D stretching modes at 2145 and 2164 cm-1 (Mátrai and Gal, 1984) corresponding to the two forms. Force constants were calculated for these vibrations and these confirm the theoretical calculations, which show the equatorial bonds to be shorter and stronger. The force constant for the equatorial C-H stretching is 2% higher than for the axial.
Ab initio study of magnetic single layer MPX3 metal-phosphorous-trichalcogenides
NASA Astrophysics Data System (ADS)
Chittari, Bheema Lingam; Hwang, Euyheon; Jung, Jeil; MacDonald, Allan H.
We analyze the electronic structure of two dimensional (2D) MPX3 (M= V, Cr, Mn, Fe, Co, Ni, Cu, Zn, and X = S, Se, Te) transition metal thiophosphates, viewing them as single layer van der Waals materials that can exhibit magnetic order. Our ab initio calculations for MPX3 single layer compounds predict both semiconducting phases with variable band gap sizes and metallic phases, and an intimate interplay between magnetic order and the presence of a gap. A systematic trend of decreasing band gaps in antiferromagnetic states is observed as the chalcogen atoms S, Se, and Te change from smaller to larger atomic number, Ferromagnetic, antiferromagnetic, and nonmagnetic phases, and lattice constant changes accompanied by distortions in crystal symmetry, occur as the metal atom is varied. The sensitive interdependence between magnetic, structural, and electronic properties suggests the important potential of this class of 2D magnetic van der Waals materials for strain and field-effect carrier tunable spintronics.
Ab initio study of pressure induced structural and electronic properties in TmPo
Makode, Chandrabhan Pataiya, Jagdish; Sanyal, Sankar P.; Panwar, Y. S.; Aynyas, Mahendra
2015-06-24
We report an ab initio calculation of pressure induced structural phase transition and electronic properties of Thulium Polonide (TmPo).The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). It is found that TmPo is stable in NaCl-type (B{sub 1}-phase) structure to CsCl-type (B{sub 2}-phase) structure of this compound in the pressure range of 7.0 GPa. We also calculate the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure and density of states. From energy diagram it is observed that TmPo exhibit metallic behavior. The calculated values of equilibrium lattice parameter and bulk modulus are in general good agreement.
Viennois, Romain; Jund, Philippe; Colinet, Catherine; Tedenac, Jean-Claude
2012-09-15
First principles calculations are done for Mg{sub 2}X (X=Si, Ge or Sn) antifluorite compounds and their solid solutions in order to investigate their pseudo-binary phase diagram. The formation energies of the end-member compounds agree qualitatively with the experiments. For X=Si and Ge, there is a complete solubility, but we observe a miscibility gap in the pseudo-binary phase diagram Mg{sub 2}Si-Mg{sub 2}Sn. This agrees with the most recent experiments and phase diagram assessments. Calculated electronic properties of Mg{sub 2}Si{sub 1-x}Sn{sub x} alloys qualitatively agree with experiments and in particular the energy bandgap decreases when Si is substituted by Sn. Supercell calculations are also done in order to determine the most stable defects and the doping induced by these defects in the three end-member compounds. We find that the intrinsic n-doping in pure Mg{sub 2}Si can be attributed to the presence of magnesium atoms in interstitial positions. In Mg{sub 2}Ge and Mg{sub 2}Sn, since other defects are stable, they can be also of p-type. - Graphical abstract: Evidence of a miscibility gap from the plot of the formation energy vs x{sub Si} (silicon content) for the solid solutions Mg{sub 2}Si-Mg{sub 2}Sn. Highlights: Black-Right-Pointing-Pointer First-principles study of the stability of Mg{sub 2}Si-Mg{sub 2}X alloys (X=Ge or Sn) and their defects. Black-Right-Pointing-Pointer Mg{sub 2}Si-Mg{sub 2}Ge alloys form a complete series of solid solutions. Black-Right-Pointing-Pointer Miscibility gap is found in Mg{sub 2}Si-Mg{sub 2}Sn alloys. Black-Right-Pointing-Pointer Interstitial defects are more stable in Mg{sub 2}Si and induce n-doping.
NASA Astrophysics Data System (ADS)
Amari, S.; Bouhafs, B.
2016-09-01
Based on the first-principles methods, the structural, elastic, electronic, properties and magnetic ordering of californium monopnictides CfX (X = P) have been studied using the full-potential augmented plane wave plus local orbitals (FP-L/APW + lo) method within the framework of density functional theory (DFT). The electronic exchange correlation energy is described by generalized gradient approximation GGA and GGA+U (U is the Hubbard correction). The GGA+U method is applied to the rare-earth 5f states. We have calculated the lattice parameters, bulk modulii and the first pressure derivatives of the bulk modulii. The elastic properties of the studied compounds are only investigated in the most stable calculated phase. In order to gain further information, we have calculated Young's modulus, shear modulus, anisotropy factor and Kleinman parameter by the aid of the calculated elastic constants. The results mainly show that californium monopnictides CfX (X = P) have an antiferromagnetic spin ordering. Density of states (DOS) and charge densities for both compounds are also computed in the NaCl (B1) structure.
Ab initio calculations of the optical properties of crystalline and liquid InSb
Sano, Haruyuki; Mizutani, Goro
2015-11-15
Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.
Thürmer, Stephan; Seidel, Robert; Winter, Bernd; Ončák, Milan; Slavíček, Petr
2011-06-16
The effect of hydration on the electronic structure of H(2)O(2) is investigated by liquid-jet photoelectron spectroscopy measurements and ab initio calculations. Experimental valence electron binding energies of the H(2)O(2) orbitals in water are, on average, 1.9 eV red-shifted with respect to the gas-phase molecule. A smaller width of the first peak was observed in the photoelectron spectrum from the solution. Our experiment is complemented by simulated photoelectron spectra, calculated at the ab initio level of theory (with EOM-IP-CCSD and DFT methods), and using path-integral sampling of the ground-state density. The observed shift in ionization energy upon solvation is attributed to a combination of nonspecific electrostatic effects (long-range polarization) and of the specific interactions between H(2)O(2) and H(2)O molecules in the first solvation shell. Changes in peak widths are found to result from merging of the two lowest ionized states of H(2)O(2) in water due to conformational changes upon solvation. Hydration effects on H(2)O(2) are stronger than on the H(2)O molecule. In addition to valence spectra, we report oxygen 1s core-level photoelectron spectra from H(2)O(2)(aq), and observed energies and spectral intensities are discussed qualitatively.
Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces
NASA Astrophysics Data System (ADS)
Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos
2016-08-01
Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.
Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces
Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos
2016-01-01
Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew–Burke–Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C−H and O−H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C−H and O−H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C−H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C−H bond of methanol is more facile than the O−H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O−H bond activation is enhanced, becoming slightly more facile than C−H bond activation. PMID:27503889
Cosmic-Ray Modulation: an Ab Initio Approach
NASA Astrophysics Data System (ADS)
Engelbrecht, N. E.; Burger, R. A.
2014-10-01
A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three-dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented.
The hydration structure of carbon monoxide by ab initio methods
NASA Astrophysics Data System (ADS)
Awoonor-Williams, Ernest; Rowley, Christopher N.
2017-01-01
The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO-H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration using the TIP3P water model is in good agreement with the experiment (9.3 kJ mol-1 expt. vs 10.7 kJ mol-1 calc.). The calculated diffusivity of CO (aq) in TIP3P-model water was 5.1 ×10-5 cm2/s calc., more than double the experimental value of 2.3 ×10-5 cm2/s. The hydration energy calculated using the TIP4P-FB water model is in poorer agreement with the experiment (ΔG = 6.8 kJ/mol) but the diffusivity is in better agreement (D =2.5 ±0.1 ×10-5 cm2/s).
Efficient conformational space exploration in ab initio protein folding simulation
Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A. Z. M. Dayem; Rahman, M. Sohel
2015-01-01
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554
Ab initio valence-space theory for exotic nuclei
NASA Astrophysics Data System (ADS)
Holt, Jason
2015-10-01
Recent advances in ab initio nuclear structure theory have led to groundbreaking predictions in the exotic medium-mass region, from the location of the neutron dripline to the emergence of new magic numbers far from stability. Playing a key role in this progress has been the development of sophisticated many-body techniques and chiral effective field theory, which provides a systematic basis for consistent many-nucleon forces and electroweak currents. Within the context of valence-space Hamiltonians derived from the nonperturbative in-medium similarity renormalization group (IM-SRG) approach, I will discuss the importance of 3N forces in understanding and making new discoveries in the exotic sd -shell region. Beginning in oxygen, we find that the effects of 3N forces are decisive in explaining why 24O is the last bound oxygen isotope, validating first predictions of this phenomenon from several years ago. Furthermore, 3N forces play a key role in reproducing spectroscopy, including signatures of doubly magic 22,24O, and physics beyond the dripline. Similar improvements are obtained in new spectroscopic predictions for exotic fluorine and neon isotopes, where agreement with recent experimental data is competitive with state-of-the-art phenomenology. Finally, I will discuss first applications of the IM-SRG to effective valence-space operators, such as radii and E 0 transitions, as well as extensions to general operators crucial for our future understanding of electroweak processes, such as neutrinoless double-beta decay. This work was supported by NSERC and the NRC Canada.
Efficient conformational space exploration in ab initio protein folding simulation.
Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel
2015-08-01
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.
Resonance and aromaticity: an ab initio valence bond approach.
Rashid, Zahid; van Lenthe, Joop H; Havenith, Remco W A
2012-05-17
Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randić's conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.
AN AB INITIO MODEL FOR COSMIC-RAY MODULATION
Engelbrecht, N. E.; Burger, R. A.
2013-07-20
A proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays (CRs) is of vital importance for a better understanding of CR modulation in the heliosphere. This study presents an ab initio model for CR modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for solar minimum heliospheric conditions, utilizing boundary values chosen so that model results are in reasonable agreement with spacecraft observations of turbulence quantities in the solar ecliptic plane and along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modeled slab and two-dimensional (2D) turbulence energy spectra. The modeled 2D spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers. There currently exist no models or observations for the wavenumber where this drop-off occurs, and it is considered to be the only free parameter in this study. The modeled spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on CR drifts are modeled in a self-consistent way, also employing a recently developed model for wavy current sheet drift. The resulting diffusion and drift coefficients are applied to the study of galactic CR protons and antiprotons using a 3D, steady-state CR modulation code, and sample solutions in fair to good agreement with multiple spacecraft observations are presented.
High pressure behaviour of uranium dicarbide (UC2): Ab-initio study
NASA Astrophysics Data System (ADS)
Sahoo, B. D.; Mukherjee, D.; Joshi, K. D.; Kaushik, T. C.
2016-08-01
The structural stability of uranium dicarbide has been examined under hydrostatic compression employing evolutionary structure search algorithm implemented in the universal structure predictor: evolutionary Xtallography (USPEX) code in conjunction with ab-initio electronic band structure calculation method. The ab-initio total energy calculations involved for this purpose have been carried out within both generalized gradient approximations (GGA) and GGA + U approximations. Our calculations under GGA approximation predict the high pressure structural sequence of tetragonal → monoclinic → orthorhombic for this material with transition pressures of ˜8 GPa and 42 GPa, respectively. The same transition sequence is predicted by calculations within GGA + U also with transition pressures placed at ˜24 GPa and ˜50 GPa, respectively. Further, on the basis of comparison of zero pressure equilibrium volume and equation of state with available experimental data, we find that GGA + U approximation with U = 2.5 eV describes this material better than the simple GGA approximation. The theoretically predicted high pressure structural phase transitions are in disagreement with the only high experimental study by Dancausse et al. [J. Alloys. Compd. 191, 309 (1993)] on this compound which reports a tetragonal to hexagonal phase transition at a pressure of ˜17.6 GPa. Interestingly, during lowest enthalpy structure search using USPEX, we do not see any hexagonal phase to be closer to the predicted monoclinic phase even within 0.2 eV/f. unit. More experiments with varying carbon contents in UC2 sample are required to resolve this discrepancy. The existence of these high pressure phases predicted by static lattice calculations has been further substantiated by analyzing the elastic and lattice dynamic stability of these structures in the pressure regimes of their structural stability. Additionally, various thermo-physical quantities such as equilibrium volume, bulk modulus, Debye
Lucas, J. M.; Andres, J. de; Sogas, J.; Alberti, M.; Aguilar, A.; Bofill, J. M.; Bassi, D.; Ascenzi, D.; Tosi, P.
2009-07-14
Reactive collisions between Li{sup +} ions and i-C{sub 3}H{sub 7}Cl molecules have been studied in the 0.20-12.00 eV center-of-mass energy range using an octopole radio frequency guided-ion beam apparatus recently developed in our laboratory. At low collision energies, dehydrohalogenation reactions giving rise to Li(C{sub 3}H{sub 6}){sup +} and Li(HCl){sup +} are the main reaction channels, while at higher ones C{sub 3}H{sub 7}{sup +} and C{sub 2}H{sub 3}{sup +} become dominant, all their reactive cross sections having been measured as a function of the collision energy. To obtain information about the potential energy surfaces (PESs) on which the reactive processes take place, ab initio calculations at the MP2 level have been performed. For dehydrohalogenations, the reactive ground singlet PES shows ion-molecule adduct formation in both the reactant and product sides of the surface. Following the minimum energy path connecting both minima, an unstable intermediate and the corresponding barriers, both lying below the reactant's energy, have been characterized. The entrance channel ion-molecule adduct is also involved in the formation of C{sub 3}H{sub 7}{sup +}, which then generates C{sub 2}H{sub 3}{sup +} via an CH{sub 4} unimolecular elimination. A qualitative interpretation of the experimental results based on ab initio calculations is also included.
NASA Astrophysics Data System (ADS)
Mazzola, Guglielmo; Sorella, Sandro
2017-01-01
We propose an ab initio molecular dynamics method, capable of dramatically reducing the autocorrelation time required for the simulation of classical and quantum particles at finite temperatures. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix S . Here, we apply this technique to both Lennard-Jones models, to demonstrate the accuracy and speeding-up of the sampling, and within a quantum Monte Carlo based wave function approach, for determining the phase diagram of high-pressure hydrogen with simulations much longer than the autocorrelation time. With the proposed method, we are able to equilibrate in a few hundred steps even close to the liquid-liquid phase transition (LLT). Within our approach, we find that the LLT transition is consistent with recent density functionals predicting a much larger transition pressure when the long range dispersive forces are taken into account.
The ideal strength of gold under uniaxial stress: an ab initio study.
Wang, Hao; Li, Mo
2010-07-28
We employ an ab initio calculation based on density functional theory to investigate the ideal strength of face-centered cubic crystal Au under uniaxial stress along the [100] direction. We show that the stability of the perfect Au crystal under tensile stress is determined by the tetragonal shear stiffness modulus, with an ideal tensile strength of 4.2 GPa and the corresponding Lagrangian tensile strain of ∼ 0.07. The potential bifurcation from the primary uniaxial loading path is along the tetragonal shear. Under compressive stress, there is a stress-free body-centered cubic phase, which is unstable and ready to transform to a stress-free body-centered tetragonal phase with lower internal energy. The stable region is from - 1.6 to 4.2 GPa in the ideal strength, or from - 0.07 to 0.07 in the Lagrangian strain.
Ab initio electron scattering cross-sections and transport in liquid xenon
NASA Astrophysics Data System (ADS)
Boyle, G. J.; McEachran, R. P.; Cocks, D. G.; Brunger, M. J.; Buckman, S. J.; Dujko, S.; White, R. D.
2016-09-01
Ab initio fully differential cross-sections for electron scattering in liquid xenon are developed from a solution of the Dirac-Fock scattering equations, using a recently developed framework (Boyle et al 2015 J. Chem. Phys. 142 154507) which considers multipole polarizabilities, a non-local treatment of exchange, and screening and coherent scattering effects. A multi-term solution of Boltzmann’s equation accounting for the full anisotropic nature of the differential cross-section is used to calculate transport properties of excess electrons in liquid xenon. The results were found to agree to within 25% of the measured mobilities and characteristic energies over the reduced field range of 10-4-1 Td. The accuracies are comparable to those achieved in the gas phase. A simple model, informed by highly accurate gas-phase cross-sections, is presented to improve the liquid cross-sections, which was found to enhance the accuracy of the transport coefficient calculations.
NASA Astrophysics Data System (ADS)
Menezla, S.; Kadri, A.; Zitouni, K.; Djelal, A.; Djermouni, M.; Hallouche, A.; Zaoui, A.
2015-12-01
We present an ab-initio theoretical study of structural and elastic properties of GaAs1-xBix alloys in the Zinc-Blende (ZB) phase. We use a recent version of Wien2k package code based on Density Functional Theory (DFT) Full Potential and Linearized Augmented Plane Waves (FP-LAPW) method including recent Tran-Blaha modified Becke-Johnson correction of the exchange potential (TB-mBJ) and the spin-orbit interaction (SO). The calculations are performed within the Local Density Approximation (LDA) as well as the Generalized Gradient Approximation (GGA). We study first the structural properties of GaAs1-xBix alloys by solving Murnaghan equation of state. Our results show that the ZB phase is the lowest equilibrium crystal structure of GaAs1-xBix in the whole alloy composition range, in agreement with previous theoretical predictions. The variations versus Bi contents of the ZB GaAs1-xBix lattice constant a0, bulk modulus B0 and its pressure derivative B0‧ are also found very close to other theoretical and experimental data, but with much smaller bowing effects indicating a better resolution thanks to TB-mBJ correction. The variations of B0 versus the reverse equilibrium volume of the unit cell (1/V0) are found to be described by the simple linear empirical expression B0 = -0.21068 + 0.16695/V0 which is close to the theoretical prediction for III-V semiconductors with, however, somewhat lower linear coefficients values, suggesting a more metallic behavior. In a second part of this work, we use Birch-Murnaghan approach to study the elastic properties of GaAs1-xBix alloys. The elastic stiffness coefficients, C11, C12 and C44, and their variations versus alloy composition were determined for ZB GaAs1-xBix alloy. Their values in GaAs and GaBi binary compounds are found in very good agreement with available experimental and/or theoretical data. Their variations in GaAs1-xBix alloy show a monotonic decrease with increasing Bi contents, indicating a softening behavior as is
Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.
Martí-Rujas, Javier; Kawano, Masaki
2013-02-19
Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific
An investigation of ab initio shell-model interactions derived by no-core shell model
NASA Astrophysics Data System (ADS)
Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing
2016-09-01
The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.
Autrey, Tom; Brown, Aaron K; Camaioni, Donald M; Dupuis, Michel; Foster, Nancy S; Getty, April
2004-03-31
Photoacoustic signals from dilute ( approximately 30 mM) solutions of H2O2 were measured over the temperature range from 10 to 45 degrees C to obtain the reaction enthalpy and volume change for H2O2(aq) --> 2 OH(aq) from which we ultimately determined DeltafG degrees , DeltafH degrees and partial molal volume, v degrees , of OH (aq). We find DeltarH = 46.8 +/- 1.4 kcal/mol, which is 4 kcal/mol smaller than the gas-phase bond energy, and DeltaVr = 6.5 +/- 0.4 mL/mol. The v degrees for OH in water is 14.4 +/- 0.4 mL/ml: smaller than the v degrees of water. Using ab intio continuum theory, the hydration free energy is calculated to be -3.9 +/- 0.3 kcal/mol (for standard states in number density concentration units) by a novel approach devised to capture in the definition of the solute cavity the strength and specific interactions of the solute with a water solvent molecule. The shape of the cavity is defined by "rolling" a three-dimensional electron density isocontour of water on the ab initio water-OH minimum interaction surface. The value of the contour is selected to reproduce the volume of OH in water. We obtain for OH(aq): DeltafH degrees = -0.2 +/- 1.4 and DeltafG degrees = 5.8 +/- 0.4 kcal/mol that are in agreement with literature values. The results provide confidence in the pulsed PAC technique for measuring aqueous thermochemistry of radicals and open the way to obtaining thermochemistry for most radicals that can be formed by reaction of OH with aqueous substrates while advancing the field of continuum solvation theory toward ab initio-defined solute cavities.
Ab initio study of the optical properties of carbon nanotubes
NASA Astrophysics Data System (ADS)
Chang, Eric
2006-03-01
We present an ab initio study of the optical properties of carbon nanotubes. We use state-of-the-art electronic structure methods based on many-body perturbation theory to compute the optical absorption and resonance Raman spectra of large tubes which have up to 200 atoms [1,2]. Our symmetry-based method makes the study of large tubes feasible within the many- body framework and also allows us to understand the symmetry properties of the excitons and selection rules. We include a study of the so-called dark excitons which are crucial for understanding luminescence efficiency in carbon nanotubes. The mechanism that explains the dark-bright splitting can be understood within our symmetry-based approach. Finally, we present an analysis of the two-photon spectra for several carbon nanotubes, a theoretical analysis which, in conjunction with combined one- and two-photon experiments, allows one to measure the binding energy of excitons. We find in all cases that the excitonic binding energy is large, ranging from 0.5 to 0.9 eV depending on the diameter of the tube, and that the excitonic wavefunction is Wannier-like and extended over many atoms. Our studies for the one- and two-photon absorption and resonance Raman spectra have been fruitful for understanding the corresponding experiments. In particular, our theoretical results are in good agreement with one- and two-photon absorption experiments [3-5]. The results for resonance Raman show that such a spectroscopic technique is a good alternative to optical absorption since it allows for the selection of tubes of a given diameter while probing the same excited states. 1. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. Lett. 92, 196401 (2004). 2. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. B 72, 195423 (2005). 3. M. Y. Sfeir et al., Science 306, 1540 (2004). 4. J. Maultzsch et al., to be published in Phys. Rev. B, see also cond-mat/0505150. 5. Z. M. Li et. al., Phys. Rev. Lett. 87, 127401 (2001).
Ab initio computational applications to complex biomolecular systems
NASA Astrophysics Data System (ADS)
Liang, Lei
A series of biomaterial related systems---including water and DNA molecules---have been studied using ab initio (first-principles) methods. By investigating the properties of water as the preliminary step, the hydrogen bond (HB) interactions, which play important roles in biomolecules, were better understood from the quantum mechanical viewpoint. The calculated K-edge x-ray absorption near edge structure (XANES) spectra of all 340 oxygen atoms in the model have been accumulated to reproduce the experimental one. The spectra were shown to be very sensitive to the HB configurations of O atoms, which could be used to elucidate the subtle structural variations in complex biomolecules. The simulation of single-molecule DNA overstretching experiments under torsionally constrained condition has been carried out afterwards. The initial DNA models were stretched stepwisely and eventually gained an extension of 1.5-fold (150% x the original length). The variation of total energy, atomic configuration, and the electronic structure during this process were analyzed in details. At the extension of ˜1.3-fold, the ring opening reactions occurred in the backbones. The backbone nicks appeared at elongations of ˜1.40-fold. The whole process was accompanied by HB breaking and charge transfers. We have proposed an overstretched structure named O-DNA (Opened-DNA) to clarify the confusion in understanding the behavior of DNA under high force load. With more experiences gained, a comprehensive methodology revealing the underlying principles of bioprocesses from the quantum mechanical viewpoint eventually come up. For the purpose of better computational accuracy, the scheme of implementing the generalized gradient approximation (GGA) exchange-correlation functionals into the Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) program suite has been discussed, and the computational efficiency has been analyzed correspondingly. Moreover, the parallel strategy for performing
ab initio MD simulations of geomaterials with ~1000 atoms
NASA Astrophysics Data System (ADS)
Martin, G. B.; Kirtman, B.; Spera, F. J.
2009-12-01
In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in
Borges, P. D. E-mail: lscolfaro@txstate.edu; Scolfaro, L. E-mail: lscolfaro@txstate.edu
2014-12-14
The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.
NASA Astrophysics Data System (ADS)
Autrey, Daniel; Choo, Jaebum; Laane, Jaan
2000-10-01
The ring-twisting vibration of 1,3-cyclohexadiene has been studied using Raman and infrared spectroscopy of the molecule in the vapor phase. The Raman spectrum shows five ring-twisting transitions in the 150 - 200 cm-1 region. The far-infrared spectrum shows only two transitions for this vibration, which is infrared forbidden in the C_2v (planar) approximation. Three ring-twisting combination bands were also observed off a fundamental vibration at 926.1 cm-1. A coordinate dependent kinetic energy expansion for the ring-twisting motion was calculated, and this was used to determine the ring-twisting potential function. Ab initio calculations were performed using Moller-Plesset perturbation theory (MP2) using different basis sets. The barrier to planarity of 1150 cm-1 was determined from the spectroscopic data. The various ab initio calculations gave barriers to planarity in the 1197 - 1593 cm-1 range.
Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study
Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z
2014-04-01
The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Effect of composition on antiphase boundary energy in Ni3Al based alloys: Ab initio calculations
NASA Astrophysics Data System (ADS)
Gorbatov, O. I.; Lomaev, I. L.; Gornostyrev, Yu. N.; Ruban, A. V.; Furrer, D.; Venkatesh, V.; Novikov, D. L.; Burlatsky, S. F.
2016-06-01
The effect of composition on the antiphase boundary (APB) energy of Ni-based L 12-ordered alloys is investigated by ab initio calculations employing the coherent potential approximation. The calculated APB energies for the {111} and {001} planes reproduce experimental values of the APB energy. The APB energies for the nonstoichiometric γ' phase increase with Al concentration and are in line with the experiment. The magnitude of the alloying effect on the APB energy correlates with the variation of the ordering energy of the alloy according to the alloying element's position in the 3 d row. The elements from the left side of the 3 d row increase the APB energy of the Ni-based L 12-ordered alloys, while the elements from the right side slightly affect it except Ni. The way to predict the effect of an addition on the {111} APB energy in a multicomponent alloy is discussed.
Ab initio tight-binding description of morphology-dependent resonance in a bisphere
NASA Astrophysics Data System (ADS)
Miyazaki, H.; Jimba, Y.
2000-09-01
Morphology-dependent resonance (MDR) of the electric field in a bisphere is investigated with respect to the electromagnetic energy stored within the spheres. The energy spectra clearly reveal the fine structure of the bonding and antibonding branches originating from the Mie resonance of a single sphere. The electric field distribution can directly provide information on the formation of the bonding and antibonding states. On the basis of this detailed information, we establish the ab initio tight-binding (TB) formalism of the MDR in a bishpere. The single-mode TB model combined with the linearization of the phase shift clarifies the meaning of the overlap integral. It also gives a qualitative explanation of the MDR. By dividing the Mie resonance modes into the relevant modes and the reservoir modes and incorporating the latter perturbationally, it is shown that the double-mode TB model can reproduce the exact numerical results fairly well.
Ab initio determination of the proton affinities of small neutral and anionic molecules
NASA Technical Reports Server (NTRS)
DeFrees, D. J.; McLean, A. D.
1986-01-01
The proton affinity of a molecule in the gas phase is a fundamental measure of its basicity and is the factor controlling the course of many ion-molecule reactions. In this article, ab initio molecular orbital theory at the MP4/6-311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol-1. Furthermore, the errors are random, indicating that there are likely no systematic errors in either the experimental or theoretical PA's. Also, this level of theory is used to calibrate less sophisticated theoretical models which are suitable for larger molecules; the MP4/6-311 ++ G(2d, 2p) and MP2/6-311 ++ G(d, p) theoretical models should be particularly useful. A procedure for predicting the vibrational frequencies for anion is proposed and applied to CH3-, NH2-, OH-, and CN-.
Many-Body Potentials for Aqueous Be(2+) Derived from ab Initio Calculations.
Winter, Nicolas D
2016-12-08
An effective three-body potential for the aqueous Be(2+) ion has been constructed from a large number of high-level ab initio cluster calculations. The new potential was validated in subsequent molecular dynamics simulations of both gas phase ion-water clusters and bulk liquid. The structures of the first and second solvation shells were studied using radial distribution functions and angular distribution functions. The vibrational spectrum of Be(2+) and first shell waters was examined by computing power spectra from the molecular dynamics simulations. The observed bands showed reasonable agreement with experimental spectroscopic frequencies. The potential of mean force for water exchange between the first and second solvation shells was calculated and the energy barrier for exchange was found to have improved agreement with experiment relative to two-body force fields. Examination of the solvation structure near the transition state yielded results consistent with an associative mechanism.
NASA Astrophysics Data System (ADS)
Wachter, Georg; Lemell, Christoph; Burgdörfer, Joachim; Sato, Shunsuke A.; Tong, Xiao-Min; Yabana, Kazuhiro
2014-08-01
We theoretically investigate the generation of ultrafast currents in insulators induced by strong few-cycle laser pulses. Ab initio simulations based on time-dependent density functional theory give insight into the atomic-scale properties of the induced current signifying a femtosecond-scale insulator-metal transition. We observe the transition from nonlinear polarization currents during the laser pulse at low intensities to tunnelinglike excitation into the conduction band at higher laser intensities. At high intensities, the current persists after the conclusion of the laser pulse considered to be the precursor of the dielectric breakdown on the femtosecond scale. We show that the transferred charge sensitively depends on the orientation of the polarization axis relative to the crystal axis, suggesting that the induced charge separation reflects the anisotropic electronic structure. We find good agreement with very recent experimental data on the intensity and carrier-envelope phase dependence [A. Schiffrin et al., Nature (London) 493, 70 (2013)].
AB INITIO Modeling of Thermomechanical Properties of Mo-Based Alloys for Fossil Energy Conversion
Ching, Wai-Yim
2013-12-31
In this final scientific/technical report covering the period of 3.5 years started on July 1, 2011, we report the accomplishments on the study of thermo-mechanical properties of Mo-based intermetallic compounds under NETL support. These include computational method development, physical properties investigation of Mo-based compounds and alloys. The main focus is on the mechanical and thermo mechanical properties at high temperature since these are the most crucial properties for their potential applications. In particular, recent development of applying ab initio molecular dynamic (AIMD) simulations to the T1 (Mo{sub 5}Si{sub 3}) and T2 (Mo{sub 5}SiB{sub 2}) phases are highlighted for alloy design in further improving their properties.
Ab initio-based approach to structural change of compound semiconductor surfaces during MBE growth
NASA Astrophysics Data System (ADS)
Ito, Tomonori; Akiyama, Toru; Nakamura, Kohji
2009-01-01
Phase diagrams of GaAs and GaN surfaces are systematically investigated by using our ab initio-based approach in conjunction with molecular beam epitaxy (MBE). The phase diagrams are obtained as a function of growth parameters such as temperature and beam equivalent pressure (BEP). The versatility of our approach is exemplified by the phase diagram calculations for GaAs(0 0 1) surfaces, where the stable phases and those phase boundaries are successfully determined as functions of temperature and As 2 and As 4 BEPs. The initial growth processes are clarified by the phase diagram calculations for GaAs(1 1 1)B-(2×2). The calculated results demonstrate that the As-trimer desorption on the GaAs(1 1 1)B-(2×2) with Ga adatoms occurs beyond 500-700 K while the desorption without Ga adatoms does beyond 800-1000 K. This self-surfactant effect induced by Ga adsorption crucially affects the initial growth of GaAs on the GaAs(1 1 1)B-(2×2). Furthermore, the phase diagram calculations for GaN(0 0 0 1) suggests that Ga adsorption or desorption during GaN MBE growth can easily change the pseudo-(1×1) to the (2×2)-Ga via newly found (1×1) and vice versa. On the basis of this finding, the possibility of ghost island formation during MBE growth is discussed.
Huang, Ying; Chen, Shi-Yi; Deng, Feilong
2016-01-01
In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools.
An ab initio-based Er–He interatomic potential in hcp Er
Yang, Li; ye, Yeting; Fan, K. M.; Shen, Huahai; Peng, Shuming; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei
2014-09-01
We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations. The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.
Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization
NASA Astrophysics Data System (ADS)
Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng
With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.
Ab initio calculation of (hyper)polarizabilities using a sum-over-states formalism.
NASA Astrophysics Data System (ADS)
Taylor, Caroline M.; Chaudhuri, Rajat K.; Potts, Davin M.; Freed, Karl F.
2001-03-01
Hyperpolarizabilities are relevant to a wide range of non-linear optical properties. Ab initio computations often require a high level of correlation for accurate determination of β and γ , and especially of thier frequency dependence. While sum-over-states methods are widely used within semi-empirical frameworks, they have not been employed with high level ab initio methods because of the computational costs associated with calculating a sufficient number of states. The effective valence shell Hamiltonian method (H^v) is a highly correlated, size-extensive, ab initio, multireference, perturbative (``perturb-then-diagonalize'') method. A single H^v calculation yields a large number of states, making it ideal for use with the sum-over-states fomalism for determination of molecular properties. The method has been used to calculate the (hyper)polarizabilities of small polyene systems.
Classical and ab-initio molecular dynamic simulation of an amorphous silica surface
NASA Astrophysics Data System (ADS)
Mischler, C.; Kob, W.; Binder, K.
2002-08-01
We present the results of a classical molecular dynamic simulation as well as of an ab-initio molecular dynamic simulation of an amorphous silica surface. In the case of the classical simulation we use the potential proposed by van Beest et al. (BKS) whereas the ab-initio simulation is done with a Car-Parrinello method (CPMD). We find that the surfaces generated by BKS have a higher concentration of defects (e.g., concentration of two-membered rings) than those generated with CPMD. In addition also the distribution functions of the angles and of the distances are different for the short rings. Hence we conclude that whereas the BKS potential is able to correctly reproduce the surface on the length scale beyond ≈5 Å, it is necessary to use an ab-initio method to reliably predict the structure at small scales.
Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening
NASA Astrophysics Data System (ADS)
de Jonge, Marc R.; Vinkers, H. Maarten; van Lenthe, Joop H.; Daeyaert, Frits; Bush, Ian J.; van Dam, Huub J. J.; Sherwood, Paul; Guest, Martyn F.
2007-09-01
We present a new and completely parallel method for protein ligand docking. The potential of the docking target structure is obtained directly from the electron density derived through an ab initio computation. A large subregion of the crystal structure of Isocitrate Lyase, was selected as docking target. To allow the full ab initio treatment of this region special care was taken to assign optimal basis functions. The electrostatic potential is tested by docking a small charged molecule (succinate) into the binding site. The ab initio grid yields a superior result by producing the best binding orientation and position, and by recognizing it as the best. In contrast the same docking procedure, but using a classical point-charge based potential, produces a number of additional incorrect binding poses, and does not recognize the correct pose as the best solution.
Autrey, Thomas; Brown, Aaron K.; Camaioni, Donald M.; Dupuis, Michel; Foster, Nancy S.; Getty, April D.
2004-03-31
Photoacoustic signals from dilute ({approx}30 mM) solutions of H{sub 2}O{sub 2} were measured over the temperature range from 10-45 C to obtain the reaction enthalpy and volume change for H{sub 2}O{sub 2}(aq) {yields} 2 OH(aq) from which we ultimately determined {Delta}{sub f}G{sup o}, {Delta}{sub f}H{sup o} and partial molal volume, v{sup o}, of OH (aq). We find {Delta}{sub r}H = 46.8 {+-} 1.4 kcal/mol, which is 4 kcal/mol smaller than the gas phase bond energy, and {Delta}V{sub r} = 6.5 {+-} 0.4 mL/mol. The v{sup o} for OH in water is 14.4 {+-} 0.4 mL/ml: smaller than the v{sup o} of water. Using ab initio continuum theory, the hydration free energy is calculated to be -3.9 {+-} 0.3 kcal/mol (for standard states in number density concentration units) by a novel approach devised to capture in the definition of the solute cavity the strength and specific interactions of the solute with a water solvent molecule. The shape of the cavity is defined by ''rolling'' a 3 dimensional electron density isocontour of water on the ab initio water-OH minimum interaction surface. The value of the contour is selected to reproduce the volume of OH in water. We obtain for OH(aq): {Delta}{sub f}H{sup o} = -0.2 {+-} 1.4 and {Delta}{sub f}G{sup o} = 5.8 {+-} 0.4 kcal/mol that are in agreement with literature values. The results provide confidence in the pulsed PAC technique for measuring aqueous thermochemistry of radicals and open the way to obtaining thermochemistry for most radicals that can be formed by reaction of OH with aqueous substrates while advancing the field of continuum solvation theory towards ab initio-defined solute cavities.
Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J
2015-02-01
AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.
Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations
NASA Technical Reports Server (NTRS)
Good, Brian S.
2003-01-01
We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.
Ab initio study of collective excitations in a disparate mass molten salt.
Bryk, Taras; Klevets, Ivan
2012-12-14
Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.
Khaliullin, Rustam Z; Kühne, Thomas D
2013-10-14
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.
A density functional and ab initio investigation of the p-aminobenzoic acid molecule
NASA Astrophysics Data System (ADS)
Lago, A. F.; Dávalos, J. Z.; de Brito, A. Naves
2007-08-01
The p-aminobenzoic acid (C 7H 7NO 2) molecule has been investigated at different levels of theory. DFT methods (B3LYP and PBE1PBE), second order Møller-Plesset perturbation theory (MP2) and composite ab initio methods (G3MP2 and CBS) have been employed, in conjunction with large basis sets. Important informations on the electronic structure and thermochemistry of this molecule have been extracted, and the performance of the density functional and ab initio methods has been evaluated, based on the comparison of the calculated and the available experimental data.
NASA Astrophysics Data System (ADS)
de Boer, K.; Jansen, A. P. J.; van Santen, R. A.
1994-06-01
We have developed a new method for deriving parameters for the shell model of silica polymorphs. All parameters for the shell model are derived in a self-consistent way from ab initio energy surfaces, polarizabilities and dipole moments of small clusters. This yields an ab initio partial charge shell model potential. The predictive power of our potential is demonstrated by presenting predictions for the structure of α-quartz, α-cristobalite, coesite, stishovite and the IR spectrum of α-quartz which are compared with experiment and predictions of the widely used potentials of Jackson and Catlow, and Kramer, Farragher, van Beest and van Santen.
Ab-initio simulations of materials using VASP: Density-functional theory and beyond.
Hafner, Jürgen
2008-10-01
During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science-promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces
NASA Astrophysics Data System (ADS)
John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.
2016-04-01
We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.
Ab initio calculation of structural stability, electronic and optical properties of Ag{sub 2}Se
Rameshkumar, S.; Jayalakshmi, V.; Jaiganesh, G.; Palanivel, B.
2015-06-24
The structural stability, electronic and optical properties of Ag{sub 2}Se compound is studied using ab initio packages. Ag{sub 2}Se is found to crystallize in orthorhombic structure with two different space groups i.e. P2{sub 1}2{sub 1}2{sub 1} (No. 19) and P222{sub 1} (No. 17). For this compound in these two space groups, the total energy has been computed as a function of volume. Our calculated results suggest that the P2{sub 1}2{sub 1}2{sub 1}–phase is more stable than that of the P222{sub 1}–phase. The band structure calculation show that Ag{sub 2}Se is semimetallic with an overlap of about 0.014 eV in P2{sub 1}2{sub 1}2{sub 1}–phase whereas is metallic in nature in P222{sub 1}–phase. Moreover, the optical properties including the dielectric function, energy loss spectrum are obtained and analysed.
Ab initio lattice stability of fcc and hcp Fe-Mn random alloys.
Gebhardt, T; Music, D; Hallstedt, B; Ekholm, M; Abrikosov, I A; Vitos, L; Schneider, J M
2010-07-28
We have studied the lattice stability of face centred cubic (fcc) versus hexagonal close packed (hcp) Fe-Mn random alloys using ab initio calculations. In the calculations we considered the antiferromagnetic order of local moments, which for fcc alloys models the magnetic configuration of this phase at room temperature (below its Néel temperature) as well as their complete disorder, corresponding to paramagnetic fcc and hcp alloys. For both cases, the results are consistent with our thermodynamic calculations, obtained within the Calphad approach. For the room temperature magnetic configuration, the cross-over of the total energies of the hcp phase and the fcc phase of Fe-Mn alloys is at the expected Mn content, whereas for the magnetic configuration above the fcc Néel temperature, the hcp lattice is more stable within the whole composition range studied. The increase of the total energy difference between hcp and antiferromagnetic fcc due to additions of Mn as well as the stabilizing effect of antiferromagnetic ordering on the fcc phase are well displayed. These results are of relevance for understanding the deformation mechanisms of these random alloys.
Slavícek, Petr; Winter, Bernd; Faubel, Manfred; Bradforth, Stephen E; Jungwirth, Pavel
2009-05-13
Vertical ionization energies of the nucleosides cytidine and deoxythymidine in water, the lowest ones amounting in both cases to 8.3 eV, are obtained from photoelectron spectroscopy measurements in aqueous microjets. Ab initio calculations employing a nonequilibrium polarizable continuum model quantitatively reproduce the experimental spectra and provide molecular interpretation of the individual peaks of the photoelectron spectrum, showing also that lowest ionization originates from the base. Comparison of calculated vertical ionization potentials of pyrimidine bases, nucleosides, and nucleotides in water and in the gas phase underlines the dramatic effect of bulk hydration on the electronic structure. In the gas phase, the presence of sugar and, in particular, of phosphate has a strong effect on the energetics of ionization of the base. Upon bulk hydration, the ionization potential of the base in contrast becomes rather insensitive to the presence of the sugar and phosphate, which indicates a remarkable screening ability of the aqueous solvent. Accurate aqueous-phase vertical ionization potentials provide a significant improvement to the corrected gas-phase values used in the literature and represent important information in assessing the threshold energies for photooxidation and oxidation free energies of solvent-exposed DNA components. Likewise, such energetic data should allow improved assessment of delocalization and charge-hopping mechanisms in DNA ionized by radiation.
Ab initio investigation of the elastic properties of Ni3Fe
NASA Astrophysics Data System (ADS)
Wang, Guisheng; Hu, Qing-Miao; Kokko, Kalevi; Johansson, Börje; Vitos, Levente
2013-11-01
Ab initio alloy theory, formulated within the exact muffin-tin orbitals method in combination with the coherent-potential approximation, is used to determine the elastic properties of Ni-Fe alloys with Fe:Ni ratio 1:3. The interplay between magnetic and chemical effects is investigated by computing the lattice parameters and the single- and polycrystal elastic moduli for different partially ordered structures in the ferro- and paramagnetic states. It is found that the influence of long-range chemical order on the bulk properties strongly depends on the magnetic state. The largest magnetic-order-induced changes are obtained for the chemically ordered L12 phase. The ferromagnetic L12 system possesses ˜5.4% larger elastic Debye temperature than the paramagnetic L12 phase, which in turn has a similar ΘD as the chemically disordered face-centered cubic phase in either the ferro- or paramagnetic state. It is concluded that magnetic ordering has a substantially larger impact on the bulk parameters of Ni3Fe than chemical ordering. The calculated trends are explained based on the electronic structure of nonmagnetic, ferromagnetic, and paramagnetic ordered and disordered phases.
An efficient method for electron-atom scattering using ab-initio calculations
NASA Astrophysics Data System (ADS)
Xu, Yuan; Yang, Yonggang; Xiao, Liantuan; Jia, Suotang
2017-02-01
We present an efficient method based on ab-initio calculations to investigate electron-atom scatterings. Those calculations profit from methods implemented in standard quantum chemistry programs. The new approach is applied to electron-helium scattering. The results are compared with experimental and other theoretical references to demonstrate the efficiency of our method.
Ab initio molecular dynamics simulations of a binary system of ionic liquids.
Brüssel, Marc; Brehm, Martin; Voigt, Thomas; Kirchner, Barbara
2011-08-14
This work presents first insights into the structural properties of a binary mixture of ionic liquids from the perspective of ab initio molecular dynamics simulations. Simulations were carried out for a one-to-one mixture of 1-ethyl-3-methyl-imidazolium thiocyanate and 1-ethyl-3-methyl-imidazolium chloride and compared to pure 1-ethyl-3-methyl-imidazolium thiocyanate.
Ab initio prediction of vacancy properties in concentrated alloys: The case of fcc Cu-Ni
NASA Astrophysics Data System (ADS)
Zhang, Xi; Sluiter, Marcel H. F.
2015-05-01
Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total energies in a consistent manner without a statistical model. Essential features of such a model are knowledge of the chemical potential and imposition of invariants. In the present work, we derive the simplest model that satisfies these requirements and we compare it with models in the literature. As illustration we compute ab initio vacancy properties of fcc Cu-Ni alloys as a function of composition and temperature. Ab initio density functional calculations were performed for SQS supercells at various compositions with and without vacancies. Various methods of extracting alloy vacancy properties were examined. A ternary cluster expansion yielded effective cluster interactions (ECIs) for the Cu-Ni-Vac system. Composition and temperature dependent alloy vacancy concentrations were obtained using statistical thermodynamic models with the ab initio ECIs. An Arrhenius analysis showed that the heat of vacancy formation was well represented by a linear function of temperature. The positive slope of the temperature dependence implies a negative configurational entropy contribution to the vacancy formation free energy in the alloy. These findings can be understood by considering local coordination effects.
Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R
2016-07-07
Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.
Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)
NASA Astrophysics Data System (ADS)
Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang
2001-01-01
Semiempirical PM3, ab initio HF/3-21g ∗, and DFT B3LYP/6-31g ∗ calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.
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…
NASA Astrophysics Data System (ADS)
Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.
2016-07-01
Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.
An efficient and accurate molecular alignment and docking technique using ab initio quality scoring
Füsti-Molnár, László; Merz, Kenneth M.
2008-01-01
An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561
Ab-initio kinetics and thermodynamics studies of ammonia-borane for hydrogen storage
NASA Astrophysics Data System (ADS)
Miranda, Caetano R.; Ceder, Gerbrand
2007-03-01
Ammonia-borane (BH3NH3) is a promising chemical hydrogen storage material given its high gravimetry and volumetric properties. However, the ammonia-borane (AB) thermal hydrogen release is not very efficient, being mainly limited by the kinetics of hydrogenation. Using ab initio calculations, we have investigated the thermodynamics and kinetics of hydrogen release on AB by calculating the free energies of the H2 release reactions for different possible decomposition products. Our results indicate that AB regeneration through the ammonia-borane polymeric and borazine-cyclotriborazane cycles is very unlikely due to the strong exothermic character of the reactions. The kinetics of hydrogen release is further investigated with the recently developed metadynamics method. This method allows us to calculate the multidimensional free energy surface of hydrogen release on AB. Our simulations reveal the atomistic mechanism of hydrogenation and provide the free energies barriers and transition states involved in inter and intramolecule H2 release on AB.
Ab Initio Enhanced calphad Modeling of Actinide-Rich Nuclear Fuels
Morgan, Dane; Yang, Yong Austin
2013-10-28
The process of fuel recycling is central to the Advanced Fuel Cycle Initiative (AFCI), where plutonium and the minor actinides (MA) Am, Np, and Cm are extracted from spent fuel and fabricated into new fuel for a fast reactor. Metallic alloys of U-Pu-Zr-MA are leading candidates for fast reactor fuels and are the current basis for fast spectrum metal fuels in a fully recycled closed fuel cycle. Safe and optimal use of these fuels will require knowledge of their multicomponent phase stability and thermodynamics (Gibbs free energies). In additional to their use as nuclear fuels, U-Pu-Zr-MA contain elements and alloy phases that pose fundamental questions about electronic structure and energetics at the forefront of modern many-body electron theory. This project will validate state-of-the-art electronic structure approaches for these alloys and use the resulting energetics to model U-Pu-Zr-MA phase stability. In order to keep the work scope practical, researchers will focus on only U-Pu-Zr-{Np,Am}, leaving Cm for later study. The overall objectives of this project are to: Provide a thermodynamic model for U-Pu-Zr-MA for improving and controlling reactor fuels; and, Develop and validate an ab initio approach for predicting actinide alloy energetics for thermodynamic modeling.
Engineering superconductors with ab initio methods: the example of LiB
NASA Astrophysics Data System (ADS)
Curtarolo, Stefano
2007-03-01
The identification of novel crystal structures is a fundamental step for predicting new stable compounds in alloys. While performing ab initio data mining of intermetallic compounds [1], we discover a new family of layered metal borides [2], of which MgB2 is one particular element (the new phases are called Metal Sandwich (MS)). Thermodynamic stability and electronic properties of these MS phases are investigated in details, leading to the prediction of a hypothetical novel superconductor MS-LiB [2,3]. Calculations show that the MS phases in the Li-B system exhibit electronic features similar to those of MgB2 [2,3] and CaC6 [4]. Although the predicted critical temperature of LiB is lower than that of MgB2 (references [4] and [5] for MS2-LiB and MS1-LiB, respectively), the peculiarities of MS-LiB in terms of electronic structure, layer arrangements and doping capabilities allow a lot of freedom in the search for higher Tc systems [5]. We acknowledge the San Diego Supercomputer Center for computational resources. [1] S. Curtarolo et al., Phys. Rev. Lett. 91, 135503 (2003). [2] A.N. Kolmogorov, S. Curtarolo, Phys. Rev. B 73, 180501(R) (2006). [3] A.N. Kolmogorov, S. Curtarolo, in press, Phys. Rev B 74 (2006), condmat/0607654. [4] A.Y. Liu, I.I. Mazin, cond-mat/0610057. [5] M. Calandra, A.N. Kolmogorov, S. Curtarolo, submitted (2006).
Ab initio calculation of the electronic absorption spectrum of liquid water
Martiniano, Hugo F. M. C.; Galamba, Nuno; Cabral, Benedito J. Costa
2014-04-28
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.
Ab initio calculation of the electronic absorption spectrum of liquid water.
Martiniano, Hugo F M C; Galamba, Nuno; Cabral, Benedito J Costa
2014-04-28
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O-H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.
Liu, Shi-Yu; Liu, Shiyang; Li, De-Jun; Wang, Sanwu; Guo, Jing; Shen, Yaogen
2015-02-14
Utilizing a combination of ab initio density-functional theory and thermodynamics formalism, we have established the microscopic mechanisms for oxidation of the binary and ternary alloy surfaces and provided a clear explanation for the experimental results of the oxidation. We construct three-dimensional surface phase diagrams (SPDs) for oxygen adsorption on three different Nb-X(110) (X = Ti, Al or Si) binary alloy surfaces. On the basis of the obtained SPDs, we conclude a general microscopic mechanism for the thermodynamic oxidation, that is, under O-rich conditions, a uniform single-phase SPD (type I) and a nonuniform double-phase SPD (type II) correspond to the sustained complete selective oxidation and the non-sustained partial selective oxidation by adding the X element, respectively. Furthermore, by revealing the framework of thermodynamics for the oxidation mechanism of ternary alloys through the comparison of the surface energies of two separated binary alloys, we provide an understanding for the selective oxidation behavior of the Nb ternary alloy surfaces. Using these general microscopic mechanisms, one could predict the oxidation behavior of any binary and multi-component alloy surfaces based on thermodynamics considerations.
Ab initio calculation of the electronic absorption spectrum of liquid water
NASA Astrophysics Data System (ADS)
Martiniano, Hugo F. M. C.; Galamba, Nuno; Cabral, Benedito J. Costa
2014-04-01
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O-H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.
NASA Astrophysics Data System (ADS)
Ohta, Ayumi; Kobayashi, Osamu; Danielache, Sebastian O.; Nanbu, Shinkoh
2017-03-01
The ultra-fast photoisomerization reactions between 1,3-cyclohexadiene (CHD) and 1,3,5-cis-hexatriene (HT) in both hexane and ethanol solvents were revealed by nonadiabatic ab initio molecular dynamics (AI-MD) with a particle-mesh Ewald summation method and our Own N-layered Integrated molecular Orbital and molecular Mechanics model (PME-ONIOM) scheme. Zhu-Nakamura version trajectory surface hopping method (ZN-TSH) was employed to treat the ultra-fast nonadiabatic decaying process. The results for hexane and ethanol simulations reasonably agree with experimental data. The high nonpolar-nonpolar affinity between CHD and the solvent was observed in hexane solvent, which definitely affected the excited state lifetimes, the product branching ratio of CHD:HT, and solute (CHD) dynamics. In ethanol solvent, however, the CHD solute was isomerized in the solvent cage caused by the first solvation shell. The photochemical dynamics in ethanol solvent results in the similar property to the process appeared in vacuo (isolated CHD dynamics).
NASA Astrophysics Data System (ADS)
López, E.; Lucas, J. M.; de Andrés, J.; Albertí, M.; Bofill, J. M.; Bassi, D.; Aguilar, A.
2014-10-01
Collisions between potassium ions and neutral i-C3H7Br and i-C3H7OH, all in their electronic ground state, have been studied in the 0.10-10.00 eV center of mass (CM) collision energy range, using the radiofrequency-guided ion beam technique. In K+ + i-C3H7Br collisions KHBr+ formation was observed and quantified, while the analogous KH2O+ formation in K+ + i-C3H7OH was hardly detected. Moreover, formation of the ion-molecule adducts and their decomposition leading to C3H7+ and either KBr or KOH, respectively, have been observed. For all these processes, absolute cross-sections were measured as a function of the CM collision energy. Ab initio structure calculations at the MP2 level have given information about the potential energy surfaces (PESs) involved. In these, different stationary points have been characterized using the reaction coordinate method, their connectivity being ensured by using the intrinsic-reaction-coordinate method. From the measured excitation function for KHBr+ formation the corresponding thermal rate constant at 303 K has been calculated. The topology of the calculated PESs allows an interpretation of the main features of the reaction dynamics of both systems, and in particular evidence the important role played by the potential energy wells in controlling the reactivity for the different reaction channels.
NASA Astrophysics Data System (ADS)
French, Martin
2010-11-01
Since the interior structure of giant planets inside or outside our solar system cannot be probed directly by experiments, planetary models have been developed to gain further insight. Such models require accurate equations of state (EOS) for the major components (H, He, and heavier compounds like water) up to extreme thermodynamic conditions (pressures of several ten megabars and temperatures of more than ten thousand degrees Kelvin) [1]. Ab initio methods that combine finite temperature density functional theory (FT-DFT) for the electrons with classical molecular dynamics (MD) for the ions have proven to be a powerful tool to calculate such accurate EOS data. In addition, the FT-DFT-MD also generates structural information, transport and optical properties and, most important, information on phase diagrams and demixing regions. Based on our recently calculated ab initio data for H, He, and water, we derive interior models of Saturn and Jupiter and discuss the role of H-He demixing [2] and of the plasma phase transition in hydrogen on the planetary interiors. We also present new models for Uranus and Neptune which offer conditions to allow the formation of the exotic superionic phase of water [3]. The ab initio data can also be applied in planetary evolution scenarios and dynamo simulations of solar and extrasolar planets.[4pt] [1] J. J. Fortney, N. Nettelmann, Space Sci. Rev. 152, 423 (2010)[0pt] [2] W. Lorenzen, B. Holst, R. Redmer, Phys. Rev. Lett. 102, 115701 (2009)[0pt] [3] M. French, T. R. Mattsson, N. Nettelmann, R. Redmer, Phys. Rev. B 79, 054107 (2009)
Peterson, Charles; Penchoff, Deborah A.; Wilson, Angela K.
2015-11-21
An effective approach for the determination of lanthanide energetics, as demonstrated by application to the third ionization energy (in the gas phase) for the first half of the lanthanide series, has been developed. This approach uses a combination of highly correlated and fully relativistic ab initio methods to accurately describe the electronic structure of heavy elements. Both scalar and fully relativistic methods are used to achieve an approach that is both computationally feasible and accurate. The impact of basis set choice and the number of electrons included in the correlation space has also been examined.
Ab initio many-body calculations of nucleon-4He scattering with three-nucleon forces
Hupin, Guillaume; Langhammer, Joachim; Navratil, Petr; ...
2013-11-27
We extend the ab initio no-core shell model/resonating-group method to include three-nucleon (3N) interactions for the description of nucleon-nucleus collisions. We outline the formalism, give algebraic expressions for the 3N-force integration kernels, and discuss computational aspects of two alternative implementations. The extended theoretical framework is then applied to nucleon-4He elastic scattering using similarity-renormalization-group (SRG)-evolved nucleon-nucleon plus 3N potentials derived from chiral effective field theory. We analyze the convergence properties of the calculated phase shifts and explore their dependence upon the SRG evolution parameter. We include up to six excited states of the 4He target and find significant effects from themore » inclusion of the chiral 3N force, e.g., it enhances the spin-orbit splitting between the 3/2– and 1/2– resonances and leads to an improved agreement with the phase shifts obtained from an accurate R-matrix analysis of the five-nucleon experimental data. As a result, we find remarkably good agreement with measured differential cross sections at various energies below the d+3H threshold, while analyzing powers manifest larger deviations from experiment for certain energies and angles.« less
Ab initio investigations on the stability of seven-fold approximants
NASA Astrophysics Data System (ADS)
Orsini-Rosenberg, Heinrich; Steurer, Walter
2011-07-01
The stability of theoretical heptagonal approximants was investigated. No approximant phase has yet been confirmed consisting of all three heptagonal rhomb prototiles. To solve this problem, two new approximant structures were constructed from supertiles taken from the ThB4 and YCrB4 structure types. In order to compare structural stability, the total energy convex hulls were calculated for the ternary systems B-Cr-RE (RE = Dy, Er, Ho, Y), as well as B-Mn-Dy and B-Mn-Y, by means of ab initio calculations, using density functional theory. This included all known stable monary, binary and ternary phases. Additionally, several layered boride structure types, which are not stable in the respective ternary systems but show four-, five-, six- or seven-fold local environments, were included by chemical substitution. In all ternary systems, the theoretical approximants were found to be mechanically stable, but chemically unstable by an amount of energy larger than the margin of error. A tendency towards the stabilization of structures showing five- or 10-fold local environments was observed. This is consistent with the findings of decagonal approximants in the systems B-Ti-Ru and B-Mg-Ru.
Ab initio prediction of superdense tetragonal and monoclinic polymorphs of carbon
Li, Zhen -Zhen; Wang, Jian -Tao; Xu, Li -Fang; Chen, Changfeng
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_{1}c, P4_{3}2_{1}2, 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 in 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.
Ab initio prediction of superdense tetragonal and monoclinic polymorphs of carbon
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¯21c, P43212, P21/c, and C2 symmetry, respectively. These carbon polymorphs have large 32-atom unit cells in all-sp3 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 in the range of 5.19–5.41 eV,more » 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
Ab initio diffuse-interface model for lithiated electrode interface evolution
NASA Astrophysics Data System (ADS)
Stournara, Maria E.; Kumar, Ravi; Qi, Yue; Sheldon, Brian W.
2016-07-01
The study of chemical segregation at interfaces, and in particular the ability to predict the thickness of segregated layers via analytical expressions or computational modeling, is a fundamentally challenging topic in the design of novel heterostructured materials. This issue is particularly relevant for the phase-field (PF) methodology, which has become a prominent tool for describing phase transitions. These models rely on phenomenological parameters that pertain to the interfacial energy and thickness, quantities that cannot be experimentally measured. Instead of back-calculating these parameters from experimental data, here we combine a set of analytical expressions based on the Cahn-Hilliard approach with ab initio calculations to compute the gradient energy parameter κ and the thickness λ of the segregated Li layer at the LixSi-Cu interface. With this bottom-up approach we calculate the thickness λ of the Li diffuse interface to be on the order of a few nm, in agreement with prior experimental secondary ion mass spectrometry observations. Our analysis indicates that Li segregation is primarily driven by solution thermodynamics, while the strain contribution in this system is relatively small. This combined scheme provides an essential first step in the systematic evaluation of the thermodynamic parameters of the PF methodology, and we believe that it can serve as a framework for the development of quantitative interface models in the field of Li-ion batteries.
Liquid boron: x-ray measurements and ab initio molecular dynamics simulations.
Price, D. L.; Alatas, A.; Hennet, L.; Jakse, N.; Krishnan, S.; Pasturel, A.; Pozdnyakova, I.; Saboungi, M. L.; Said, A.; Scheunemann, R.; Schirmacher, W.; Sinn, H.; Centre de Recherche sure les Conditions Extremes et Materiaux; Lab. de Physique ed Modelisantion des Milieux Condensees; KLA-Tencor; Containerless Research, Inc.; Univ. Munchen; DESY
2009-01-01
We report results of a comprehensive study of liquid boron with x-ray measurements of the atomic structure and dynamics coupled with ab initio molecular dynamics simulations. There is no evidence of survival into the liquid of the icosahedral arrangements that characterize the crystal structures of boron but many atoms appear to adopt a geometry corresponding to the pentagonal pyramids of the crystalline phases. Despite similarities in the melting behavior of boron and silicon, there is little evidence of a significant structural shift with temperature that might suggest an eventual liquid-liquid phase transition. Relatively poor agreement with the observed damping of the sound excitations is obtained with the simple form of mode-coupling theory that has proved successful with other monatomic liquids, indicating that higher-order correlation functions arising from directional bonding and short-lived local structures are playing a crucial role. The large ratio of the high frequency to the isothermal sound velocity indicates a much stronger viscoelastic stiffening than in other monatomic liquids.
Ab initio prediction of superdense tetragonal and monoclinic polymorphs of carbon
NASA Astrophysics Data System (ADS)
Li, Zhen-Zhen; Wang, Jian-Tao; Xu, Li-Fang; Chen, Changfeng
2016-11-01
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 t 32 , t 32* , m 32 , and m 32* structures in P 4 ¯21c , P 43212 , P 21/c , and C 2 symmetry, respectively. These carbon polymorphs have large 32-atom unit cells in all-s p3 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 in 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. The present results establish different types of carbon phases and offer insights into their outstanding structural and electronic properties.
Ab initio investigation of high-entropy alloys of 3d elements
NASA Astrophysics Data System (ADS)
Tian, Fuyang; Varga, Lajos Karoly; Chen, Nanxian; Delczeg, Lorand; Vitos, Levente
2013-02-01
Single-phase high-entropy alloys are investigated using the exact muffin-tin orbitals (EMTO) method in combination with the coherent potential approximation (CPA). Choosing the paramagnetic face-centered-cubic NiCoFeCr alloy as an example, we compare the CPA results with those obtained using the supercell (SC) method. For the equilibrium Wigner-Seitz radius and elastic properties, the single-site mean-field approximation turns out to yield consistent results with the SC approach. Next, we employ the EMTO-CPA method to study the bulk properties of CuNiCoFeCrTix (x=0.0-0.5,1.0) and NiCoFeCrTi high-entropy alloys. A detailed comparison between the theoretical results and the available experimental data demonstrates that ab initio theory can properly describe the fundamental properties of this important class of engineering alloys. Theory predicts NiCoFeCr and CuNiCoFeCr to be more isotropic and less ductile than the Ti-containing single-phase alloys (CuNiCoFeCrTix with x≳0.4 and NiCoFeCrTi).
NASA Technical Reports Server (NTRS)
Allen, B. Danette; Alexandrov, Natalia
2016-01-01
Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that
López, E.; Lucas, J. M.; Andrés, J. de; Albertí, M.; Aguilar, A.; Bofill, J. M.; Bassi, D.
2014-10-28
Collisions between potassium ions and neutral i-C{sub 3}H{sub 7}Br and i-C{sub 3}H{sub 7}OH, all in their electronic ground state, have been studied in the 0.10–10.00 eV center of mass (CM) collision energy range, using the radiofrequency-guided ion beam technique. In K{sup +} + i-C{sub 3}H{sub 7}Br collisions KHBr{sup +} formation was observed and quantified, while the analogous KH{sub 2}O{sup +} formation in K{sup +} + i-C{sub 3}H{sub 7}OH was hardly detected. Moreover, formation of the ion-molecule adducts and their decomposition leading to C{sub 3}H{sub 7}{sup +} and either KBr or KOH, respectively, have been observed. For all these processes, absolute cross-sections were measured as a function of the CM collision energy. Ab initio structure calculations at the MP2 level have given information about the potential energy surfaces (PESs) involved. In these, different stationary points have been characterized using the reaction coordinate method, their connectivity being ensured by using the intrinsic-reaction-coordinate method. From the measured excitation function for KHBr{sup +} formation the corresponding thermal rate constant at 303 K has been calculated. The topology of the calculated PESs allows an interpretation of the main features of the reaction dynamics of both systems, and in particular evidence the important role played by the potential energy wells in controlling the reactivity for the different reaction channels.
AB Initio Study of the Structure and Spectroscopic Properties of Halogenated Thioperoxy Radicals
NASA Technical Reports Server (NTRS)
Munoz, Luis A.; Binning, R. C., Jr.; Weiner, Brad R.; Ishikawa, Yasuyuki
1997-01-01
Thioperoxy (XSO or XOS) radicals exist in a variety of chemical environments, and they have as a consequence drawn some interest. HSO, an important species in the chemistry of the troposphere, has been examined both experimentally. The halogenated (X = F, Cl or Br) peroxy species and isovalent thioperoxy species have been studied less, but they too are potentially interesting because oxidized sulfur species and halogen sources are present in the atmosphere. Learning the fate of XSO and XOS radicals is important to understanding the atmospheric oxidation chemistry of sulfur compounds. Of these, FSO and ClSO are particularly interesting because they have been directly detected spectroscopically. Recent studies in our laboratory on the photochemistry of thionyl halides (X2SO; where X = F or Cl) have suggested new ways to generate XSO species. The laser-induced photodissociation of thionyl fluoride, F2SO, at 193 nm and thionyl chloride, ClSO, at 248 nm is characterized by a radical mechanism, X2SO -> XSO + X. The structure of FSO has been characterized experimentally by Endo et cd. employing microwave spectroscopy. Using the unrestricted Hartree-Fock (UHF) self-consistent field (SCF) method, Sakai and Morokuma computed the electronic structure of the ground (sup 2)A" and the first excited (sup 2)A' states of FSO. Electron correlation was not taken into account in their study. In a laser photodissociation experiment, Huber et al. identified ClSO mass spectromctrically. ClSO has also been detected in low temperature matrices by EPR and in the gas phase by far IR laser magnetic resonance. Although the structure of FSO is known in detail, the only study, experimental or theoretical, of CISO has been an ab initio HFSCF study by Hinchliffe. Electron correlation corrections were also excluded from this study. In order to better understand the isomerization and dissociation dynamics of the radical species, we have performed ab initio correlated studies of the potential energy
Giansiracusa, Marcus J; Vonci, Michele; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette
2016-06-06
Optimization of literature synthetic procedures has afforded, in moderate yield, homogeneous and crystalline samples of the five analogues Na11[{RE(OH2)}3CO3(PW9O34)2] (1-RE; RE = Y, Tb, Dy, Ho, and Er). Phase-transfer methods have allowed isolation of the mixed salts (Et4N)9Na2[{RE(OH2)}3CO3(PW9O34)2] (2-RE; RE = Y and Er). The isostructural polyanions in these compounds are comprised of a triangular arrangement of trivalent rare-earth ions bridged by a μ3-carbonate ligand and sandwiched between two trilacunary Keggin {PW9O34} polyoxometalate ligands. Alternating-current (ac) magnetic susceptibility studies of 1-Dy, 1-Er, and 2-Er reveal the onset of frequency dependence for the out-of-phase susceptibility in the presence of an applied magnetic field at the lowest measured temperatures. Inelastic neutron scattering (INS) spectra of 1-Ho and 1-Er exhibit transitions between the lowest-lying crystal-field (CF) split states of the respective J = 8 and (15)/2 ground-state spin-orbit multiplets of the Ho(III) and Er(III) ions. Complementary ab initio calculations performed for these two analogues allow excellent reproduction of the experimental magnetic susceptibility and low-temperature magnetization data and are in reasonable agreement with the experimental INS data. The ab initio calculations reveal that the slight difference in coordination environments of the three Ln(III) ions in each complex gives rise to differences in the CF splitting that are not insignificant. This theoretical result is consistent with the observation of multiple relaxation processes by ac magnetic susceptibility and the broadness of the measured INS peaks. The ab initio calculations also indicate substantial mixing of the MJ contributions to the CF split energy levels of each Ln(III) ion. Calculations indicate that the CF ground states of the Ho(III) centers in 1-Ho are predominantly comprised of contributions from small MJ, while those of the Er(III) centers in 1-Er are predominantly
Melting of sodium under high pressure. An ab-initio study
González, D. J.; González, L. E.
2015-08-17
We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil
2015-05-15
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.
Ab initio calculations on the magnetic properties of transition metal complexes
Bodenstein, Tilmann; Fink, Karin
2015-12-31
We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes.
Point defect modeling in materials: Coupling ab initio and elasticity approaches
NASA Astrophysics Data System (ADS)
Varvenne, Céline; Bruneval, Fabien; Marinica, Mihai-Cosmin; Clouet, Emmanuel
2013-10-01
Modeling point defects at an atomic scale requires careful treatment of the long-range atomic relaxations. This elastic field can strongly affect point defect properties calculated in atomistic simulations because of the finite size of the system under study. This is an important restriction for ab initio methods which are limited to a few hundred atoms. We propose an original approach coupling ab initio calculations and linear elasticity theory to obtain the properties of an isolated point defect for reduced supercell sizes. The reliability and benefit of our approach are demonstrated for three problematic cases: the self-interstitial in zirconium, clusters of self-interstitials in iron, and the neutral vacancy in silicon.
Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions
Navratil, P; Ormand, W E; Forssen, C; Caurier, E
2004-11-30
There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
Zen, Andrea; Luo, Ye Mazzola, Guglielmo Sorella, Sandro; Guidoni, Leonardo
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Effects of Mg II and Ca II ionization on ab-initio solar chromosphere models
NASA Technical Reports Server (NTRS)
Rammacher, W.; Cuntz, M.
1991-01-01
Acoustically heated solar chromosphere models are computed considering radiation damping by (non-LTE) emission from H(-) and by Mg II and Ca II emission lines. The radiative transfer equations for the Mg II k and Ca II K emission lines are solved using the core-saturation method with complete redistribution. The Mg II k and Ca II K cooling rates are compared with the VAL model C. Several substantial improvements over the work of Ulmschneider et al. (1987) are included. It is found that the rapid temperature rises caused by the ionization of Mg II are not formed in the middle chromosphere, but occur at larger atmospheric heights. These models represent the temperature structure of the 'real' solar chromosphere much better. This result is a major precondition for the study of ab-initio models for solar flux tubes based on MHD wave propagation and also for ab-initio models for the solar transition layer.
B28: the smallest all-boron cage from an ab initio global search
NASA Astrophysics Data System (ADS)
Zhao, Jijun; Huang, Xiaoming; Shi, Ruili; Liu, Hongsheng; Su, Yan; King, R. Bruce
2015-09-01
Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures.Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures. Electronic supplementary information (ESI) available: Planar isomer structures of B28 and spatial distributions of front molecular orbitals. See DOI: 10.1039/c5nr04034e
Ab initio electron mobility and polar phonon scattering in GaAs
NASA Astrophysics Data System (ADS)
Zhou, Jin-Jian; Bernardi, Marco
2016-11-01
In polar semiconductors and oxides, the long-range nature of the electron-phonon (e -ph ) interaction is a bottleneck to compute charge transport from first principles. Here, we develop an efficient ab initio scheme to compute and converge the e -ph relaxation times (RTs) and electron mobility in polar materials. We apply our approach to GaAs, where by using the Boltzmann equation with state-dependent RTs, we compute mobilities in excellent agreement with experiment at 250 -500 K . The e -ph RTs and the phonon contributions to intravalley and intervalley e -ph scattering are also analyzed. Our work enables efficient ab initio computations of transport and carrier dynamics in polar materials.
NASA Astrophysics Data System (ADS)
Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.
2015-02-01
The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.
Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study
Rio, B. G. del; González, L. E.
2015-08-17
Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.
Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon
2013-01-01
The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%. PMID:23445785
Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.
2015-02-27
The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.
Properties of metals during the heating by intense laser irradiation using ab initio simulations
NASA Astrophysics Data System (ADS)
Holst, Bastian; Recoules, Vanina; Torrent, Marc; Mazevet, Stephane
2011-10-01
Ultrashort laser pulses irradiating a target heat the electrons to very high temperatures. In contrast, the ionic lattice is unaffected on the time scale of the laser pulse since the heat capacity of electrons is much smaller than that of the lattice. This non-equilibrium system can be described as a composition of two subsystems: one consisting of hot electrons and the other of an ionic lattice at low temperature. We studied the effect of this intense electronic excitations on the optical properties of gold using ab initio simulations. We additionally use ab initio linear response to compute the phonon spectrum and the electron-phonon coupling constant within Density Functional Theory for several electronic temperatures of few eV. LULI, Ecole Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau, France.
Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy
NASA Astrophysics Data System (ADS)
Chen, Xi H.; Zhang, John Z. H.
2004-06-01
In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.
Pospíšil, Miroslav; Kovář, Petr; Vácha, Robert; Svoboda, Michal
2012-01-01
Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreement with ab initio calculations obtained in the Gaussian03 program. Dihedral torsions of active groups of betulin were determined for both procedures, and related calculated structures were compared successfully. The selected force field was used for subsequent optimization of betulin in a water environment, and a conformational search was performed using quench molecular dynamics. The total energies of betulin and its interactions in water bulk were calculated, and the influence of water on betulin structure was investigated.
Ab initio studies of equations of state and chemical reactions of reactive structural materials
NASA Astrophysics Data System (ADS)
Zaharieva, Roussislava
subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated
Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.
Yang, Jianjun; Tse, John S
2011-11-17
The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.
Ab initio simulation of atomic-scale imaging in noncontact atomic force microscopy.
Caciuc, V; Hölscher, H
2009-07-01
In this paper, we summarize some results of our ab initio simulations aimed at investigating the mechanism of the NC-AFM image contrast on semiconductor and metallic surfaces. We start with an introduction into the basic ideas behind the ab initio simulation process of the NC-AFM experimental results. Our simulations reveal that the interaction of a clean silicon tip with a semiconductor surface like InAs(110) might lead to bond-formation and bond-breaking processes during the approach and retraction of the tip. This imaging mechanism is very similar to that observed on a metallic surface like Ag(110). Interestingly, a clean silicon tip can become contaminated with Ag surface atoms. On both types of surface we observe a significant energy dissipation which is caused by a hysteresis in the tip-sample force curves calculated on the approach and retraction path.
[Photoelectron Spectra of CCl2-: Ab Initio Calculation and Franck-Condon Analysis].
Wu, Jun
2015-12-01
Geometry optimization and harmonic vibrational frequency calculations were performed on the X¹A₁ state of CCl₂ and X²B₁ state of CCl₂⁻ at the B3LYP, MP2, CCSD levels. Franck-Condon analysis and spectral simulations were carried out on the photoelectron band of CCl₂⁻ including Duschinsky effects. The simulated spectra obtained are in excellent agreement with the experiment. Note that Duschinsky effect between bending vibration and the symmetric stretch modes should be considered in the CCl₂ (X¹A₁)-CCl₂⁻ (X²B₁) photodetachment process. By combining ab initio calculations with Franck-Condon analyses, the assignment of spectrum observed is firmly established to the X¹A₁-X²B₁ photodetachment process of the CCl₂⁻ radical, and the recommended geometric parameters of which in the literature are confirmed again base on ab initio theory and IFCA process.
Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation
NASA Astrophysics Data System (ADS)
Correa, J. D.; Cisternas, E.
2016-09-01
By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.
Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2014-04-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and lead (l-Pb). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2015-05-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2016-05-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.
Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna
2016-01-01
Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo.
Zen, Andrea; Luo, Ye; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Halasyamani, Shiv; Fennie, Craig
2016-11-03
We have focused on the synthesis, characterization, and ab initio theory on multi-functional mixed-metal fluorides. With funding from the DOE, we have successfully synthesized and characterized a variety of mixed metal fluoride materials.
An ab initio study of the polytypism in InP
Dacal, Luis C. O.; Cantarero, A.
2016-01-01
The existence of polytypism in semiconductor nanostructures gives rise to the appearance of stacking faults which many times can be treated as quantum wells. In some cases, despite of a careful growth, the polytypism can be hardly avoided. In this work, we perform an ab initio study of zincblende stacking faults in a wurtzite InP system, using the supercell approach and taking the limit of low density of narrow stacking faults regions. Our results confirm the type II band alignment between the phases, producing a reliable qualitative description of the band gap evolution along the growth axis. These results show an spacial asymmetry in the zincblende quantum wells, that is expected due to the fact that the wurtzite stacking sequence (ABAB) is part of the zincblende one (ABCABC), but with an unexpected asymmetry between the valence and the conduction bands. We also present results for the complex dielectric function, clearly showing the influence of the stacking on the homostructure values and surprisingly proving that the correspondent bulk results can be used to reproduce the polytypism even in the limit we considered. PMID:27666092
Slavíček, Petr; Fárník, Michal
2011-07-14
In this perspective article, we focus on the photochemistry of five-membered nitrogen containing heterocycles (pyrrole, imidazole and pyrazole) in clusters. These heterocycles represent paradigmatic structures for larger biologically active heterocyclic molecules and complexes. The dimers of the three molecules are also archetypes of different bonding patterns: N-H···π interaction, N-H···N hydrogen bond and double hydrogen bond. We briefly review available data on photochemistry of the title molecules in the gas phase, but primarily we focus on the new reaction channels opened upon the complexation with other heterocycles or solvent molecules. Based on ab initio calculations we discuss various possible reactions in the excited states of the clusters: (1) hydrogen dissociation, (2) hydrogen transfer between the heterocyclic units, (3) molecular ring distortion, and (4) coupled electron-proton transfer. The increasing photostability with complexity of the system can be inferred from experiments with photodissociation in these clusters. A unified view on photoinduced processes in five-membered N-heterocycles is provided. We show that even though different deactivation channels are energetically possible for the complexed heterocycles, in most cases the major result is a fast reconstruction of the ground state. The complexed or solvated heterocycles are thus inherently photostable although the stability can in principle be achieved via different reaction routes.
Ab initio Structure Determination of Mg10Ir19B16
Xu, Qiang; Klimczuk, T.; Gortenmulder, T.; Jansen, J.; McGuire, Michael A; Cava, R. J.; Zandbergen, H
2009-01-01
The ab initio structure determination of a novel unconventional noncentro-symmetric superconductor Mg{sub 10}Ir{sub 19}B{sub 16} (T{sub c} = 5 K) has been performed using a method that involves a combination of experimental data and calculations. Electron diffraction, X-ray powder diffraction, phase estimation routines, quantum mechanical calculations, high-resolution electron microscopy, and structural chemistry arguments are used. With the strengths of different methods used to eliminate the ambiguities encountered in others, the complete structure, including a very light B atom, has been determined with a high accuracy from impure polycrystalline powder samples, which suggests that the type of analysis described may be used to successfully address other similar intractable problems. The solved structure of Mg{sub 10}Ir{sub 19}B{sub 16} shows a complex nature that irregular coordination environments preclude a conversional description of compact packing of coordination polyhedra; however, it can be easier understood as ordered in an onion-skin-like series of nested polyhedra.
Ottonello, G; Zuccolini, M Vetuschi; Belmonte, D
2010-09-14
We present the results of a computational investigation with ab initio procedures of the structure-energy and vibrational properties of silica clusters in a dielectric continuum with dielectric constant ε=3.8, through density functional theory/B3LYP gas phase calculations coupled with a polarized continuum model approach [integral equation formalism applied to a polarized continuum (IEFPCM)] and those of the periodical structure D(6h) which leads to the α-cristobalite polymorph of silica when subjected to symmetry operations with the same functional within the linear combination of atomic orbitals (LCAO) approximation and in the framework of Bloch's theorem. Based on the computed energies and vibrational features, an aggregate of the D(6h) network and the monomer locally ordered in the short-medium range and both present in the glass in a mutual arrangement lacking of spatial continuity reproduces satisfactorily the experimentally observed low T heat capacity and the deviation from the Debye T(3) law. Above T(g), the experimental heat capacity of the liquid is perfectly reproduced summing to the internal modes the translational and rotational contributions to the bulk heat capacity and subtracting the (acoustic) terms arising from coherent motion (no longer existent).
Superhard F-carbon predicted by ab initio particle-swarm optimization methodology.
Tian, Fei; Dong, Xiao; Zhao, Zhisheng; He, Julong; Wang, Hui-Tian
2012-04-25
A simple (5 + 6 + 7)-sp(3) carbon (denoted as F-carbon) with eight atoms per unit cell predicted by a newly developed ab initio particle-swarm optimization methodology on crystal structure prediction is proposed. F-carbon can be seen as the reconstruction of AA-stacked or 3R-graphite, and is energetically more stable than 2H-graphite beyond 13.9 GPa. Band structure and hardness calculations indicate that F-carbon is a transparent superhard carbon with a gap of 4.55 eV at 15 GPa and a hardness of 93.9 GPa at zero pressure. Compared with the previously proposed Bct-, M- and W-carbons, the simulative x-ray diffraction pattern of F-carbon also well matches the superhard intermediate phase of the experimentally cold-compressed graphite. The possible transition route and energy barrier were observed using the variable cell nudged elastic band method. Our simulations show that the cold compression of graphite can produce some reversible metastable carbons (e.g. M- and F-carbons) with energy barriers close to diamond or lonsdaleite.
NASA Astrophysics Data System (ADS)
Mullaney, John C.; Zaleski, Daniel P.; Tew, David Peter; Walker, Nick; Legon, Anthony
2016-06-01
An isolated, gas-phase dimer of imidazole is generated through laser vaporisation of a solid rod containing a 1:1 mixture of imidazole and copper in the presence of an argon buffer gas undergoing supersonic expansion. The complex is characterised through broadband rotational spectroscopy and is shown to have a twisted, hydrogen-bonded geometry. Calculations at the CCSD(T)(F12*)/cc-pVDZ-F12 level of theory confirm this to be the lowest-energy conformer of the imidazole dimer. The distance between the respective centres of mass of the imidazole monomer subunits is determined to be 5.2751(1) Å, and the twist angle γ describing rotation of one monomer with respect to the other about a line connecting the centres of mass of the monomers is determined to be 87.9(4)o. Four out of six intermolecular parameters in the model geometry are precisely determined from the experimental rotational constants and are consistent with results calculated ab initio.
Ab initio Mapping of Interlayer Coupling in Transition Metal Dichalcogenides and Graphene
NASA Astrophysics Data System (ADS)
Fang, Shiang; Kaxiras, Efthimios
Two-dimensional layered materials cover a wide variety of physics phenomena, such as topological phases, superconductivity, magnetism and charge density waves. Owing to the layered geometry and the van der Waals interactions in between, stacks of these van der Waals layered materials provide a venue to create a heterostructure with various physics properties. The interaction between different physics properties is particular interesting to engineer the material with the desired properties. One of the crucial ingredient in understanding the heterostructure is the interlayer coupling in between. In the literature, such kind of coupling has been proposed in various empirical forms. However, a true ab initio coupling model is still lacking. For the first time, here we have derived such interlayer coupling model from the first principle calculations based on the Wannier transformation of graphene stacks. We further investigate the Fermi velocity renormalization, van Hove singularities and the moire pattern for electron localization. Such microscopic understanding of the interlayer coupling would shed light on orbital hybridization and transport in multilayer stacks. This work was supported by the STC Center for Integrated Quantum Materials, NSF Grant No. DMR-1231319, and by ARO MURI Award No. W911NF-14-0247.
An ab initio investigation of some hydrogen-bonded complexes of methanethiol
NASA Astrophysics Data System (ADS)
Bricknell, Bradley C.; Ford, Thomas A.
2010-07-01
The hydrogen-bonded complexes formed between methanethiol, as proton donor, and trimethyl amine, dimethyl ether, methyl fluoride, trimethyl phosphine, dimethyl sulphide and methyl chloride, as proton acceptors, have been studied by means of ab initio calculations at the second order level of Møller-Plesset perturbation theory and using the 6-311++G(d,p) basis set. The hydrogen bond energies were found to correlate with the gas phase basicities of the proton acceptors. The increases of the SH bond lengths, the shifts of the wavenumbers of the SH stretching modes and the increases of their infrared intensities were also found to be dependent on the interaction energies. The results for the CH 3SH·S(CH 3) 2 complex are anomalous, and this is attributed to deficiencies with the basis set used for sulphur. The data for the CH 3SH complex closely mirror the behaviour of the corresponding complexes of CH 3OH and (CH 3) 2NH, with the perturbations of the various properties varying consistently in the order CH 3OH > (CH 3) 2NH > CH 3SH.
Steady-state ab initio laser theory for N-level lasers.
Cerjan, Alexander; Chong, Yidong; Ge, Li; Stone, A Douglas
2012-01-02
We show that Steady-state Ab initio Laser Theory (SALT) can be applied to find the stationary multimode lasing properties of an N-level laser. This is achieved by mapping the N-level rate equations to an effective two-level model of the type solved by the SALT algorithm. This mapping yields excellent agreement with more computationally demanding N-level time domain solutions for the steady state.
NASA Astrophysics Data System (ADS)
Yurchenko, Sergei N.; Carvajal, Miguel; Thiel, Walter; Jensen, Per
2006-09-01
We report a six-dimensional CCSD(T)/aug-cc-pVTZ dipole moment surface for the electronic ground state of PH 3 computed ab initio on a large grid of 10 080 molecular geometries. Parameterized, analytical functions are fitted through the ab initio data, and the resulting dipole moment functions are used, together with a potential energy function determined by refining an existing ab initio surface in fittings to experimental wavenumber data, for simulating absorption spectra of the first three polyads of PH 3, i.e., ( ν2, ν4), ( ν1, ν3, 2 ν2, 2 ν4, ν2 + ν4), and ( ν1 + ν2, ν3 + ν2, ν1 + ν4, ν3 + ν4, 2 ν2 + ν4, ν2 + 2 ν4, 3 ν2, 3 ν4). The resulting theoretical transition moments show excellent agreement with experiment. A line-by-line comparison of the simulated intensities of the ν2/ ν4 band system with 955 experimental intensity values reported by Brown et al. [L.R. Brown, R.L. Sams, I. Kleiner, C. Cottaz, L. Sagui, J. Mol. Spectrosc. 215 (2002) 178-203] gives an average absolute percentage deviation of 8.7% (and a root-mean-square deviation of 0.94 cm -1 for the transition wavenumbers). This is very remarkable since the calculations rely entirely on ab initio dipole moment surfaces and do not involve any adjustment of these surfaces to reproduce the experimental intensities. Finally, we predict the line strengths for transitions between so-called cluster levels (near-degenerate levels formed at high rotational excitation) for J up to 60.
Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule
Párraga, H.; Arranz, F. J. Benito, R. M.; Borondo, F.
2013-11-21
An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system.
First fully ab initio potential energy surface of methane with a spectroscopic accuracy
NASA Astrophysics Data System (ADS)
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2016-09-01
Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.
Ab initio equation of state of hydrogen for inertial fusion applications
NASA Astrophysics Data System (ADS)
Benedict, Lorin X.; Morales, Miguel A.; Schwegler, Eric; Tamblyn, Isaac; Bonev, Stanimir A.; Correa, Alfredo A.; Clark, Daniel S.; Haan, Steven W.; LLNL Collaboration
2011-06-01
We describe ab initio electronic structure calculations (DFT molecular dynamics and quantum Monte Carlo) of the equation of state of hydrogen in a regime relevant for ICF applications. We find the computed EOS to be quite close to that of the most recent SESAME table (constructed by G. Kerley, 2004). A simple density-dependent correction brings the recent SESAME EOS into nearly perfect agreement with ours in the chosen region. Simulations of ICF applications with this corrected SESAME table are discussed.
Ab initio molecular dynamics study of liquid sodium and cesium up to critical point
Yuryev, Anatoly A.; Gelchinski, Boris R.
2015-08-17
Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.
Ab initio molecular dynamics study of liquid sodium and cesium up to critical point
NASA Astrophysics Data System (ADS)
Yuryev, Anatoly A.; Gelchinski, Boris R.
2015-08-01
Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.
Ab initio study of optical absorption spectra of semiconductors and conjugated polymers
Tiago, M.L.; Chang, Eric K.; Rohlfing, Michael; Louie, Steven G.
2000-04-30
The effects of electron-hole interaction on the optical properties of a variety of materials have been calculated using an ab initio method based on solving the Bethe-Salpeter equation. Results on selected semiconductors, insulators, and semiconducting polymers are presented. In the cases of alpha-quartz (SiO2) and poly-phenylene-vinylene, resonant excitonic states qualitatively alter the absorption spectra.
Monge-Palacios, M; Rangel, C; Espinosa-Garcia, J
2013-02-28
A full-dimensional analytical potential energy surface (PES) for the OH + NH3 → H2O + NH2 gas-phase reaction was developed based exclusively on high-level ab initio calculations. This reaction presents a very complicated shape with wells along the reaction path. Using a wide spectrum of properties of the reactive system (equilibrium geometries, vibrational frequencies, and relative energies of the stationary points, topology of the reaction path, and points on the reaction swath) as reference, the resulting analytical PES reproduces reasonably well the input ab initio information obtained at the coupled-cluster single double triple (CCSD(T)) = FULL/aug-cc-pVTZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical PES we perform an extensive kinetics study using variational transition-state theory with semiclassical transmission coefficients over a wide temperature range, 200-2000 K. The forward rate constants reproduce the experimental measurements, while the reverse ones are slightly underestimated. However, the detailed analysis of the experimental equilibrium constants (from which the reverse rate constants are obtained) permits us to conclude that the experimental reverse rate constants must be re-evaluated. Another severe test of the new surface is the analysis of the kinetic isotope effects (KIEs), which were not included in the fitting procedure. The KIEs reproduce the values obtained from ab initio calculations in the common temperature range, although unfortunately no experimental information is available for comparison.
NASA Astrophysics Data System (ADS)
Shen, Shiyu; Guirgis, Gamil A.; Gao, Jian; Durig, James R.
2001-12-01
The infrared spectra (3200-50 cm -1) of gaseous and solid and Raman spectra (3200-10 cm -1) of the liquid with qualitative depolarization ratios and solid 3-bromo-3,3-difluoropropene CH 2CHCBrF 2 have been recorded. Both the gauche and cis conformers have been identified in the fluid phase, but the gauche conformer is thermodynamically more stable than the cis rotamer and it is the only rotamer present in the spectrum of the annealed solid. Variable temperature (-105 to -150°C) studies of the infrared spectra of the sample dissolved in liquid krypton has been carried out. From these data, the enthalpy difference has been determined to be 281±28 cm -1 (3.36±0.33 kJ mol -1), with the gauche conformer as the more stable rotamer, which is in agreement with the ab initio predictions at all levels of calculations. It is estimated that there is only 11% of the cis conformer present at an ambient temperature. A complete vibration assignment is proposed for the gauche conformer which is based on infrared band contours, depolarization values, and group frequencies which is supported by normal coordinate calculations utilizing the force constants from ab initio MP2/6-31G (d) calculations. The conformational stabilities, barriers to internal rotation, and fundamental vibrational frequencies which have been determined experimentally are compared to those obtained from the ab initio calculations. The results are discussed and compared with the corresponding properties of some similar molecules.
Resolution of ab initio shapes determined from small-angle scattering.
Tuukkanen, Anne T; Kleywegt, Gerard J; Svergun, Dmitri I
2016-11-01
Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.
Sibambo, Sibongile R; Pillay, Viness; Choonara, Yahya E; Khan, Riaz A; Sweet, Joe L
2007-09-01
This study elucidated the in vitro physicomechanical transitions of a crosslinked polylactic-co-glycolic acid (PLGA) scaffold, utilizing quantum mechanics to compute the ab initio energy requirements of a salted-out and subsequently crosslinked PLGA scaffold interacting with simulated physiological fluid, phosphate buffered saline (PBS) (pH 7.4, 37 degrees C) at a molecular level. Twenty-six salted-out PLGA scaffolds were formulated using a four factor, two centerpoint quadratic Face-Centered Central Composite Design (FCCD). PLGA molecular mass, PLGA concentration, water volume and salting-out reaction time were the dependant formulation variables. Subsequent to PLGA solubilization in dimethyl formamide (DMF), protonated water was added to induce salting-out of PLGA into a scaffolds that were immersed in PBS, oscillated at 100 rpm, and analyzed at pre-determined time intervals for their physicomechanical and ab initio quantum energy transitions. Results indicated that the matrix resilience (MR) decreased with longer incubation periods (MR=35-45%) at day 30. Scaffolds salted-out using higher PLGA concentrations exhibited minimal changes in MR and the matrix ability to absorb energy was found to closely correlate with the scaffold residence time in PBS. Spartan-based ab initio quantum energy predictions elucidated the potential scaffold stability from a molecular viewpoint and its suitability for use in rate-modulated drug delivery.
Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.
Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim
2016-10-17
For CO and N2 on Mg(2+) sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies. With the achieved accuracy (estimated uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE+D2, B3LYP+D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of experimental values derived from fitting isotherms or from variable-temperature IR studies.
An ab initio calculation of the fundamental and overtone HCl stretching vibrations for the HCl dimer
NASA Astrophysics Data System (ADS)
Jensen, Per; Bunker, P. R.; Epa, V. C.; Karpfen, A.
1992-02-01
We have previously determined an analytical ab initio six-dimensional potential energy surface for the HCl dimer, and have used it to determine the minimum energy path for the trans-tunneling motion. In the present paper we refine this path by fitting to data. We calculate a further 178 ab initio points in order to determine the HCl stretching energies, and HCl stretching dipole moment functions, at eight positions along the minimum energy path. We use these ab initio results to compute the stretching wavenumbers and transition moments from the v1 = v2 = 0 state to all states of (HCl) 2 that have v1 + v2 ≤ 3, where v1 and v2 are the local mode quantum numbers for the HCl stretching vibrations. In doing this calculation we have assumed an adiabatic separation of the HCl stretching motion from the other vibrational motions in the dimer, and have used the semirigid bender Hamiltonian to average over the trans-tunneling motion. We obtain the fundamental "free-H" stretch v1 at 2877 cm -1 and the fundamental "bound-H" stretch v2 at 2861 cm -1; the experimental values are 2880 and 2854 cm -1, respectively.
Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation
NASA Astrophysics Data System (ADS)
Yang, Lina; Minnich, Austin J.
2017-03-01
Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.
NASA Astrophysics Data System (ADS)
Tachikawa, Masanori; Shiga, Motoyuki
2004-09-01
We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.
Resolution of ab initio shapes determined from small-angle scattering
Tuukkanen, Anne T.; Kleywegt, Gerard J.; Svergun, Dmitri I.
2016-01-01
Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models. PMID:27840683
Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation
Yang, Lina; Minnich, Austin J.
2017-01-01
Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials. PMID:28290484
Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.
Yang, Lina; Minnich, Austin J
2017-03-14
Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.
Dominant Modes in Light Nuclei - Ab Initio View of Emergent Symmetries
NASA Astrophysics Data System (ADS)
Draayer, J. P.; Dytrych, T.; Launey, K. D.; Dreyfuss, A. C.; Langr, D.
2015-01-01
An innovative symmetry-guided concept is discussed with a focus on emergent symmetry patterns in complex nuclei. In particular, the ab initio symmetry-adapted no-core shell model (SA-NCSM), which capitalizes on exact as well as partial symmetries that underpin the structure of nuclei, provides remarkable insight into how simple symmetry patterns emerge in the many-body nuclear dynamics from first principles. This ab initio view is complemented by a fully microscopic no-core symplectic shell-model framework (NCSpM), which, in turn, informs key features of the primary physics responsible for the emergent phenomena of large deformation and alpha-cluster substructures in studies of the challenging Hoyle state in Carbon-12 and enhanced collectivity in intermediate-mass nuclei. Furthermore, by recognizing that deformed configurations often dominate the low-energy regime, the SA-NCSM provides a strategy for determining the nature of bound states of nuclei in terms of a relatively small subspace of the symmetry-reorganized complete model space, which opens new domains of nuclei for ab initio investigations, namely, the intermediate-mass region, including isotopes of Ne, Mg, and Si.
Exploring the free energy surface using ab initio molecular dynamics
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-22
Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO_{2} and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO_{2} and the hcp to fcc phase transition in Ti.
Exploring the free energy surface using ab initio molecular dynamics
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-22
Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method inmore » collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.« less
Thermodynamically constrained correction to ab initio equations of state
French, Martin; Mattsson, Thomas R.
2014-07-07
We show how equations of state generated by density functional theory methods can be augmented to match experimental data without distorting the correct behavior in the high- and low-density limits. The technique is thermodynamically consistent and relies on knowledge of the density and bulk modulus at a reference state and an estimation of the critical density of the liquid phase. We apply the method to four materials representing different classes of solids: carbon, molybdenum, lithium, and lithium fluoride. It is demonstrated that the corrected equations of state for both the liquid and solid phases show a significantly reduced dependence of the exchange-correlation functional used.
Ab Initio Simulation Beryllium in Solid Molecular Hydrogen: Elastic Constant
NASA Astrophysics Data System (ADS)
Guerrero, Carlo L.; Perlado, Jose M.
2016-03-01
In systems of inertial confinement fusion targets Deuterium-Tritium are manufactured with a solid layer, it must have specific properties to increase the efficiency of ignition. Currently there have been some proposals to model the phases of hydrogen isotopes and hence their high pressure, but these works do not allow explaining some of the structures present at the solid phase change effect of increased pressure. By means of simulation with first principles methods and Quantum Molecular Dynamics, we compare the structural difference of solid molecular hydrogen pure and solid molecular hydrogen with beryllium, watching beryllium inclusion in solid hydrogen matrix, we obtain several differences in mechanical properties, in particular elastic constants. For C11 the difference between hydrogen and hydrogen with beryllium is 37.56%. This may produce a non-uniform initial compression and decreased efficiency of ignition.
Benjamin A. Frandsen; Brunelli, Michela; Page, Katharine; ...
2016-05-11
Here, we present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ~1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominatedmore » by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. Furthermore, the Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.« less
Ab-Initio Description and Prediction of Properties of Carbon-Based and Other Non-Metallic Materials
NASA Technical Reports Server (NTRS)
Bagayoko, D.; Zhao, G. L.; Hasan, S.
2001-01-01
We have resolved the long-standing problem consisting of 30%-50% theoretical underestimates of the band gaps of non-metallic materials. We describe the Bagayoko, Zhao, and Williams (BZW) method that rigorously circumvents the basis-set and variational effect presumed to be a cause of these underestimates. We present ab-initio, computational results that are in agreement with experiment for diamond (C), silicon (Si), silicon carbides (3C-SiC and 4H-SiC), and other semiconductors (GaN, BaTiO3, AlN, ZnSe, ZnO). We illustrate the predictive capability of the BZW method in the case of the newly discovered cubic phase of silicon nitride (c-Si3N4) and of selected carbon nanotabes [(10,0), and (8,4)]. Our conclusion underscores the inescapable need for the BZW method in ab-initio calculations that employ a basis set in a variational approach. Current nanoscale trends amplify this need. We estimate that the potential impact of applications of the BZW method in advancing our understanding of nonmetallic materials, in informing experiment, and particularly in guiding device design and fabrication is simply priceless.
Rodríguez-Santiago, Luis; Alí-Torres, Jorge; Vidossich, Pietro; Sodupe, Mariona
2015-05-28
Several lines of evidence supporting the role of metal ions in amyloid aggregation, one of the hallmarks of Alzheimer's disease (AD), have turned metal ion chelation into a promising therapeutic treatment. The design of efficient chelating ligands requires proper knowledge of the electronic and molecular structure of the complexes formed, including their hydration properties. Among various potential chelators, clioquinol (5-chloro-7-iodo-8-hydroxyquinoline, CQH) has been evaluated with relative success in in vitro experiments and even in phase 2 clinical trials. Clioquinol interacts with Zn(ii) to lead to a binary metal/ligand 1 : 2 stoichiometric complex in which the phenolic group of CQH is deprotonated, resulting in Zn(CQ)2 neutral complexes, to which additional water molecules may coordinate. In the present work, the coordinative properties of clioquinol in aqueous solution have been analyzed by means of static, minimal cluster based DFT calculations and explicit solvent ab initio molecular dynamics simulations. Results from static calculations accounting for solvent effects by means of polarized continuum models suggest that the preferred metal coordination environment is tetrahedral Zn(CQ)2, whereas ab initio molecular dynamics simulations point to quasi degenerate penta Zn(CQ)2(H2O) and hexa Zn(CQ)2(H2O)2 coordinated complexes. The possible reasons for these discrepant results are discussed.
Thermodynamics of mixing in MgSiO 3-Al 2O 3 perovskite and ilmenite from ab initio calculations
NASA Astrophysics Data System (ADS)
Jung, D. Y.; Vinograd, V. L.; Fabrichnaya, O. B.; Oganov, A. R.; Schmidt, M. W.; Winkler, B.
2010-07-01
The thermodynamic mixing functions of MgSiO 3-Al 2O 3 solid solutions in perovskite and ilmenite structures were modeled based on the results of ab initio calculations applied to a set of supercell structures containing 64 and 48 exchangeable sites, respectively. The sampled structures were constructed from the supercells of the end-members MgSiO 3 perovskite and Al 2O 3 corundum by inserting double AlAl and MgSi defects, respectively, at all possible distances. From these calculations the pairwise effective interactions were derived and used to calculate enthalpy differences between successive configurations produced in Monte Carlo simulation runs. The temperature dependent enthalpies of mixing of the solid solutions were evaluated as averages over the Monte Carlo runs while the free energies of mixing were calculated with the method of thermodynamic integration. The phase equilibria of perovskite, ilmenite and garnet in the Mg-Si-Al-O system were calculated using the computed models of mixing and the standard thermodynamic properties of the end-members from the data base of Fabrichnaya (1999). The obtained activity-composition models are in good agreement with available experimental constraints, thereby showing that the thermodynamic effects of mixing in silicate solid solutions with coupled substitutions can be reliably predicted based on ab initio calculated total energies of a small set of supercell structures.
NASA Astrophysics Data System (ADS)
Frandsen, Benjamin A.; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J.; Staunton, Julie B.; Billinge, Simon J. L.
2016-05-01
We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ˜1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.
NASA Astrophysics Data System (ADS)
Masrour, R.; Jabar, A.; Hlil, E. K.; Hamedoun, M.; Benyoussef, A.; Hourmatallah, A.; Rezzouk, A.; Bouslykhane, K.; Benzakour, N.
2017-04-01
Self-consistent ab initio calculations, based on Density Functional Theory (DFT) approach and using Full potential Linear Augmented Plane Wave (FLAPW) method, are performed to investigate both electronic and magnetic properties of the Mn2NiAl. Magnetic moment considered to lie along (001) axes are computed. Obtained data from ab initio calculations are used as input for Monte Carlo simulations to compute other magnetic parameters. Also, the magnetic properties of Mn2NiAl are studied using the Monte Carlo simulations. The variation of magnetization and magnetic susceptibility with the reduced temperature of Mn2NiAl are investigated. The transition temperature of this system is deduced for different values exchange interaction and crystal field. The thermal total magnetization has been obtained, and the magnetic hysteresis cycle is established. The total magnetic moment is superior to those obtained by the other method and is mainly determined by the antiparallel aligned MnI, MnII and Ni spin moments. The superparamagnetic phase is found at the neighborhood of transition temperature.
Matrix-isolation study and ab initio calculations of the structure and spectra of hydroxyacetone.
Sharma, Archna; Reva, Igor; Fausto, Rui
2008-07-03
The structure of hydroxyacetone (HA) isolated in an argon matrix (at 12 K) and in a neat solid phase (at 12-175 K) was characterized by using infrared (IR) spectroscopy. The interpretation of the experimental results was supported by high-level quantum chemical calculations, undertaken by using both ab initio (MP2) and density functional theory methods. A potential-energy surface scan, carried out at the MP2/6-311++G(d,p) level of theory, predicted four nonequivalent minima, Cc, Tt, Tg, and Ct, all of them doubly degenerate by symmetry. The energy barriers for conversion between most of the symmetrically related structures and also between some of the nonequivalent minima (e.g., Tg --> Tt and Ct --> Tt) are very small and stay below the zero-point vibrational level associated with the isomerization coordinate in the higher-energy form in each pair. Therefore, only Cc and Tt conformers have physical significance, with populations of 99 and 1%, respectively, in gas phase at room temperature. For the matrix-isolated compound, only the most stable Cc conformer was observed. On the other hand, the polarizable continuum model calculations indicated that in water solution, the population of Tt and Ct conformers might be high enough (ca. 6 and 11%, respectively) to enable their experimental detection, thus supporting the conclusions of a previous IR spectroscopy study [ Spectrochim. Acta A 2005, 61, 477] in which the presence of more than one HA conformer in aqueous solution was postulated. The signatures of these minor conformers, however, do not appear in the spectra of the neat HA crystal, and the crystal structure was rationalized in terms of centrosymmetric hydrogen-bonded dimers consisting of two Cc-like units. Finally, we calculated (1)H, (13)C, and (17)O NMR chemical shifts at different levels of theory and found them to agree with available experimental data.
Ab initio calculations of the photoionization of diatomic molecules
NASA Astrophysics Data System (ADS)
Lefebvre-Brion, Helene; Raşeev, Georges
2003-01-01
A review is presented of the calculation of photoionization spectra, particularly in the spectral range where electron autoionization of diatomic molecules takes place. In addition to some interesting results obtained over years that compare favourably with experiment, the emphasis here is put on the relation between the methods developed for the calculation of observables associated with the continuum energy spectrum of the electrons and the Alchemy system of programs. This system of programs serves as a basis for initial and intermediate calculations. The examples presented show that diatomic molecules not only in gas phase but also oriented in space or physisorbed at surfaces may be studied readily.
Unified ab initio treatment of attosecond photoionization and Compton scattering
NASA Astrophysics Data System (ADS)
Yudin, G. L.; Bondar, D. I.; Patchkovskii, S.; Corkum, P. B.; Bandrauk, A. D.
2009-10-01
We present a new theoretical approach to attosecond laser-assisted photo- and Compton ionization. Attosecond x-ray absorption and scattering are described by \\hat{\\mathscr{S}}^{(1,2)} -matrices, which are coherent superpositions of 'monochromatic' \\skew{3}\\hat{S}^{(1,2)} -matrices in a laser-modified Furry representation. Besides refining the existing theory of the soft x-ray photoelectron attosecond streak camera and spectral phase interferometry (ASC and ASPI), we formulate a theory of hard x-ray photoelectron and Compton ASC and ASPI. The resulting scheme has a simple structure and leads to closed-form expressions for ionization amplitudes. We investigate Compton electron interference in the separable Coulomb-Volkov continuum with both Coulomb and laser fields treated non-perturbatively. We find that at laser-field intensities below 1013 Wcm-2 normalized Compton lines almost coincide with the lines obtained in the laser-free regime. At higher intensities, attosecond interferences survive integration over electron momenta, and feature prominently in the Compton lines themselves. We define a regime where the electron ground-state density can be measured with controllable accuracy in an attosecond time interval. The new theory provides a firm basis for extracting photo- and Compton electron phases and atomic and molecular wavefunctions from experimental data.
Putungan, Darwin Barayang; Lin, Shi-Hsin; Kuo, Jer-Lai
2016-07-27
We systematically investigated the potential of single-layer VS2 polytypes as Na-battery anode materials via density functional theory calculations. We found that sodiation tends to inhibit the 1H-to-1T structural phase transition, in contrast to lithiation-induced transition on monolayer MoS2. Thus, VS2 can have better structural stability in the cycles of charging and discharging. Diffussion of Na atom was found to be very fast on both polytypes, with very small diffusion barriers of 0.085 eV (1H) and 0.088 eV (1T). Ab initio random structure searching was performed in order to explore stable configurations of Na on VS2. Our search found that both the V top and the hexagonal center sites are preferred adsorption sites for Na, with the 1H phase showing a relatively stronger binding. Notably, our random structures search revealed that Na clusters can form as a stacked second layer at full Na concentration, which is not reported in earlier works wherein uniform, single-layer Na adsorption phases were assumed. With reasonably high specific energy capacity (232.91 and 116.45 mAh/g for 1H and 1T phases, respectively) and open-circuit voltage (1.30 and 1.42 V for 1H and 1T phases, respectively), VS2 is a promising alternative material for Na-ion battery anodes with great structural sturdiness. Finally, we have shown the capability of the ab initio random structure searching in the assessment of potential materials for energy storage applications.
CL-20 photodecomposition: ab initio foundations for identification of products.
Kholod, Yana; Kosenkov, Dmytro; Okovytyy, Sergiy; Gorb, Leonid; Qasim, Mohammad; Leszczynski, Jerzy
2008-11-01
1,5-Dihydrodiimidazo[4,5-b:4'5'e]pyrazine, 1H-imidazo[4,5-b]pyrazine, and 1H-imidazole were considered as possible products of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) photodecomposition. Since we took as a reference the product obtained after CL-20 irradiation in methanol solution, the nature of intermolecular bonds between heterocycles under study and methanol molecules was analyzed in detail. Existing hydrogen bonds were found to be quite strong, so dependence of calculations results on an influence of solvent was taken into account using both the polarizable continuum model (PCM) and the supermolecular approach. Electronic spectra of 1,5-dihydrodiimidazo[4,5-b:4'5'e]pyrazine, 1H-imidazo[4,5-b]pyrazine and 1H-imidazole were simulated using time dependent density functional theory (TD-DFT) and single-excitation configuration interaction (CIS) method. We observed that TD-DFT excitation energies are lower if compared to corresponding values obtained by the CIS method. Results of calculations with PCM and the supermolecular approach are very close. It was found that differences between calculated gas phase excitation energies and those values obtained by applying solvent models increases when the number of conjugated bonds in a molecule increases. Oscillator strengths of UV bands of the considered molecules are higher in the gas phase than in modeled methanol solutions. We found that the predicted spectrum of 1H-imidazole is in close agreement with the experimental UV spectrum of the CL-20 photolysis product.
NASA Astrophysics Data System (ADS)
Morales, Miguel A.; Benedict, Lorin X.; Clark, Daniel S.; Schwegler, Eric; Tamblyn, Isaac; Bonev, Stanimir A.; Correa, Alfredo A.; Haan, Steven W.
2012-03-01
We describe ab initio electronic structure calculations (density functional theory molecular dynamics and coupled electron-ion quantum Monte Carlo) of the equation of state (EOS) of hydrogen in a pressure-temperature regime relevant for simulating the initial phase of an inertial confinement fusion capsule implosion. We find the computed EOS to be quite close to that of the most recent SESAME table (constructed by G. Kerley, 2003). A simple density-dependent but temperature-independent correction brings the 2003-Kerley EOS into excellent agreement with ours in the chosen region of the hydrogen phase diagram. Simulations of fusion ignition experiments on the National Ignition Facility (NIF) with this modified 2003-Kerley table are shown to produce results nearly indistinguishable from those of the 2003-Kerley EOS, which was used to design the capsule. In this sense, we do not expect that further improvements to the hydrogen EOS in this particular regime will impact the capsule design.
NASA Astrophysics Data System (ADS)
Lahnsteiner, Jonathan; Kresse, Georg; Kumar, Abhinav; Sarma, D. D.; Franchini, Cesare; Bokdam, Menno
2016-12-01
The high efficiency of lead organo-metal-halide perovskite solar cells has raised many questions about the role of the methylammonium (MA) molecules in the Pb-I framework. Experiments indicate that the MA molecules are able to "freely" spin around at room temperature even though they carry an intrinsic dipole moment. We have performed large supercell (2592 atoms) finite-temperature ab initio molecular dynamics calculations to study the correlation between the molecules in the framework. An underlying long-range antiferroelectric ordering of the molecular dipoles is observed. The dynamical correlation between neighboring molecules shows a maximum around room temperature in the mid-temperature phase. In this phase, the rotations are slow enough to (partially) couple to neighbors via the Pb-I cage. This results in a collective motion of neighboring molecules in which the cage acts as the mediator. At lower and higher temperatures, the motions are less correlated.
Towards ab initio extremely metal-poor stars
NASA Astrophysics Data System (ADS)
Ritter, Jeremy S.; Safranek-Shrader, Chalence; Milosavljević, Miloš; Bromm, Volker
2016-12-01
Extremely metal-poor stars have been the focus of much recent attention owing to the expectation that their chemical abundances can shed light on the metal and dust yields of the earliest supernovae. We present our most realistic simulation to date of the astrophysical pathway to the first metal-enriched stars. We simulate the radiative and supernova hydrodynamic feedback of a 60 M⊙ Population III star starting from cosmological initial conditions realizing Gaussian density fluctuations. We follow the gravitational hydrodynamics of the supernova remnant at high spatial resolution through its freely expanding, adiabatic, and radiative phases, until gas, now metal-enriched, has resumed runaway gravitational collapse. Our findings are surprising: while the Population III progenitor exploded with a low energy of 1051 erg and injected an ample metal mass of 6 M⊙, the first cloud to collapse after the supernova explosion is a dense surviving primordial cloud on which the supernova blast wave deposited metals only superficially, in a thin, unresolved layer. The first metal-enriched stars can form at a very low metallicity, of only 2-5 × 10-4 Z⊙, and can inherit the parent cloud's highly elliptical, radially extended orbit in the dark matter gravitational potential.
Ab initio structure determination of n-diamond
Li, Da; Tian, Fubo; Chu, Binhua; Duan, Defang; Sha, Xiaojing; Lv, Yunzhou; Zhang, Huadi; Lu, Nan; Liu, Bingbing; Cui, Tian
2015-01-01
A systematic computational study on the crystal structure of n-diamond has been performed using first-principle methods. A novel carbon allotrope with hexagonal symmetry R32 space group has been predicted. We name it as HR-carbon. HR-carbon composed of lonsdaleite layers and unique C3 isosceles triangle rings, is stable over graphite phase above 14.2 GPa. The simulated x-ray diffraction pattern, Raman, and energy-loss near-edge spectrum can match the experimental results very well, indicating that HR-carbon is a likely candidate structure for n-diamond. HR-carbon has an incompressible atomic arrangement because of unique C3 isosceles triangle rings. The hardness and bulk modulus of HR-carbon are calculated to be 80 GPa and 427 GPa, respectively, which are comparable to those of diamond. C3 isosceles triangle rings are very important for the stability and hardness of HR-carbon. PMID:26299905
Ab initio structure determination of n-diamond.
Li, Da; Tian, Fubo; Chu, Binhua; Duan, Defang; Sha, Xiaojing; Lv, Yunzhou; Zhang, Huadi; Lu, Nan; Liu, Bingbing; Cui, Tian
2015-08-24
A systematic computational study on the crystal structure of n-diamond has been performed using first-principle methods. A novel carbon allotrope with hexagonal symmetry R32 space group has been predicted. We name it as HR-carbon. HR-carbon composed of lonsdaleite layers and unique C3 isosceles triangle rings, is stable over graphite phase above 14.2 GPa. The simulated x-ray diffraction pattern, Raman, and energy-loss near-edge spectrum can match the experimental results very well, indicating that HR-carbon is a likely candidate structure for n-diamond. HR-carbon has an incompressible atomic arrangement because of unique C3 isosceles triangle rings. The hardness and bulk modulus of HR-carbon are calculated to be 80 GPa and 427 GPa, respectively, which are comparable to those of diamond. C3 isosceles triangle rings are very important for the stability and hardness of HR-carbon.
The ab initio simulation of the Earth's core.
Alfè, D; Gillan, M J; Vocadlo, L; Brodholt, J; Price, G D
2002-06-15
The Earth has a liquid outer and solid inner core. It is predominantly composed of Fe, alloyed with small amounts of light elements, such as S, O and Si. The detailed chemical and thermal structure of the core is poorly constrained, and it is difficult to perform experiments to establish the properties of core-forming phases at the pressures (ca. 300 GPa) and temperatures (ca. 5000-6000 K) to be found in the core. Here we present some major advances that have been made in using quantum mechanical methods to simulate the high-P/T properties of Fe alloys, which have been made possible by recent developments in high-performance computing. Specifically, we outline how we have calculated the Gibbs free energies of the crystalline and liquid forms of Fe alloys, and so conclude that the inner core of the Earth is composed of hexagonal close packed Fe containing ca. 8.5% S (or Si) and 0.2% O in equilibrium at 5600 K at the boundary between the inner and outer cores with a liquid Fe containing ca. 10% S (or Si) and 8% O.
Ab Initio Thermal Conductivity Model of the Earth's Lower Mantle
NASA Astrophysics Data System (ADS)
Tsuchiya, T.; Dekura, H.; Tsuchiya, J.
2012-12-01
Lattice thermal conductivity of minerals under pressure and temperature is a key property to understanding dynamics and evolution of the Earth's interior. However, determination of the thermal conductivity still remains technically challenging both experimentally and theoretically particularly at the deep mantle and core conditions. Here we show a new technique to calculate lattice thermal conductivity of minerals non-empirically. Since the anharmonic coupling strength is calculated efficiently based on the density functional perturbation theory, our technique can be applicable to minerals even with complex structure and chemistry such as perovskite and post-perovskite MgSiO3. Calculated lattice thermal conductivity of perovskite agrees satisfactorily with an experimental value at ambient condition, and those of perovskite and post-perovskite are found quite different at deep mantle pressures and temperatures. This indicates that the D" discontinuity is not only the phase transition boundary but also the boundary of conductivity. Using the obtained thermal conductivities, we determine the effective conductivity of the Earth's lower mantle and estimate the energy flow carried across the core-mantle boundary (CMB). Our results demonstrate that the CMB heat flux could change significantly from place to place by reflecting a possible temperature heterogeneity located atop the core. Research supported by KAKENHI and Grant from Senior Research Fellow Center, Ehime University.
Treatment of dilute clusters of methanol and water by ab initio quantum mechanical calculations.
Ruckenstein, Eli; Shulgin, Ivan L; Tilson, Jeffrey L
2005-02-10
Large molecular clusters can be considered as intermediate states between gas and condensed phases, and information about them can help us understand condensed phases. In this paper, ab initio quantum mechanical methods have been used to examine clusters formed of methanol and water molecules. The main goal was to obtain information about the intermolecular interactions and the structure of methanol/water clusters at the molecular level. The large clusters (CH(4)O...(H(2)O)(12) and H(2)O...(CH(4)O)(10)) containing one molecule of one component (methanol or water) and many (12, 10) molecules of the other component were considered. Møller-Plesset perturbation theory (MP2) was used in the calculations. Several representative cluster geometries were optimized, and nearest-neighbor interaction energies were calculated for the geometries obtained in the first step. The results of the calculations were compared to the available experimental information regarding the liquid methanol/water mixtures and to the molecular dynamics and Monte Carlo simulations, and good agreement was found. For the CH(4)O...(H(2)O)(12) cluster, it was shown that the molecules of water can be subdivided into two classes: (i) H bonded to the central methanol molecule and (ii) not H bonded to the central methanol molecule. As expected, these two classes exhibited striking energy differences. Although they are located almost the same distance from the carbon atom of the central methanol molecule, they possess very different intermolecular interaction energies with the central molecule. The H bonding constitutes a dominant factor in the hydration of methanol in dilute aqueous solutions. For the H(2)O...(CH(4)O)(10) cluster, it was shown that the central molecule of water has almost three H bonds with the methanol molecules; this result differs from those in the literature that concluded that the average number of H bonds between a central water molecule and methanol molecules in dilute solutions of
Quarti, Claudio; Mosconi, Edoardo; De Angelis, Filippo
2015-04-14
The last two years have seen the unprecedentedly rapid emergence of a new class of solar cells, based on hybrid organic-inorganic halide perovskites. The success of this class of materials is due to their outstanding photoelectrochemical properties coupled to their low cost, mainly solution-based, fabrication techniques. Solution processed materials are however often characterized by an inherent flexible structure, which is hardly mapped into a single local minimum energy structure. In this perspective, we report on the interplay between structural and electronic properties of hybrid lead iodide perovskites investigated using ab initio molecular dynamics (AIMD) simulations, which allow the dynamical simulation of disordered systems at finite temperature. We compare the prototypical MAPbI3 (MA = methylammonium) perovskite in its cubic and tetragonal structure with the trigonal phase of FAPbI3 (FA = formamidinium), investigating different starting arrangements of the organic cations. Despite the relatively short time scale amenable to AIMD, typically a few tens of ps, this analysis demonstrates the sizable structural flexibility of this class of materials, showing that the instantaneous structure could significantly differ from the time and thermal averaged structure. We also highlight the importance of the organic-inorganic interactions in determining the fluxional properties of this class of materials. A peculiar spatial localization of the valence and conduction band edges is also found, with a dynamics in the range of 0.1 ps, which is associated with the positional dynamics of the organic cations within the cubo-octahedral perovskite cage. This asymmetry in the spatial localization of the band edges is expected to ease exciton dissociation and assist the initial stages of charge separation, possibly constituting one of the key factors for the impressive photovoltaic performances of hybrid lead-iodide perovskites.
Ab initio calculation of Ti NMR shieldings for titanium oxides and halides
NASA Astrophysics Data System (ADS)
Tossell, J. A.
Titanium NMR shielding constants have been calculated using ab initio coupled Hartree-Fock perturbation theory and polarized double-zeta basis sets for TiF 4, TiF 62-, TiCI 4, Ti(OH) 4, Ti(OH 2) 64+, Ti(OH) 4O, and Ti(OH) 3O -. In all cases the calculations were performed at Hartree-Fuck energy-optimized geometries. For Ti(OH) 4 a S4-symmetry geometry with nonlinear ∠ TiOH was employed. Relative shieldings are in reasonable agreement with experiment for TiF 62-, TiCI 4, and Ti(OR) 4, where R = H or alkyl. Ti(OH 2) 64+ is predicted to be more highly shielded than Ti(OH) 4 by about 340 ppm. The five-coordinate complex Ti(OH) 4O, whose calculated structure matches well that measured by extended X-ray absorption fine structure in K 2O · TiO 2 · SiO 2 glass, is actually deshielded compared to Ti(OH) 4 by about 40 ppm. X-ray absorption-near-edge spectral energies have also been calculated for TiF 4, TiCI 4, Ti(OH) 4, and Ti(OH) 4O using an equivalent ionic core virtual-orbital method and the observed reduction in term energy for the five-coordinate species compared to Ti(OH) 4 has been reproduced. Replacement of the H atoms in Ti(OH) 4 by point charges has only a slight effect upon σTi, suggesting a possible means of incorporating second-neighbor effects in NMR calculations for condensed phases.
Ab initio study of carbon-chlorine bond cleavage in carbon tetrachloride.
Zhang, Nianliu; Blowers, Paul; Farrell, James
2005-01-15
Chlorinated solvents in groundwater are known to undergo reductive dechlorination reactions with Fe(ll)-containing minerals and with corroding metals in permeable-barrier treatment systems. This research investigated the effect of the reaction energy on the reaction pathway for C-Cl bond cleavage in carbon tetrachloride (CCl4). Hartree-Fock, density functional theory, and modified complete basis set ab initio methods were used to study adiabatic electron transfer to aqueous-phase CCl4. The potential energies associated with fragmentation of the carbon tetrachloride anion radical (CCl4-) into a trichloromethyl radical (CCl3) and a chloride ion (Cl-) were explored as a function of the carbon-chlorine bond distance during cleavage. The effect of aqueous solvation was investigated using a continuum conductor-like screening model. Solvation significantly lowered the energies of the reaction products, suggesting that dissociative electron transfer was enhanced by solvation. The potential energy curves in an aqueous medium indicate that reductive cleavage undergoes a change from an inner-sphere to an outer-sphere mechanism as the overall energy change for the reaction is increased. The activation energy for the reaction was found to be a linear function of the overall energy change, and the Marcus-Hush model was used to relate experimentally measured activation energies for CCl4 reduction to overall reaction energies. Experimentally measured activation energies for CCl4 reduction by corroding iron correspond to reaction energies that are insufficiently exergonic for promoting the outer-sphere mechanism. This suggests that the different reaction pathways that have been observed for CCl4 reduction by corroding iron arise from different catalytic interactions with the surface, and not from differences in energy of the transferred electrons.
EL2-like defects in InP nanowires: An ab initio total energy investigation
NASA Astrophysics Data System (ADS)
Miwa, R. H.; Schmidt, T. M.; Fazzio, A.
2007-04-01
We have performed an ab initio total energy investigation, within the density-functional theory, of antisite defects in InP nanowires (InP NWs) grown along the [111] direction. Our total energy results indicate that (i) P antisites (PIn) are the most likely antisite defect compared with In antisites (InP) and (ii) the formation energies of P and In antisites do not depend on the NW diameter. In particular, in thin InP NWs, with diameters of ˜13Å , the PIn antisite exhibits a trigonal symmetry, lying at 0.15Å from the Td site, followed by a metastable configuration with PIn in an interstitial position ( 1.15Å from the Td site). We find a PIn-P dissociation energy of 0.33eV , and there is no EL2-like center for such a thin InP NW. However, EL2-like defects occur by increasing the NW diameter. For diameters of ˜18Å , the PIn-P dissociation energy increases to 0.53eV , which is 0.34eV lower compared with the PIn-P dissociation energy for the InP bulk phase, 0.87eV . We mapped the atomic displacements and calculated the relaxation energy, Franck-Condon shift, upon single excitation of PIn induced states in InP NW. The formation (or not) of EL2-like defects, PIn dissociation energy barrier, and the Franck-Condon energy shift can be tuned by the NW diameter.
Ab-initio simulations of H2O interaction with b-SiC surfaces.
NASA Astrophysics Data System (ADS)
Cicero, Giancarlo
2006-03-01
We report on the interaction of gas phase water molecules with polar and non polar stoichiometric surfaces of cubic silicon carbide, a leading candidate semiconductor for bio-compatible devices. Finite temperature ab-initio molecular dynamics shows that the specific geometric arrangement of atoms on the outermost surface layer is responsible for water orientation and coordination and thus plays a major role in determining the surface reactivity. In particular, irrespective of coverage, water spontaneously dissociates on both polar[1] Si-terminated (001) and non-polar[2] (110) surfaces, while the C-terminated1 (001) surface is non-reactive and hydrophobic. Based on our results, we propose that STM images and photoemission experiments may detect specific changes induced by water on both the structural and electronic properties of SiC surfaces. We completed our investigation by studying a realistic solid/liquid interface[3] for the case of Si-SiC(001), after full hydroxylation takes place. We observed the formation of a thin ( 3 /AA) interfacial layer, which presents a higher density than bulk water. The liquid does not uniformly ‘wet’ the surface, rather molecules preferably bind along directions parallel to the Si dimer rows. Our calculations also predict that at 1 nm, the structural and electronic properties of liquid water are weakly affected by one-dimensional confinement between hydrophilic, solid substrates. [1] G. Cicero, A. Catellani and G. Galli Phys Rev. Lett. 93 (2004), 0161102; G. Cicero, A. Catellani and G. Galli J. Phys. Chem. B 108 (2004), 16518. [2] A. Catellani, G. Cicero and G. Galli J. Chem. Phys., in press. [3] G. Cicero, J. Grossman, A. Catellani and G. Galli J. Am. Chem. Soc. 127 (2005), 6830.
Ab Initio Calculations of the Interaction between CO _{2} and the Acetate Ion
Steckel, Janice A.
2012-11-29
A series of ab initio calculations designed to investigate the interaction of CO{sub 2} with acetate are presented. The lowest energy structure, AC–CO{sub 2}-η{sup 2}, is predicted by CCSD(T)/aVTZ to be bound by -10.6 kcal/mol. Six of the bound complexes have binding energies on the order of -8 kcal/mol, but analysis shows that the η{sup 1}-CT complex is fundamentally different from the others. The η{sup 1}-CT complex is characterized by geometric distortion, large polarization and induction effects and charge transfer whereas the other five complexes have little geometric distortion and negligible charge transfer. The amount of charge that is transferred from the anion to the CO{sub 2} in the η{sup 1}-CT complex is estimated to be about half an electron by NPA, DMA, CHELPG, and Mulliken analyses, whereas the EDA-ALMO-CTA (B3LYP) approach predicts a charge transfer of 75 me{sup –}. However, the transfer of this small amount of charge leads to an energy lowering of -56 kcal/mol, without which the complex would not be bound. The RI-MP2 geometries closely approximate those resulting from the CCSD optimizations, and the optimized second-order opposite spin (O2) method performs well for all the complexes except for the η{sup 1}-CT complex. DFT methods do not reproduce all the ab initio geometries, binding energies and/or energy ordering of these complexes although the range-separated hybrid meta-GGA (M11) and nonlocal (VV10 and vdwDF10) functionals are shown to yield results significantly better than other functionals considered for this system. The fact that there is such variation among DFT methods has implications for DFT-based ab initio molecular dynamics simulations and for the parametrization of classical force fields based on DFT calculations.
An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry
Matthew Neurock; David A. Walthall
2006-05-07
One of the greatest societal challenges over the next decade is the production of cheap, renewable energy for the 10 billion people that inhabit the earth. This will require the development of various different energy sources potentially including fuels derived from methane, coal, and biomass and alternatives sources such as solar, wind and nuclear energy. One approach will be to synthesize gasoline and other fuels from simpler hydrocarbons such as CO derived from methane or other U.S. based sources such as coal. Syngas (CO and H{sub 2}) can be readily converted into higher molecular weight hydrocarbons through Fischer-Tropsch synthesis. Fischer-Tropsch synthesis involves the initiation or activation of CO and H{sub 2} bonds, the subsequent propagation steps including hydrogenation and carbon-carbon coupling, followed by chain termination reactions. Commercially viable catalysts include supported Co and Co-alloys. Over the first two years of this project we have used ab initio methods to determine the adsorption energies for all reactants, intermediates, and products along with the overall reaction energies and their corresponding activation barriers over the Co(0001) surface. Over the third year of the project we developed and advanced an ab initio-based kinetic Monte Carlo simulation code to simulate Fischer Tropsch synthesis. This report details our work over the last year which has focused on the derivation of kinetic parameters for the elementary steps involved in FT synthesis from ab initio density functional theoretical calculations and the application of the kinetic Monte Carlo algorithm to simulate the initial rates of reaction for FT over the ideal Co(0001) surface. The results from our simulations over Co(0001) indicate the importance of stepped surfaces for the activation of adsorbed CO. In addition, they demonstrate that the dominant CH{sub x}* surface intermediate under steady state conditions is CH*. This strongly suggests that hydrocarbon coupling
NASA Astrophysics Data System (ADS)
Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär
2017-02-01
The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.
NASA Astrophysics Data System (ADS)
Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei
2014-06-01
New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).
Liu, Lihong; Wang, Yating; Fang, Qiu
2017-02-14
Ethylene-bridged azobenzene (br-AB) has aroused broad interests due to its unique photoswitching properties. Numerous dynamical simulations have been performed for the br-AB photoisomerization, which focused mainly on the conformational effect and the funnel role of minimum-energy conical intersection (MECI) on the mechanism. In the present work, we use the "full quantum" ab initio multiple spawning method to simulate the br-AB photoisomerization, which provides new insights into the mechanism. Upon irradiation of br-AB to the first excited singlet state (S1), most of the excess energies are trapped in the azo-moiety. Since the intramolecular vibrational energy redistribution is slower than the S1 relaxation processes, the nonadiabatic transition from S1 to the ground state (S0) occurs in the vicinity of high-energy crossing seam and even the largest probabilities of the S1 → S0 transition are not distributed in the MECI regions. Once decaying to the S0 state through the high-energy region, the subsequent isomerization and re-formation of the initial isomer are ultrafast processes in the S0 state. It is the nonergodic behavior of the S1 and S0 dynamics that is mainly responsible for the unique photoswitching properties of the ethylene-bridged azobenzene, which will be discussed in detail.
NASA Astrophysics Data System (ADS)
Liu, Lihong; Wang, Yating; Fang, Qiu
2017-02-01
Ethylene-bridged azobenzene (br-AB) has aroused broad interests due to its unique photoswitching properties. Numerous dynamical simulations have been performed for the br-AB photoisomerization, which focused mainly on the conformational effect and the funnel role of minimum-energy conical intersection (MECI) on the mechanism. In the present work, we use the "full quantum" ab initio multiple spawning method to simulate the br-AB photoisomerization, which provides new insights into the mechanism. Upon irradiation of br-AB to the first excited singlet state (S1), most of the excess energies are trapped in the azo-moiety. Since the intramolecular vibrational energy redistribution is slower than the S1 relaxation processes, the nonadiabatic transition from S1 to the ground state (S0) occurs in the vicinity of high-energy crossing seam and even the largest probabilities of the S1 → S0 transition are not distributed in the MECI regions. Once decaying to the S0 state through the high-energy region, the subsequent isomerization and re-formation of the initial isomer are ultrafast processes in the S0 state. It is the nonergodic behavior of the S1 and S0 dynamics that is mainly responsible for the unique photoswitching properties of the ethylene-bridged azobenzene, which will be discussed in detail.
Multiferroicity in TTF-CA Organic Molecular Crystals Predicted through Ab Initio Calculations
NASA Astrophysics Data System (ADS)
Giovannetti, Gianluca; Kumar, Sanjeev; Stroppa, Alessandro; van den Brink, Jeroen; Picozzi, Silvia
2009-12-01
We show by means of ab initio calculations that the organic molecular crystal TTF-CA is multiferroic: it has an instability to develop spontaneously both ferroelectric and magnetic ordering. Ferroelectricity is driven by a Peierls transition of the TTF-CA in its ionic state. Subsequent antiferromagnetic ordering strongly enhances the opposing electronic contribution to the polarization. It is so large that it switches the direction of the total ferroelectric moment. Within an extended Hubbard model, we capture the essence of the electronic interactions in TTF-CA, confirm the presence of a multiferroic groundstate, and clarify how this state develops microscopically.
Ab-initio method for X-ray absorption spectra simulation of hydride molecular ions
NASA Astrophysics Data System (ADS)
Puglisi, Alessandra; Sisourat, Nicolas; Carniato, Stéphane
2017-03-01
Soft X-ray absorption spectra of molecular ions are important data for the modeling and understanding of laboratory and astrophysical plasma. In this work, we present an ab-initio method, based on the Configuration Interaction (CI) approach, for the calculations of energy positions and oscillator strengths of X-ray absorption spectra. Furthermore, we investigate the effects of the choice of the nature and number of spin-orbitals used in the CI expansion on the spectra. The method is applied on three hydride molecular ions, namely CH+, OH+ and SiH+. However, the approach proposed here is general and may thus be applied to any kind of molecular ions.
Ab initio research of energy loss for energetic protons in solid-density Be
NASA Astrophysics Data System (ADS)
He, Bin; Meng, Xu-Jun; Wang, Zhi-Gang; Wang, Jian-Guo
2017-03-01
Ab initio research of energy loss for energetic protons in solid-density Be is made based on the average atom model. Our results are found in good agreement with the recent experiment for both warm and cool matter. Our results are compared with the local density approximation model and the reason for their difference is also explored. The energy loss at smaller projectile energies is predicted by our model and local density approximation, which helps probe the higher reliability of the proving model and judge the existence of the non-Fermi-Dirac velocity distribution for free electrons exists in dense plasmas in future.
Application of ab-initio calculations to modeling of nanoscale diffusion and activation in silicon
NASA Astrophysics Data System (ADS)
Diebel, Milan
As ULSI devices enter the nanoscale, ultra-shallow and highly electrically active junctions become necessary. New materials and 3D device structures as well as new process technologies are under exploration to meet the requirements of future devices. A detailed understanding of the atomistic mechanisms of point-defect/dopant interactions which govern diffusion and activation behavior is required to overcome the challenges in building these devices. This dissertation describes how ab-initio calculations can be used to develop physical models of diffusion and activation in silicon. A hierarchy of approaches (ab-initio, kinetic lattice Monte Carlo, continuum) is used to bridge the gaps in time scale and system size between atomistic calculations and nanoscale devices. This modeling approach is demonstrated by investigating two very different challenges in process technology: F co-implantation and stress effects on dopant diffusion/activation. In the first application, ab-initio calculations are used to understand anomalous F diffusion behavior. A set of strongly bound fluorine vacancy complexes (FnVm ) were found. The decoration of vacancies/dangling silicon bonds by fluorine leads to fluorine accumulating in vacancy rich regions, which explains the fluorine redistribution behavior reported experimentally. The revealed interactions of F with point-defects explain the benefits of F co-implantation for B and P activation and diffusion. Based on the insight gained, a simplified F diffusion model at the continuum level (50--100 nm scale) is extracted that accounts for co-implantation effects on B and P for various implant energies and doses. The second application addresses the effect of stress on point-defect/dopant equilibrium concentration, diffusion, and activation. A methodology is developed to extract detailed stress effects from ab-initio calculations. The approach is used to extract induced strains and elasticity tensors for various defects and impurities in order
A high-precision ab initio determination of the equilibrium geometry and force field of HOC(+)
NASA Technical Reports Server (NTRS)
Defrees, D. J.; Bunker, P. R.; Binkley, J. S.; Mclean, A. D.
1987-01-01
The results of an ab initio molecular orbital investigation of the isoformyl cation, HOC(+), shape are reported. The effects of expanding the basis set to near the Hartree-Fock limit and of electron correlation were examined, and the results indicate that near the Hartree-Fock limit the HOC(+) is linear. An analytic potential function is presented, from which the calculated rotational energies are only 0.03 percent different from the experimental values. This represents a nearly two orders of magnitude reduction in error from earlier work.
NASA Astrophysics Data System (ADS)
Ishimura, Hiromi; Kadoya, Ryushi; Suzuki, Tomoya; Murakawa, Takeru; Shulga, Sergiy; Kurita, Noriyuki
2015-07-01
Alzheimer's disease is caused by accumulation of amyloid-β (Aβ) peptides in a brain. To suppress the production of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) by secretases. However, because the secretases also play important roles to produce vital proteins for human body, inhibitors for the secretases may have side effects. To propose new agents for protecting the cleavage site of APP from the attacking of the γ-secretase, we have investigated here the specific interactions between a short APP peptide and curcumin derivatives, using protein-ligand docking as well as ab initio molecular simulations.
Ab Initio Study on Atomic Structures and Physical Properties of CdSe Quantum Nanodots
2009-11-25
CdSe quantum dots , with magic number (( CdSe )13, ( CdSe )19, ( CdSe )33 and ( CdSe )34 ). Effects of organic ligand binding on the stability of CdSe as well...calculations of optical absorption spectra for CdSe quantum dots , with magic number (( CdSe )13, ( CdSe )19, ( CdSe )33 and ( CdSe )34 ), have been calculated in...1 AOARD-08-4037 Title of Proposed Project: Ab initio study on atomic structures and physical
NASA Astrophysics Data System (ADS)
Curchod, Basile F. E.; Rauer, Clemens; Marquetand, Philipp; González, Leticia; Martínez, Todd J.
2016-03-01
Full multiple spawning is a formally exact method to describe the excited-state dynamics of molecular systems beyond the Born-Oppenheimer approximation. However, it has been limited until now to the description of radiationless transitions taking place between electronic states with the same spin multiplicity. This Communication presents a generalization of the full and ab initio multiple spawning methods to both internal conversion (mediated by nonadiabatic coupling terms) and intersystem crossing events (triggered by spin-orbit coupling matrix elements) based on a spin-diabatic representation. The results of two numerical applications, a model system and the deactivation of thioformaldehyde, validate the presented formalism and its implementation.
Structure and dynamics of the Lu2Si2O7 lattice: Ab initio calculation
NASA Astrophysics Data System (ADS)
Nazipov, D. V.; Nikiforov, A. E.
2017-01-01
The ab initio calculations have been carried out for the crystal structure and Raman spectrum of a single crystal of lutetium pyrosilicate Lu2Si2O7. The types of fundamental vibrations and their frequencies and intensities in the Raman spectrum for two polarizations of the crystal have been determined. The calculations have been performed within the framework of the density functional theory (DFT) using the hybrid functionals. The ions involved in the vibrations have been identified using the method of isotopic substitution. The results of the calculations are in good agreement with the experiment.
NASA Astrophysics Data System (ADS)
Persico, Maurizio; Cacelli, Ivo; Ferretti, Alessandro
1991-04-01
We have determined ab initio potential energy surfaces of the S0 and S1 states of dimethylnitrosamine, with particular care for the N-N bond dissociation pathway. The electronic correlation has been taken into account by a multireference perturbation method, CIPSI. Classical trajectories in the S1 surface have been run with statistically determined initial conditions. Computed lifetimes and orientation parameters for the recoil velocity and the NO fragment angular momentum are in agreement with experimental data. Large amplitude internal motions are of primary importance in determining such quantities.
NASA Astrophysics Data System (ADS)
Kubota, Yoshiyuki; Ohnuma, Toshiharu; Bučko, Tomáš
2017-03-01
The reaction of carbon dioxide (CO2) with aqueous 2-aminoethanol (MEA) has been investigated using both blue moon ensemble and metadynamics approaches combined with ab initio molecular dynamics (AIMD) simulations. The AIMD simulations predicted the spontaneous deprotonation of the intermediate compound, MEA zwitterion, and they were used to study two possible routes for subsequent proton transfer reactions: the formation of the protonated MEA and the formation of MEA carbamic acid. The free-energy curve depicted by blue moon ensemble technique supported the favorable deprotonation of MEA zwitterion. The overall free-energy profile showed the favorable formation of the ionic products of MEA carbamate ion and protonated MEA.
Flexible Ab initio boundary conditions: simulating isolated dislocations in bcc Mo and Ta.
Woodward, C; Rao, S I
2002-05-27
We report the first ab initio density-functional study of the strain field and Peierls stress of isolated <111> screw dislocations in bcc Mo and Ta. The local dislocation strain field is self-consistently coupled to the long-range elastic field using a flexible boundary condition method. This reduces the mesoscopic atomistic calculation to one involving only degrees of freedom near the dislocation core. The predicted equilibrium core for Mo is significantly different from previous atomistic results and the Peierls stress shows significant non-Schmid behavior as expected for the bcc metals.
Ab initio study on electronically excited states of lithium isocyanide, LiNC
NASA Astrophysics Data System (ADS)
Yasumatsu, Hisato; Jeung, Gwang-Hi
2014-01-01
The electronically excited states of the lithium isocyanide molecule, LiNC, were studied by means of ab initio calculations. The bonding nature of LiNC up to ∼10 eV is discussed on the basis of the potential energy surfaces according to the interaction between the ion-pair and covalent states. The ion-pair states are described by Coulomb attractive interaction in the long distance range, while the covalent ones are almost repulsive or bound with a very shallow potential dent. These two states interact each other to form adiabatic potential energy surfaces with non-monotonic change in the potential energy with the internuclear distance.
Ab initio no core calculations of light nuclei and preludes to Hamiltonian quantum field theory
Vary, J. P.; Maris, P.; Honkanen, H.; Li, J.; Shirokov, A. M.; Brodsky, S. J.; Harindranath, A.
2009-12-17
Recent advances in ab initio quantum many-body methods and growth in computer power now enable highly precise calculations of nuclear structure. The precision has attained a level sufficient to make clear statements on the nature of 3-body forces in nuclear physics. Total binding energies, spin-dependent structure effects, and electroweak properties of light nuclei play major roles in pinpointing properties of the underlying strong interaction. Eventually, we anticipate a theory bridge with immense predictive power from QCD through nuclear forces to nuclear structure and nuclear reactions. Light front Hamiltonian quantum field theory offers an attractive pathway and we outline key elements.
Ab initio no core calculations of light nuclei and preludes to Hamiltonian quantum field theory
Vary, J.P.; Maris, P.; Shirokov, A.M.; Honkanen, H.; li, J.; Brodsky, S.J.; Harindranath, A.; Teramond, G.F.de; /Costa Rica U.
2009-08-03
Recent advances in ab initio quantum many-body methods and growth in computer power now enable highly precise calculations of nuclear structure. The precision has attained a level sufficient to make clear statements on the nature of 3-body forces in nuclear physics. Total binding energies, spin-dependent structure effects, and electroweak properties of light nuclei play major roles in pinpointing properties of the underlying strong interaction. Eventually,we anticipate a theory bridge with immense predictive power from QCD through nuclear forces to nuclear structure and nuclear reactions. Light front Hamiltonian quantum field theory offers an attractive pathway and we outline key elements.
Ab initio calculation of the deuterium quadrupole coupling in liquid water
NASA Astrophysics Data System (ADS)
Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc
1992-10-01
The quadrupole coupling constant and asymmetry parameter for the deuteron in liquid heavy water was determined using purely theoretical methods. Molecular-dynamics simulations with the ab initio potential-energy surface of Lie and Clementi were used to generate snapshots of the liquid. The electric-field gradient at the deuteron was then calculated for these configurations and averaged to obtain the liquid quadrupole coupling constant. At 300 K a quadrupole coupling constant of 256±5 kHz and an asymmetry parameter of 0.164±0.003 were obtained. The temperature dependence of the quadrupole coupling constant was investigated.
Santi, G; Dugdale, S B; Jarlborg, T
2001-12-10
The recent discovery of superconductivity coexisting with weak itinerant ferromagnetism in the d-electron intermetallic compound ZrZn2 strongly suggests spin-fluctuation mediated superconductivity. Ab initio electronic structure calculations of the Fermi surface and generalized susceptibilities are performed to investigate the viability of longitudinal spin-fluctuation-induced spin-triplet superconductivity in the ferromagnetic state. The critical temperature is estimated to be of the order of 1 K. Additionally, it is shown that in spite of a strong electron-phonon coupling ( lambda(ph) = 0.7), conventional s-wave superconductivity is inhibited by the presence of strong spin fluctuations.
The role of Metals in Amyloid Aggregation: A Test Case for ab initio Simulations
Minicozzi, V.; Rossi, G. C.; Stellato, F.; Morante, S.
2007-12-26
First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as test cases the study of the Cu coordination mode in two especially important examples: Prion protein and {beta}-amyloids. Using medium size PC-clusters as well as larger parallel platforms, we are able to deal with systems comprising 300 to 500 atoms and 1000 to 1500 electrons for as long as 2-3 ps. We present structural results which confirm indications coming from NMR and XAS data.
Trivacancy in silicon: A combined DLTS and ab-initio modeling study
NASA Astrophysics Data System (ADS)
Markevich, V. P.; Peaker, A. R.; Lastovskii, S. B.; Murin, L. I.; Coutinho, J.; Markevich, A. V.; Torres, V. J. B.; Briddon, P. R.; Dobaczewski, L.; Monakhov, E. V.; Svensson, B. G.
2009-12-01
Deep level transient spectroscopy and ab-initio modeling have been used for identification of energy levels and structure of trivacancy (V3) in Si. It is found that in the neutral charge state the V3 is bistable, with the "fourfold" configuration being lower in energy than the (1 1 0) planar configuration. V3 in the (1 1 0) planar configuration gives rise to two acceptor levels at Ec-0.36 eV and Ec-0.46 eV in the gap, while in the "fourfold" configuration the defect has trigonal symmetry and an acceptor level at Ec-0.075 eV.
Tripathi, A.N.; Smith, V.H. Jr. K7L3N6); Kaijser, P.; Siemens, A.G. ); Diercksen, G.H.F. )
1990-03-01
Isotropic scattering functions and Compton profiles together with their directional components for several directions relevant to the molecular structure of C{sub 2}H{sub 2} and C{sub 2}H{sub 4} have been evaluated for {ital ab} {ital initio} self-consistent field and configuration-interaction wave functions. The internally folded density (reciprocal form factor) {ital B}({ital r}) is calculated and discussed as are various momentum expectation values. Comparison is made with available experimental and other theoretical results.
Communication: Multiple-timestep ab initio molecular dynamics with electron correlation.
Steele, Ryan P
2013-07-07
A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Moøller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.
Communication: Multiple-timestep ab initio molecular dynamics with electron correlation
NASA Astrophysics Data System (ADS)
Steele, Ryan P.
2013-07-01
A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Møller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.
Electric-field control of magnetism in graphene quantum dots: Ab initio calculations
Agapito, Luis A.; Kioussis, Nicholas; Kaxiras, Efthimios
2011-01-01
Employing ab initio calculations we predict that the magnetic states of hydrogenated diamond-shaped zigzag graphene quantum dots (GQDs), each exhibiting unique electronic structure, can be selectively tuned with gate voltage, through Stark or hybridization electric-field modulation of the spatial distribution and energy of the spin-polarized molecular orbitals, leading to transitions between these states. Electrical read-out of the GQD magnetic state can be accomplished by exploiting the distinctive electrical properties of the various magnetic configurations. PMID:21765631
AB Initio Study of Ion-Pair States of the Iodine Molecule
NASA Astrophysics Data System (ADS)
Alekseev, Vadim A.
2013-06-01
Ion-pair states of the I_2molecule have been the subject of many experimentals studies and to date all 18 states correlating with I^+(^3P_{J=2,1,0}, ^1D_2) + I^-(^1S_0) asymptotes are known from experiment. This contribution reports on {ab initio study of the I_2 molecule with an emphasis on the ion-pair states. Figure shows experimental and calculated potentials of the ion-pair states correlating with I^+(^3P_{2}) + I^-(^1S_0) asymptote (energy is relative to I (^2P_{3/2}) + I (^2P_{3/2}) asymptote).
Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides
NASA Astrophysics Data System (ADS)
Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki
2012-09-01
Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Aβ and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Aβ and inhibit the Aβ aggregation.
An analytical ab initio potential surface and the calculated tunneling energies for the HCl dimer
NASA Astrophysics Data System (ADS)
Bunker, P. R.; Epa, V. C.; Jensen, Per; Karpfen, Alfred
1991-03-01
The six-dimensional potential energy surface of the HCl dimer has been calculated ab initio at 1654 nuclear geometries [A. Karpfen, P. R. Bunker and P. Jensen, Chem. Phys., in press]. In the present paper we have fitted an analytical function to these points; the analytical function is similar to that used previously by us for the potential surface of the HF dimer. The fitted function has 38 adjustable parameters and the standard deviation of the weighted fit is 19.0 cm -1. We have determined the minimum energy path for the trans-bending tunneling motion on this surface, and have calculated the tunneling and K-rotation energies and wavefunctions. Around equilibrium the path is qualitatively similar to that for the HF dimer in that there are two equivalent hydrogen-bonded structures of Cs symmetry (which are approximately L-shaped with a "bound" and a "free" H-atom) that can tunnel through a C2 h saddle point (the "closed" C2 h saddle point). However, away from equilibrium the path is qualitatively different from that found for the HF dimer since the HCl dimer never becomes linear along the path; in fact it passes through a second C2 h saddle point (the "open" C2 h saddle point). As a result the A-rotational constant only varies slightly along the path, and this explains the experimental observation that the tunneling splitting varies little with K-type rotation for the HCl dimer, in contrast to the situation for the HF dimer. Quantitatively it is clear that errors in the ab initio calculation, errors in the fitting of an analytic function to the points, the correction to the path that is caused by the zero point motion in the other vibrations, and the coupling between the four low-frequency modes, will all be relatively more significant than they were for the HF dimer because the full six-dimensional potential is much flatter; the ab initio dissociation energy is only ˜600 cm -1, and the ab initio tunneling barrier is only ˜70 cm -1. Therefore, we modify the
Ab Initio Electronic Structure Calculations of Cytochrome P450 -- Ligand Interactions
NASA Astrophysics Data System (ADS)
Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.
1997-03-01
The Cytochrome P450 superfamily of enzymes are of great interest in pharmacology as they participate in an enormous range of physiological processes including drug deactivation and xenobiotic detoxification. We apply ab initio electronic structure calculations to model the interactions of the haem molecule at the P450 active site with substrate and inhibitor ligands. These calculations, based on density function theory, were performed with the CETEP code which uses a plane wave basis set and pseudopotentials to perform efficient LDA, GGA and spin dependent calculations. A change in the spin state of the haem iron atom is observed on binding of a substrate molecule, consistent with the accepted reaction mechanism.
NASA Astrophysics Data System (ADS)
Wang, Shidong; Wang, Zhao; Setyawan, Wahyu; Mingo, Natalio; Curtarolo, Stefano
2011-10-01
Several thousand compounds from the Inorganic Crystal Structure Database have been considered as nanograined, sintered-powder thermoelectrics with the high-throughput ab-initio AFLOW framework. Regression analysis unveils that the power factor is positively correlated with both the electronic band gap and the carrier effective mass, and that the probability of having large thermoelectric power factors increases with the increasing number of atoms per primitive cell. Avenues for further investigation are revealed by this work. These avenues include the role of experimental and theoretical databases in the development of novel materials.
Ab initio insight into graphene nanofibers to destabilize hydrazine borane for hydrogen release
NASA Astrophysics Data System (ADS)
Qian, Zhao; Raghubanshi, Himanshu; Sterlin Leo Hudson, M.; Srivastava, O. N.; Liu, Xiangfa; Ahuja, Rajeev
2017-02-01
We report the potential destabilizing effects of graphene nanofibers on the hydrogen release property of hydrazine borane via state-of-the-art ab initio calculations for the first time. Interactions of a hydrazine borane cluster with two types of graphene patch edges which exist abundantly in our synthesized graphene nanofibers have been investigated. It is found that both zigzag and armchair edges can greatly weaken the H-host bonds (especially the middle Nsbnd H bond) of hydrazine borane. The dramatic decrease in hydrogen removal energy is caused by the strong interaction between hydrazine borane and the graphene patch edges concerning the electronic charge density redistribution.
Testing the density matrix expansion against ab initio calculations of trapped neutron drops
Bogner, S. K.; Hergert, H.; Furnstahl, R. J.; Kortelainen, Erno M; Stoitsov, M. V.; Maris, Pieter; Vary, J. P.
2011-01-01
Microscopic input to a universal nuclear energy density functional can be provided through the density matrix expansion (DME), which has recently been revived and improved. Several DME implementation strategies are tested for neutron drop systems in harmonic traps by comparing to Hartree-Fock (HF) and ab initio no-core full configuration (NCFC) calculations with a model interaction (Minnesota potential). The new DME with exact treatment of Hartree contributions is found to best reproduce HF results and supplementing the functional with fit Skyrme-like contact terms shows systematic improvement toward the full NCFC results.
Kurova, N. V. Burdov, V. A.
2013-12-15
The results of ab initio calculations of the electronic structure of Si nanocrystals doped with shallow donors (Li, P) are reported. It is shown that phosphorus introduces much more significant distortions into the electronic structure of the nanocrystal than lithium, which is due to the stronger central cell potential of the phosphorus ion. It is found that the Li-induced splitting of the ground state in the conduction band of the nanocrystal into the singlet, doublet, and triplet retains its inverse structure typical for bulk silicon.
NASA Astrophysics Data System (ADS)
Nechaev, I. A.; Krasovskii, E. E.
2016-11-01
We present a method to microscopically derive a small-size k .p Hamiltonian in a Hilbert space spanned by physically chosen ab initio spinor wave functions. Without imposing any complementary symmetry constraints, our formalism equally treats three- and two-dimensional systems and simultaneously yields the Hamiltonian parameters and the true Z2 topological invariant. We consider bulk crystals and thin films of Bi2Se3 , Bi2Te3 , and Sb2Te3 . It turns out that the effective continuous k .p models with open boundary conditions often incorrectly predict the topological character of thin films.
NASA Astrophysics Data System (ADS)
Kozlov, Maxim I.; Poddubnyy, Vladimir V.; Glebov, Ilya O.; Belov, Aleksandr S.; Khokhlov, Daniil V.
2016-02-01
The electronic properties of light-harvesting complexes determine the efficiency of energy transfer in photosynthetic antennae. Ab initio calculations of the electronic properties of bacteriochlorophylls (composing the LH1 complex of the purple bacteria Thermochromatium tepidum) were performed. Based on these calculations, the excitonic Hamiltonian of a native cyclic complex and the Hamiltonians of open complexes with several removed bacteriochlorophylls were constructed. Absorption spectra calculated based on these Hamiltonians agree well with the experimental data. We found that the parameters of interaction between the neighboring bacteriochlorophylls are significantly larger than the empirical parameters suggested previously.
Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study.
Payal, Rajdeep Singh; Balasubramanian, Sundaram
2014-09-07
Interactions determining the dissolution of a monomer of β-cellulose, i.e., cellobiose in a room temperature ionic liquid, [Emim][OAc], have been studied using ab initio molecular dynamics simulations. Although anions are the predominant species in the first coordination shell of cellobiose, cations too are present to a minor extent around it. The presence of low concentration of water in the solution does not significantly alter the nature of the coordination environment of cellobiose. All intra-molecular hydrogen bonds of anti-syn cellobiose are replaced by inter-molecular hydrogen bonds formed with the anions, whereas the anti-anti conformer retains an intramolecular hydrogen bond.
The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Jakse, N.; Pasturel, A.
2014-09-01
We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.
An accurate potential energy curve for helium based on ab initio calculations
NASA Astrophysics Data System (ADS)
Janzen, A. R.; Aziz, R. A.
1997-07-01
Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.
Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones
NASA Astrophysics Data System (ADS)
Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng
2004-04-01
A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (Δ G#) and also free energy differences (Δ G0) for benzodiazepines are reported.
Vibrational energy levels for CH4 from an ab initio potential
NASA Technical Reports Server (NTRS)
Schwenke, D. W.; Partridge, H.
2001-01-01
Many areas of astronomy and astrophysics require an accurate high temperature spectrum of methane (CH4). The goal of the present research is to determine an accurate ab initio potential energy surface (PES) for CH4. As a first step towards this goal, we have determined a PES including up to octic terms. We compare our results with experiment and to a PES based on a quartic expansion. Our octic PES gives good agreement with experiment for all levels, while the quartic PES only for the lower levels.
NASA Astrophysics Data System (ADS)
Pietrucci, Fabio; Andreoni, Wanda
2011-08-01
Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.
NASA Astrophysics Data System (ADS)
Volkov, Alexey N.; Timoshkin, Alexey Y.; Suvorov, Andrew V.
An ab initio study of the two possible pathways of ectrophilic aromatic substitution reaction catalyzed by monomeric and dimeric forms of group 13 metal halides has been performed. Optimized geometries of π, σ-complexes and corresponding transition states have been obtained at second-order Møller-Plesset/ LANL2DZ(d)+ level of theory. It is found that operation of the dimeric pathway is more favorable both thermodynamically and kinetically. Thus, it is expected that catalytical activity of the metal halide will be greatly increased if the stoichiometric ratio 2:1 is employed. Obtained results are in qualitative agreement with available experimental data.
Ab Initio Calculations of Singlet and Triplet Excited States of Chlorine Nitrate and Nitric Acid
NASA Technical Reports Server (NTRS)
Grana, Ana M.; Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)
1994-01-01
Ab initio calculations of vertical excitations to singlet and triplet excited states of chlorine nitrate and nitric acid are reported. The nature of the electronic transitions are examined by decomposing the difference density into the sum of detachment and attachment densities. Counterparts for the three lowest singlet excited states of nitric acid survive relatively unperturbed in chlorine nitrate, while other low-lying singlet states of chlorine nitrate appear to be directly dissociative in the ClO chromophore. These results suggest an assignment of the two main peaks in the experimental chlorine nitrate absorption spectrum. In addition, triplet vertical excitations and the lowest optimized triplet geometries of both molecules are studied.
Converging sequences in the ab initio no-core shell model
Forssen, C.; Vary, J. P.; Caurier, E.; Navratil, P.
2008-02-15
We demonstrate the existence of multiple converging sequences in the ab initio no-core shell model. By examining the underlying theory of effective operators, we expose the physical foundations for the alternative pathways to convergence. This leads us to propose a revised strategy for evaluating effective interactions for A-body calculations in restricted model spaces. We suggest that this strategy is particularly useful for applications to nuclear processes in which states of both parities are used simultaneously, such as for transition rates. We demonstrate the utility of our strategy with large-scale calculations in light nuclei.