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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

Energetics and solvation structure of a dihalogen dopant (I2) in (4)He clusters.

PubMed

Pérez de Tudela, Ricardo; Barragán, Patricia; Valdés, Álvaro; Prosmiti, Rita

2014-08-21

The energetics and structure of small HeNI2 clusters are analyzed as the size of the system changes, with N up to 38. The full interaction between the I2 molecule and the He atoms is based on analytical ab initio He-I2 potentials plus the He-He interaction, obtained from first-principle calculations. The most stable structures, as a function of the number of solvent He atoms, are obtained by employing an evolutionary algorithm and compared with CCSD(T) and MP2 ab initio computations. Further, the classical description is completed by explicitly including thermal corrections and quantum features, such as zero-point-energy values and spatial delocalization. From quantum PIMC calculations, the binding energies and radial/angular probability density distributions of the thermal equilibrium state for selected-size clusters are computed at a low temperature. The sequential formation of regular shell structures is analyzed and discussed for both classical and quantum treatments.

Ab Initio Density Functional Calculations and Infra-Red Study of CO Interaction with Pd Atoms on θ-Al2O3 (010) Surface.

PubMed

Narula, Chaitanya K; Allard, Lawrence F; Wu, Zili

2017-07-24

The ab initio density functional theoretical studies show that energetics favor CO oxidation on single Pd atoms supported on θ-alumina. The diffuse reflectance infra-red spectroscopy (DRIFTS) results show that carbonates are formed as intermediates when single supported Pd atoms are exposed to a gaseous mixture of CO + O 2 . The rapid agglomeration of Pd atoms under CO oxidation conditions even at 6 °C leads to the presence of Pd particles along with single atoms during CO oxidation experiments. Thus, the observed CO oxidation has contributions from both single Pd atoms and Pd particles.

Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

NASA Astrophysics Data System (ADS)

Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

1998-08-01

A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

Transition state theory thermal rate constants and RRKM-based branching ratios for the N((2)D) + CH(4) reaction based on multi-state and multi-reference ab initio calculations of interest for the Titan's chemistry.

PubMed

Ouk, Chanda-Malis; Zvereva-Loëte, Natalia; Scribano, Yohann; Bussery-Honvault, Béatrice

2012-10-30

Multireference single and double configuration interaction (MRCI) calculations including Davidson (+Q) or Pople (+P) corrections have been conducted in this work for the reactants, products, and extrema of the doublet ground state potential energy surface involved in the N((2)D) + CH(4) reaction. Such highly correlated ab initio calculations are then compared with previous PMP4, CCSD(T), W1, and DFT/B3LYP studies. Large relative differences are observed in particular for the transition state in the entrance channel resolving the disagreement between previous ab initio calculations. We confirm the existence of a small but positive potential barrier (3.86 ± 0.84 kJ mol(-1) (MR-AQCC) and 3.89 kJ mol(-1) (MRCI+P)) in the entrance channel of the title reaction. The correlation is seen to change significantly the energetic position of the two minima and five saddle points of this system together with the dissociation channels but not their relative order. The influence of the electronic correlation into the energetic of the system is clearly demonstrated by the thermal rate constant evaluation and it temperature dependance by means of the transition state theory. Indeed, only MRCI values are able to reproduce the experimental rate constant of the title reaction and its behavior with temperature. Similarly, product branching ratios, evaluated by means of unimolecular RRKM theory, confirm the NH production of Umemoto et al., whereas previous works based on less accurate ab initio calculations failed. We confirm the previous findings that the N((2)D) + CH(4) reaction proceeds via an insertion-dissociation mechanism and that the dominant product channels are CH(2)NH + H and CH(3) + NH. Copyright © 2012 Wiley Periodicals, Inc.

Ab initio density functional theory investigation of electronic properties of semiconducting single-walled carbon nanotube bundles

NASA Astrophysics Data System (ADS)

Moradian, Rostam; Behzad, Somayeh; Azadi, Sam

2008-09-01

By using ab initio density functional theory we investigated the structural and electronic properties of semiconducting (7, 0), (8, 0) and (10, 0) carbon nanotube bundles. The energetic and electronic evolutions of nanotubes in the bundling process are also studied. The effects of inter-tube coupling on the electronic dispersions of semiconducting carbon nanotube bundles are demonstrated. Our results show that the inter-tube coupling decreases the energy gap in semiconducting nanotubes. We found that bundles of (7, 0) and (8, 0) carbon nanotubes have metallic feature, while (10, 0) bundle is a semiconductor with an energy gap of 0.22 eV. To clarify our results the band structures of isolated and bundled nanotubes are compared.

Ab Initio Predictions of Hexagonal Zr(B,C,N) Polymorphs for Coherent Interface Design

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

Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G.

2017-10-27

Density functional theory calculations are used to explore hexagonal (HX) NiAs-like polymorphs of Zr(B,C,N) and compare with corresponding Zr(B,C,N) Hagg-like face-centered cubic rocksalt (B1) phases. While all predicted compounds are mechanically stable according to the Born-Huang criteria, only HX Zr(C,N) are found dynamically stable from ab initio molecular dynamics simulations and lattice dynamics calculations. HX ZrN emerges as a candidate structure with ground state energy, elastic constants, and extrinsic mechanical parameters comparable with those of B1 ZrN. Ab initio band structure and semi-classical Boltzmann transport calculations predict a metallic character and a monotonic increase in electrical conductivity with the numbermore » of valence electrons. Electronic structure calculations indicate that the HX phases gain their stability and mechanical attributes by Zr d- non-metal p hybridization and by broadening of Zr d bands. Furthermore, it is shown that the HX ZrN phase provides a low-energy coherent interface model for connecting B1 ZrN domains, with significant energetic advantage over an atomistic interface model derived from high resolution transmission electron microscopy images. The ab initio characterizations provided herein should aid the experimental identification of non-Hagg-like hard phases. Furthermore, the results can also enrich the variety of crystalline phases potentially available for designing coherent interfaces in superhard nanostructured materials and in materials with multilayer characteristics.« less

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

Ab initio/DFT/GIAO-CCSD(T) calculational study of the t-butyl cation: comparison of experimental data with structures, energetics, IR vibrational frequencies, and 13C NMR chemical shifts indicating preferred C(s) conformation.

PubMed

Rasul, Golam; Chen, Jonathan L; Prakash, G K Surya; Olah, George A

2009-06-18

The C(s) conformation of the tert-butyl cation 3 was established to be the preferred global energy minimum using a combination of ab initio, DFT, and CCSD(T) methodology with correlation-consistent basis sets. The potential energy surface of methyl rotation involving the C(3v), C(s), and C(3h) forms, however, in accord with previous studies, is quite flat. The computed IR absorptions of 3 indicate that it has the greatest degree of electron donation from C-H bonds into the C(+)-C bonds. The experimental (13)C NMR chemical shifts also agree very well with the experimental data.

An extensive ab initio study of the structures, vibrational spectra, quadratic force fields, and relative energetics of three isomers of Cl2O2

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rohlfing, Celeste MCM.; Rice, Julia E.

1992-01-01

Quantum mechanical computational methods are employed for an ab initio investigation of: (1) the molecular properties of the lowest isomers of the ClO dimer; and (2) predicted molecular and thermochemical properties. Techniques employed include electron correlation and particularly singles and doubles coupled-cluster (CCSD) theory with or without perturbational estimates of the effects of connected triple excitations. The isomers ClOClO and ClClO2 are found to have higher energies than the ClOOCl isomer, and the theoretical vibrational frequencies of the isomers are well correlated with experimental data. Experimental values of the heat of formation for the isomers are also compared with calculations based on an isodesmic reaction with Cl2O, H2O, and HOOH.

Electronic Structure of Energetic Molecules and Crystals Under Compression

NASA Astrophysics Data System (ADS)

Kay, Jeffrey

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

Sub-500 fs electronically nonadiabatic chemical dynamics of energetic molecules from the S1 excited state: Ab initio multiple spawning study

NASA Astrophysics Data System (ADS)

Ghosh, Jayanta; Gajapathy, Harshad; Konar, Arindam; Narasimhaiah, Gowrav M.; Bhattacharya, Atanu

2017-11-01

Energetic materials store a large amount of chemical energy. Different ignition processes, including laser ignition and shock or compression wave, initiate the energy release process by first promoting energetic molecules to the electronically excited states. This is why a full understanding of initial steps of the chemical dynamics of energetic molecules from the excited electronic states is highly desirable. In general, conical intersection (CI), which is the crossing point of multidimensional electronic potential energy surfaces, is well established as a controlling factor in the initial steps of chemical dynamics of energetic molecules following their electronic excitations. In this article, we have presented different aspects of the ultrafast unimolecular relaxation dynamics of energetic molecules through CIs. For this task, we have employed ab initio multiple spawning (AIMS) simulation using the complete active space self-consistent field (CASSCF) electronic wavefunction and frozen Gaussian-based nuclear wavefunction. The AIMS simulation results collectively reveal that the ultrafast relaxation step of the best energetic molecules (which are known to exhibit very good detonation properties) is completed in less than 500 fs. Many, however, exhibit sub-50 fs dynamics. For example, nitro-containing molecules (including C-NO2, N-NO2, and O-NO2 active moieties) relax back to the ground state in approximately 40 fs through similar (S1/S0)CI conical intersections. The N3-based energetic molecule undergoes the N2 elimination process in 40 fs through the (S1/S0)CI conical intersection. Nitramine-Fe complexes exhibit sub-50 fs Fe-O and N-O bond dissociation through the respective (S1/S0)CI conical intersection. On the other hand, tetrazine-N-oxides, which are known to exhibit better detonation properties than tetrazines, undergo internal conversion in a 400-fs time scale, while the relaxation time of tetrazine is very long (about 100 ns). Many other characteristics of sub-500 fs nonadiabatic decay of energetic molecules are discussed. In the end, many unresolved issues associated with the ultrafast nonadiabatic chemical dynamics of energetic molecules are presented.

A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space.

PubMed

Wu, Yao; Dai, Xiaodong; Huang, Niu; Zhao, Lifeng

2013-06-05

In force field parameter development using ab initio potential energy surfaces (PES) as target data, an important but often neglected matter is the lack of a weighting scheme with optimal discrimination power to fit the target data. Here, we developed a novel partition function-based weighting scheme, which not only fits the target potential energies exponentially like the general Boltzmann weighting method, but also reduces the effect of fitting errors leading to overfitting. The van der Waals (vdW) parameters of benzene and propane were reparameterized by using the new weighting scheme to fit the high-level ab initio PESs probed by a water molecule in global configurational space. The molecular simulation results indicate that the newly derived parameters are capable of reproducing experimental properties in a broader range of temperatures, which supports the partition function-based weighting scheme. Our simulation results also suggest that structural properties are more sensitive to vdW parameters than partial atomic charge parameters in these systems although the electrostatic interactions are still important in energetic properties. As no prerequisite conditions are required, the partition function-based weighting method may be applied in developing any types of force field parameters. Copyright © 2013 Wiley Periodicals, Inc.

Ab initio density functional theory investigation of Li-intercalated silicon carbide nanotube bundles

NASA Astrophysics Data System (ADS)

Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

2009-06-01

We present the results of ab initio density functional theory calculations on the energetic, and geometric and electronic structure of Li-intercalated ( 6,6) silicon carbide nanotube (SiCNT) bundles. Our results show that intercalation of lithium leads to the significant changes in the geometrical structure. The most prominent effect of Li intercalation on the electronic band structure is a shift of the Fermi energy which occurs as a result of charge transfer from lithium to the SiCNTs. All the Li-intercalated ( 6,6) SiCNT bundles are predicted to be metallic representing a substantial change in electronic properties relative to the undoped bundle, which is a wide band gap semiconductor. Both inside of the nanotube and the interstitial space are susceptible for intercalation. The present calculations suggest that the SiCNT bundle is a promising candidate for the anode material in battery applications.

An ab initio cluster study of the chemisorption of atomic cesium and hydrogen on reconstructed surfaces of gallium rich gallium arsenide

NASA Astrophysics Data System (ADS)

Schailey, Ronald

1999-11-01

Chemisorption properties of cesium and hydrogen atoms on the Ga-rich GaAs (100) (2 x 1), (2 x 2), and β(4 x 2) surfaces are investigated using ab initio self-consistent restricted open shell Hartree-Fock (ROHF) total energy calculations with Hay- Wadt effective core potentials. The effects of electron correlation have been included using many-body perturbation theory through second order, with the exception of β(4 x 2) symmetry due to computational limitations. The semiconductor surface is modeled by finite sized hydrogen saturated clusters. The effects of surface relaxation and reconstruction have been investigated in detail. Results are given for the energetics of chemisorption, charge population analysis, HOMO-LUMO gaps, and consequent possibilities of metallization for atomic cesium adsorption. For the chemisorption of atomic hydrogen, the experimentally verified mechanism of surface dimer bond breaking is investigated in detail.

Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1992-01-01

The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

Ab initio correlated study of the Al13H- anion: Isomers, their kinetic stability and vertical detachment energies

NASA Astrophysics Data System (ADS)

Moc, Jerzy

2012-01-01

We report correlated ab initio calculations for the Al13H- cluster anion isomers, their kinetic stability and vertical detachment energies (VDEs). Of the two most energetically favored anion structures involving H atom in terminal and threefold bridged sites of the icosahedral Al13-, the higher energy ‘threefold bridged' isomer is shown to be of low kinetic stability. Our results are consistent with the recent photoelectron spectroscopy (PE) study of Grubisic et al. who observed two distinct Al13H- isomers, one of them identified as ‘metastable'. The VDE energies computed at the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVDZ level for the ‘terminal' and ‘threefold bridged' Al13H- isomers of 3.21 and 2.32 eV are in good agreement with those determined in the PE study.

Density functional theory study of phase stability and defect thermodynamics in iron-oxyhydroxide mineral materials

NASA Astrophysics Data System (ADS)

Pinney, Nathan Douglas

Due to their high surface area and reactivity toward a variety of heavy metal and oxyanion species of environmental concern, Fe-(oxyhydr)oxide materials play an important role in the geochemical fate of natural and anthropogenic contaminants in soils, aquifers and surface water environments worldwide. In this research, ab initio simulations describe the bulk structure, magnetic properties, and relative phase stability of major Fe-(oxyhydr)oxide materials, including hematite, goethite, lepidocrocite, and ferrihydrite.These bulk models are employed in further studies of point defect and alloy/dopant thermodynamics in these materials, allowing construction of a phase stability model that better replicates the structure and composition of real materials. Li + adsorption at the predominant goethite (101) surface is simulated using ab initio methods, offering energetic and structural insight into the binding mechanisms of metal cations over a range of surface protonation conditions.

Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules

DTIC Science & Technology

2014-08-20

including zero-point energy ( ZPE ) corrections, 43.21 kcal/mol and 50.46 kcal/mol, respectively. The decomposition initiated by trans-HONO elimination can...CCSD(T)/cc-pVTZ level with ZPE corrections) of 47.00 kcal/mol and 48.27 kcal/mol, respectively. Thus, at the CCSD(T)/cc-pVTZ level, the ordering of

Axial and equatorial hydrogen-bond conformers between (CH2)3S and H(D)F: Fourier transform infrared spectroscopy and ab initio calculations.

PubMed

Madebène, B; Asselin, P; Soulard, P; Alikhani, M E

2011-08-21

The coexistence of axial and equatorial hydrogen-bonded conformers of 1 : 1 (CH(2))(3)S-HF (and -DF) has been observed in the same adiabatic expansion of a supersonic jet seeded with argon and in a static absorption cell at room temperature. High level calculations computed the axial conformer to be the most stable one with a small energy difference with respect to the equatorial one, in full agreement with previous microwave experiments. On the grounds of band contour simulations of FTIR spectra and ab initio energetic and anharmonic vibrational calculations, two pairs of ν(s) HF donor stretching bands, observed in a series of jet-FTIR spectra at 3457.9 and 3480.5 cm(-1) have been respectively assigned to the axial and equatorial forms of the 1 : 1 complex. In the jet-FTIR spectra series with HF, the assignment of an additional broad band (about 200 cm(-1) higher in frequency with respect to ν(s)) to a 1 : 2 complex has been supported by theoretical investigations. Experimental detection of both axial and equatorial forms of a cyclic trimer has been confirmed by calculated energetic and vibrational properties. The nature of hydrogen bonding has been examined within topological frameworks. The energetic partitioning within the 1 : 1 dimers has been elucidated with SAPT techniques. Interestingly, the interconversion pathway between two 1 : 1 structures has been explored and it was seen that the formation of the 1 : 1 complex affects the interconversion barrier on the ring puckering motion. The band contour analysis of gas phase FTIR experiments provided a consistent set of vibrational frequencies and anharmonic coupling constants, in good agreement with ab initio anharmonic vibrational calculations. Finally, from a series of cell-FTIR spectra recorded at different partial pressures of (CH(2))(3)S and HF monomers, the absorption signal of the 1 : 1 complex could be isolated which enabled to estimate the equilibrium constant K(p) = 0.023 at 298 K for the dimerization.

On Predicting the Crystal Structure of Energetic Materials From Quantum Mechanics

DTIC Science & Technology

2008-12-01

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

AB INITIO STUDY OF THE ELECTRONIC AND MAGNETIC PROPERTIES OF GRAPHENE WITH AND WITHOUT ADSORPTION OF M ATOM (M = C, N, O, F, Cl)

NASA Astrophysics Data System (ADS)

Ismail, Ali I.; Mubarak, A. A.

We present here an ab initio study for the energetic, electronic, magnetic and optical structures of the graphene sheet with and without the adsorption of M atom (M = C, N, O, F, Cl). The calculations are preformed using the full-potential linearized augmented plane wave (FP-LAPW) within the generalized gradient approximation (GGA) to describe the exchange-correlation potential. The calculations show that N prefers the bridge site, while C, O, F and Cl prefer the top site above the graphene sheet. The calculated M-graphene bond length is found to be inversely proportional to the adsorption energy. The hybridization between sp-states of the graphene sheet and M adatom is determined by the analysis of the partial and local density of states (PDOS and TDOS). In case of O and F as adsorbed atoms, graphene sheets show a wide energy band-gap and some significant magnetic moments. The optical properties of the studied sheets are performed in different radiation regions using the real and imaginary parts of the dielectric function. We think that the energetic, electronic, optical and magnetic properties of the M-graphene sheets are governed by two main factors; the number of unpaired valence electrons and the electronegativity of the M atom.

Ionization energies of aqueous nucleic acids: photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations.

PubMed

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 molecular dynamics of solvation effects on reactivity at electrified interfaces

DOE PAGES

Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos

2016-08-08

Using ab initio molecular dynamics (as implemented in periodic, self-consistent (GGA-PBE) density functional theory (DFT) we investigated the mechanism of methanol electro-oxidation on Pt(111). We investigated the role of solvation and electrode potential on the energetics of the first proton transfer step, methanol electro-oxidation to methoxy (CH 3O) or hydroxymethyl (CH 2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), while the binding energy 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 constrainedmore » 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. Solvation reduces the barrier for both C-H and O-H bond activation steps with respect to their vapor phase values, though 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). Furthermore, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.« less

Evaluation of synthetic linear motor-molecule actuation energetics

PubMed Central

Brough, Branden; Northrop, Brian H.; Schmidt, Jacob J.; Tseng, Hsian-Rong; Houk, Kendall N.; Stoddart, J. Fraser; Ho, Chih-Ming

2006-01-01

By applying atomic force microscope (AFM)-based force spectroscopy together with computational modeling in the form of molecular force-field simulations, we have determined quantitatively the actuation energetics of a synthetic motor-molecule. This multidisciplinary approach was performed on specifically designed, bistable, redox-controllable [2]rotaxanes to probe the steric and electrostatic interactions that dictate their mechanical switching at the single-molecule level. The fusion of experimental force spectroscopy and theoretical computational modeling has revealed that the repulsive electrostatic interaction, which is responsible for the molecular actuation, is as high as 65 kcal·mol−1, a result that is supported by ab initio calculations. PMID:16735470

Defect energetics of concentrated solid-solution alloys from ab initio calculations: Ni 0.5 Co 0.5 , Ni 0.5 Fe 0.5 , Ni 0.8 Fe 0.2 and Ni 0.8 Cr 0.2

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

Zhao, Shijun; Stocks, G. Malcolm; Zhang, Yanwen

2016-01-01

The distribution of migration energies of vacancies and interstitials in Ni 0.5Fe 0.5has a region of overlap, an indication of their comparable mobility compared to pure Ni (indicated by dotted line), which will greatly facilitate the recombination of Frenkel pairs.

Communication: Ab initio study of O{sub 4}H{sup +}: A tracer molecule in the interstellar medium?

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

Xavier, George D.; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón, E-mail: ramon@uaem.mx

2014-08-28

The structure and energetics of the protonated molecular oxygen dimer calculated via ab initio methods is reported. We find structures that share analogies with the eigen and zundel forms for the protonated water dimer although the symmetrical sharing of the proton is more prevalent. Analysis of different fragmentation channels show charge transfer processes which indicate the presence of conical intersections for various states including the ground state. An accurate estimate for the proton affinity of O{sub 4} leads to a significantly larger value (5.6 eV) than for O{sub 2} (4.4 eV), implying that the reaction H{sub 3}{sup +} + O{submore » 4} → O{sub 4}H{sup +} + H{sub 2} is exothermic by 28 Kcal/mol as opposed to the case of O{sub 2} which is nearly thermoneutral. This opens up the possibility of using O{sub 4}H{sup +} as a tracer molecule for oxygen in the interstellar medium.« less

Ab-Initio Interfacial Studies of Cobalt/Copper Multilayers

NASA Astrophysics Data System (ADS)

Villagonzalo, Cristine; Setty, Arun K.; Muratov, Leonid; Cooper, Bernard R.

2002-03-01

We present a study of the interface of cobalt/copper (Co/Cu) multilayrs. For its potential in giant magnetoresistance (GMR) device applications,(S.S.Parkin, et al.), Appl. Phys. Lett. 58 (1991) 2710 the Co/Cu system has been studied extensively. The magnitude of GMR is found to depend sensitively on the nature of the interface, however, the underlying mechanism is not well understood. Therefore, we focus on the energy-configuration of Co/Cu multilayers (of 1-4 monolayers for each element) and on the effects of interpenetration. Using an ab-initio full-potential Linear Muffin-Tin Orbital (FP-LMTO) electronic structure method, we seek a stable interfacial structure. Unlike prior studies, our computations are for the experimentally relevant (111) direction. Our preliminary results indicate that Co impurities in bulk Cu are not energetically favorable, in accord with the experimentally observed immiscibility of Co and Cu. Studies in progress of interfacial relaxation in prelude to consideration of interdiffusion and lattice buckling will also be presented.

Ab initio quantum mechanical calculation of the reaction probability for the Cl-+PH2Cl→ClPH2+Cl- reaction

NASA Astrophysics Data System (ADS)

Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.

2013-11-01

The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

Transferable atomistic model to describe the energetics of zirconia

NASA Astrophysics Data System (ADS)

Wilson, Mark; Schönberger, Uwe; Finnis, Michael W.

1996-10-01

We have investigated the energies of a number of phases of ZrO2 using models of an increasing degree of sophistication: the simple ionic model, the polarizable ion model, the compressible ion model, and finally a model including quadrupole polarizability of the oxygen ions. The three structures which are observed with increasing temperatures are monoclinic, tetragonal, and cubic (fluorite). Besides these we have studied some hypothetical structures which certain potentials erroneously predict or which occur in other oxides with this stoichiometry, e.g., the α-PbO2 structure and rutile. We have also performed ab initio density functional calculations with the full-potential linear combination of muffin-tin orbitals method to investigate the cubic-tetragonal distortion. A detailed comparison is made between the results using classical potentials, the experimental data, and our own and other ab initio results. The factors which stabilize the various structure are analyzed. We find the only genuinely transferable model is the one including compressible ions and anion polarizability to the quadrupole level.

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

DTIC Science & Technology

2011-02-10

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

Ab initio density functional theory study on the atomic and electronic structure of GaP/Si(001) heterointerfaces

NASA Astrophysics Data System (ADS)

Romanyuk, O.; Supplie, O.; Susi, T.; May, M. M.; Hannappel, T.

2016-10-01

The atomic and electronic band structures of GaP/Si(001) heterointerfaces were investigated by ab initio density functional theory calculations. Relative total energies of abrupt interfaces and mixed interfaces with Si substitutional sites within a few GaP layers were derived. It was found that Si diffusion into GaP layers above the first interface layer is energetically unfavorable. An interface with Si/Ga substitution sites in the first layer above the Si substrate is energetically the most stable one in thermodynamic equilibrium. The electronic band structure of the epitaxial GaP/Si(001) heterostructure terminated by the (2 ×2 ) surface reconstruction consists of surface and interface electronic states in the common band gap of two semiconductors. The dispersion of the states is anisotropic and differs for the abrupt Si-Ga, Si-P, and mixed interfaces. Ga 2 p , P 2 p , and Si 2 p core-level binding-energy shifts were computed for the abrupt and the lowest-energy heterointerface structures. Negative and positive core-level shifts due to heterovalent bonds at the interface are predicted for the abrupt Si-Ga and Si-P interfaces, respectively. The distinct features in the heterointerface electronic structure and in the core-level shifts open new perspectives in the experimental characterization of buried polar-on-nonpolar semiconductor heterointerfaces.

Accurate energetics of small molecules containing third-row atoms Ga-Kr: A comparison of advanced ab initio and density functional theory

NASA Astrophysics Data System (ADS)

Yockel, Scott; Mintz, Benjamin; Wilson, Angela K.

2004-07-01

Advanced ab initio [coupled cluster theory through quasiperturbative triple excitations (CCSD(T))] and density functional (B3LYP) computational chemistry approaches were used in combination with the standard and augmented correlation consistent polarized valence basis sets [cc-pVnZ and aug-cc-pVnZ, where n=D(2), T(3), Q(4), and 5] to investigate the energetic and structural properties of small molecules containing third-row (Ga-Kr) atoms. These molecules were taken from the Gaussian-2 (G2) extended test set for third-row atoms. Several different schemes were used to extrapolate the calculated energies to the complete basis set (CBS) limit for CCSD(T) and the Kohn-Sham (KS) limit for B3LYP. Zero point energy and spin orbital corrections were included in the results. Overall, CCSD(T) atomization energies, ionization energies, proton affinities, and electron affinities are in good agreement with experiment, within 1.1 kcal/mol when the CBS limit has been determined using a series of two basis sets of at least triple zeta quality. For B3LYP, the overall mean absolute deviation from experiment for the three properties and the series of molecules is more significant at the KS limit, within 2.3 and 2.6 kcal/mol for the cc-pVnZ and aug-cc-pVnZ basis set series, respectively.

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.

Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

DTIC Science & Technology

2015-07-15

There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio -Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

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2014-07-01

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40 CFR 89.126 - Denial, revocation of certificate of conformity.

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2012-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

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40 CFR 89.126 - Denial, revocation of certificate of conformity.

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2011-07-01

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Ab initio and density functional study on the mechanism of the C2H2++methanol reaction

NASA Astrophysics Data System (ADS)

Irle, Stephan; Morokuma, Keiji

1999-09-01

High level ab initio (G2MS and CASSCF) and density functional (B3LYP) calculations were carried out to study the mechanism of the ion-molecule reaction C2H2++CH3OH for four reaction channels: hydride abstraction from methanol (HA), proton transfer from acetylene cation (PT), charge transfer (CT), and covalent complex formation (CC) channel. For the CT channel, two pathways have been found: a usual nonadiabatic pathway via A'/A″ seam of crossing, and a low-energy adiabatic pathway through an initial intermediate; the latter may be the dominant process with favorable energies and a large impact parameter. The HA process involves a low-energy direct intermediate and a very low barrier to form C2H3+CH2OH+ and is also energetically favorable. The PT processes require passage over a high-energy transition state (TS) and are not important. One of the experimentally unobserved CC channels, formation of the COCC skeleton, is energetically favorable and there is no energetic reason for it not to take place; a "dynamic bottleneck" argument may have to be invoked to explain the experiment. The increase in reaction efficiency with the C-C stretch excitation may be justified by considering the TSs for two CT pathways, where the C-C distance changed substantially from that in the reactant C2H2+. Very qualitatively, the C2H2++CH3OH potential energy surface looks more like that of the C2H2++NH3 system than the C2H2++CH4 system, because of the differences in the ionization potentials: NH3˜CH3OH

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-05-01

At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08769d

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment.

PubMed

Liu, Hanchao; Wang, Yimin; Bowman, Joel M

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

NASA Astrophysics Data System (ADS)

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-01

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

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

PubMed

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

2015-12-14

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

Quantum-Chemical ab initio Calculations on the Three Isomers of Diborabenzene (C4H4B2)

NASA Astrophysics Data System (ADS)

Singh, Jaswinder; Wang, Yuekui; Raabe, Gerhard

2010-01-01

Quantum-chemical ab initio calculations up to the ZPE+CCSD(T)/aug-cc-pVTZ//MP2/6- 311++G** level were performed on three possible structural isomers of diborabenzene (C4H4B2). All three molecules were found to be local minima on the C4H4B2 energy surface and to have closed shell singlet ground states. While the ground states of the 1,3- and 1,4-isomer are planar and of C2v and D2h symmetry, respectively, 1,2-diborabenzene is non-planar with a C2 axis passing through the center of the BB bond and the middle of the opposite carbon-carbon bond as the only symmetry element. The energetically most favourable 1,3-diborabenzene was found to be about 19 and 36 kcal/mol lower in energy than the 1,2- and the 1,4-isomer. Planar 1,3- and 1,4-diborabenzene have three doubly occupied π orbitals while non-planar 1,2-diborabenzene has also three doubly occupied orbitals which can be derived from the π orbitals of its 3.7 kcal/mol energetically less favourable planar form ("π-like" orbitals). The lowest unoccupied orbitals of all three isomers have σ symmetry with large coefficients at the two boron atoms. These orbitals are lower in energy than the lowest unoccupied molecular orbitals (LUMOs) of e. g. benzene and pyridine and might cause pronounced acceptor properties which could be one of the reasons for the elusiveness of the title compounds. The results of bond separation reactions show that cyclic conjugation stabilizes all three diborabenzenes relative to their isolated fragments. The most effective stabilization energy of about 24 kcal/mol was found for the energetically lowest 1,3-isomer. This value amounts to approximately one third of the experimental value for the bond separation energy of pyridine. In all cases the energetically lowest triplet states are significantly (16 - 24 kcal/mol) higher in energy than the singlet ground states. Also among the triplets the 1,3-isomer is the energetically most fabourable species.

Ab Initio -Based Bond Order Potential to Investigate Low Thermal Conductivity of Stanene Nanostructures

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

Cherukara, Mathew J.; Narayanan, Badri; Kinaci, Alper

2016-08-28

We introduce a bond order potential (BOP) for stanene based on an ab initio derived training data set. The potential is optimized to accurately describe the energetics, as well as thermal and mechanical properties of a free-standing sheet, and used to study diverse nanostructures of stanene, including tubes and ribbons. As a representative case study, using the potential, we perform molecular dynamics simulations to study stanene’s structure and temperature-dependent thermal conductivity. We find that the structure of stanene is highly rippled, far in excess of other 2-D materials (e.g., graphene), owing to its low in-plane stiffness (stanene: ~ 25 N/m;more » graphene: ~ 480 N/ m). The extent of stanene’s rippling also shows stronger temperature dependence compared to that in graphene. Furthermore, we find that stanene based nanostructures have significantly lower thermal conductivity compared to graphene based structures owing to their softness (i.e., low phonon group velocities) and high anharmonic response. Our newly developed BOP will facilitate the exploration of stanene based low dimensional heterostructures for thermoelectric and thermal management applications.« less

Relaxation of energetic S(1D) atoms in Xe gas: comparison of ab initio calculations with experimental data.

PubMed

Bovino, S; Zhang, P; Kharchenko, V; Dalgarno, A

2011-07-14

In this paper, we report our investigation of the translational energy relaxation of fast S((1)D) atoms in a Xe thermal bath. The interaction potential of Xe-S was constructed using ab initio methods. Total and differential cross sections were then calculated. The latter have been incorporated into the construction of the kernel of the Boltzmann equation describing the energy relaxation process. The solution of the Boltzmann equation was obtained and results were compared with those reported in experiments [G. Nan, and P. L. Houston, J. Chem. Phys. 97, 7865 (1992)]. Good agreement with the measured time-dependent relative velocity of fast S((1)D) atoms was obtained except at long relaxation times. The discrepancy may be due to the error accumulation caused by the use of hard sphere approximation and the Monte Carlo analysis of the experimental data. Our accurate description of the energy relaxation process led to an increase in the number of collisions required to achieve equilibrium by an order of magnitude compared to the number given by the hard-sphere approximation.

An equilibrium ab initio atomistic thermodynamics study of chlorine adsorption on the Cu(001) surface.

PubMed

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

2011-06-07

The effect of chlorine (Cl) chemisorption on the energetics and atomic structure of the Cu(001) surface over a wide range of chlorine pressures and temperatures has been studied using equilibrium ab initio atomistic thermodynamics to elucidate the formation of cuprous chloride (CuCl) as part of the Deacon reaction on copper metal. The calculated surface free energies show that the 1/2 monolayer (ML) c(2 × 2)-Cl phase with chlorine atoms adsorbed at the hollow sites is the most stable structure for a wide range of Cl chemical potential, in agreement with experimental observations. It is also found that at very low pressure and exposure, but elevated temperature, the 1/9 ML and 1/4 ML phases become the most stable. By contrast, a high coverage of Cl does not lead to thermodynamically stable geometries. The subsurface adsorption of Cl atoms, however, dramatically increases the stability of the 1 ML and 2 ML adsorption configurations providing a possible pathway for the formation of the bulk-chloride surface phases in the kinetic regime.

Friction of water on graphene and hexagonal boron nitride from ab initio methods: very different slippage despite very similar interface structures.

PubMed

Tocci, Gabriele; Joly, Laurent; Michaelides, Angelos

2014-12-10

Friction is one of the main sources of dissipation at liquid water/solid interfaces. Despite recent progress, a detailed understanding of water/solid friction in connection with the structure and energetics of the solid surface is lacking. Here, we show for the first time that ab initio molecular dynamics can be used to unravel the connection between the structure of nanoscale water and friction for liquid water in contact with graphene and with hexagonal boron nitride. We find that although the interface presents a very similar structure between the two sheets, the friction coefficient on boron nitride is ≈ 3 times larger than that on graphene. This comes about because of the greater corrugation of the energy landscape on boron nitride arising from specific electronic structure effects. We discuss how a subtle dependence of the friction on the atomistic details of a surface, which is not related to its wetting properties, may have a significant impact on the transport of water at the nanoscale, with implications for the development of membranes for desalination and for osmotic power harvesting.

Compactness Aromaticity of Atoms in Molecules

PubMed Central

Putz, Mihai V.

2010-01-01

A new aromaticity definition is advanced as the compactness formulation through the ratio between atoms-in-molecule and orbital molecular facets of the same chemical reactivity property around the pre- and post-bonding stabilization limit, respectively. Geometrical reactivity index of polarizability was assumed as providing the benchmark aromaticity scale, since due to its observable character; with this occasion new Hydrogenic polarizability quantum formula that recovers the exact value of 4.5 a03 for Hydrogen is provided, where a0 is the Bohr radius; a polarizability based–aromaticity scale enables the introduction of five referential aromatic rules (Aroma 1 to 5 Rules). With the help of these aromatic rules, the aromaticity scales based on energetic reactivity indices of electronegativity and chemical hardness were computed and analyzed within the major semi-empirical and ab initio quantum chemical methods. Results show that chemical hardness based-aromaticity is in better agreement with polarizability based-aromaticity than the electronegativity-based aromaticity scale, while the most favorable computational environment appears to be the quantum semi-empirical for the first and quantum ab initio for the last of them, respectively. PMID:20480020

Nanomechanics of Carbon and CxByNz Nanotubes: Via a Quantum Molecular Dynamics Method

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Menon, M.; Cho, Kyeong Jae; Saini, Subhash (Technical Monitor)

1999-01-01

Nanomechanics of single-wall C, BN and BC$_3$ and B doped C nanotubes under axial compression and tension are investigated through a generalized tight-binding molecular dynamics (GTBMD) and {\\it ab-initio} electronic structure methods. The dynamic strength of BN, BC$_3$ and B doped C nanotubes for small axial strain are comparable to each other. The main difference is in the critical strain at which structural collapse occurs. For example, even a shallow doping with B lowers the value of critical strain for C nanotubes. The critical strain for BN nanotube is found to be more than that for the similar C nanotube. Once the structural collapse starts to occur we find that carbon nanotubes irreversibly go into plastic deformation regime via the formation of tetrahedral (four-fold coordinated) bonds at the location of sharp pinches or kinks. This finding is considerably different from the classical MD (molecular dynamics) simulation results known so far. The energetics and electronic densities of states of the collapsed structures, investigated with {\\it ab-initio) methods, will also be discussed.

Free energy landscape of dissociative adsorption of methane on ideal and defected graphene from ab initio simulations

NASA Astrophysics Data System (ADS)

Wlazło, M.; Majewski, J. A.

2018-03-01

We study the dissociative adsorption of methane at the surface of graphene. Free energy profiles, which include activation energies for different steps of the reaction, are computed from constrained ab initio molecular dynamics. At 300 K, the reaction barriers are much lower than experimental bond dissociation energies of gaseous methane, strongly indicating that the graphene surface acts as a catalyst of methane decomposition. On the other hand, the barriers are still much higher than on the nickel surface. Methane dissociation therefore occurs at a higher rate on nickel than on graphene. This reaction is a prerequisite for graphene growth from a precursor gas. Thus, the growth of the first monolayer should be a fast and efficient process while subsequent layers grow at a diminished rate and in a more controllable manner. Defects may also influence reaction energetics. This is evident from our results, in which simple defects (Stone-Wales defect and nitrogen substitution) lead to different free energy landscapes at both dissociation and adsorption steps of the process.

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

NASA Technical Reports Server (NTRS)

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

2012-01-01

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

Evidence for a first-order liquid-liquid transition in high-pressure hydrogen from ab initio simulations.

PubMed

Morales, Miguel A; Pierleoni, Carlo; Schwegler, Eric; Ceperley, D M

2010-07-20

Using quantum simulation techniques based on either density functional theory or quantum Monte Carlo, we find clear evidence of a first-order transition in liquid hydrogen, between a low conductivity molecular state and a high conductivity atomic state. Using the temperature dependence of the discontinuity in the electronic conductivity, we estimate the critical point of the transition at temperatures near 2,000 K and pressures near 120 GPa. Furthermore, we have determined the melting curve of molecular hydrogen up to pressures of 200 GPa, finding a reentrant melting line. 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.

Microwave Spectrum of the Ethanol-Methanol Dimer

NASA Astrophysics Data System (ADS)

Finneran, Ian A.; Carroll, Brandon; Mead, Griffin; Blake, Geoffrey

2016-06-01

The hydrogen bond donor/acceptor competition in mixed alcohol clusters remains a fundamental question in physical chemistry. Previous theoretical work on the prototype ethanol-methanol dimer has been inconclusive in predicting the energetically preferred structure. Here, we report the microwave spectrum of the ethanol-methanol dimer between 8-18 GHz, using a chirped pulse Fourier transform microwave spectrometer. With the aid of ab initio calculations, 36 transitions have been fit and assigned to a t-ethanol-acceptor, methanol-donor structure in an argon-backed expansion. In a helium-backed expansion, a second excited conformer has been observed, and tentatively assigned to a g-ethanol-acceptor, methanol-donor structure. No ethanol-donor, methanol-acceptor structures have been found, suggesting such structures are energetically disfavored.

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

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40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

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2011-07-01

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Unreacted equation of states of typical energetic materials under static compression: A review

NASA Astrophysics Data System (ADS)

Zhaoyang, Zheng; Jijun, Zhao

2016-07-01

The unreacted equation of state (EOS) of energetic materials is an important thermodynamic relationship to characterize their high pressure behaviors and has practical importance. The previous experimental and theoretical works on the equation of state of several energetic materials including nitromethane, 1,3,5-trinitrohexahydro-1,3,5-triazine (RDX), 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX), hexanitrostilbene (HNS), hexanitrohexaazaisowurtzitane (HNIW or CL-20), pentaerythritol tetranitrate (PETN), 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105), triamino-trinitrobenzene (TATB), 1,1-diamino-2,2-dinitroethene (DADNE or FOX-7), and trinitrotoluene (TNT) are reviewed in this paper. The EOS determined from hydrostatic and non-hydrostatic compressions are discussed and compared. The theoretical results based on ab initio calculations are summarized and compared with the experimental data. Project supported by the National Natural Science Foundation of China (Grant Nos. 11174045 and 11404050).

The keto-enol equilibrium in substituted acetaldehydes: focal-point analysis and ab initio limit

NASA Astrophysics Data System (ADS)

Balabin, Roman M.

2011-10-01

High-level ab initio electronic structure calculations up to the CCSD(T) theory level, including extrapolations to the complete basis set (CBS) limit, resulted in high precision energetics of the tautomeric equilibrium in 2-substituted acetaldehydes (XH2C-CHO). The CCSD(T)/CBS relative energies of the tautomers were estimated using CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z calculations with MP2/aug-cc-pVTZ geometries. The relative enol (XHC = CHOH) stabilities (ΔE e,CCSD(T)/CBS) were found to be 5.98 ± 0.17, -1.67 ± 0.82, 7.64 ± 0.21, 8.39 ± 0.31, 2.82 ± 0.52, 10.27 ± 0.39, 9.12 ± 0.18, 5.47 ± 0.53, 7.50 ± 0.43, 10.12 ± 0.51, 8.49 ± 0.33, and 6.19 ± 0.18 kcal mol-1 for X = BeH, BH2, CH3, Cl, CN, F, H, NC, NH2, OCH3, OH, and SH, respectively. Inconsistencies between the results of complex/composite energy computations methods Gn/CBS (G2, G3, CBS-4M, and CBS-QB3) and high-level ab initio methods (CCSD(T)/CBS and MP2/CBS) were found. DFT/aug-cc-pVTZ results with B3LYP, PBE0 (PBE1PBE), TPSS, and BMK density functionals were close to the CCSD(T)/CBS levels (MAD = 1.04 kcal mol-1).

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

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40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

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Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate may be deemed void ab initio. (C) The manufacturer shall bear the burden of establishing to the... be deemed void ab initio. (C) The manufacturer shall bear the burden of establishing to the... of conformity, the Administrator may deem such certificate void ab initio. (4) In any case in which...

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing... the certificate was issued, and the certificate may be deemed void ab initio. (C) The manufacturer... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing...

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

PubMed

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

2014-07-03

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

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

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

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previousmore » spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.« less

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Ab initio vel ex eventu

NASA Astrophysics Data System (ADS)

Thiessen, P. A.; Treder, H.-J.

Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

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.

Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Nanoscale High Energetic Materials: A Polymeric Nitrogen Chain N8 Confined inside a Carbon Nanotube

NASA Astrophysics Data System (ADS)

Abou-Rachid, Hakima; Hu, Anguang; Timoshevskii, Vladimir; Song, Yanfeng; Lussier, Louis-Simon

2008-05-01

We present a theoretical study of a new hybrid material, nanostructured polymeric nitrogen, where a polymeric nitrogen chain is encapsulated in a carbon nanotube. The electronic and structural properties of the new system are studied by means of ab initio electronic structure and molecular dynamics calculations. Finite temperature simulations demonstrate the stability of this nitrogen phase at ambient pressure and room temperature using carbon nanotube confinement. This nanostructured confinement may open a new path towards stabilizing polynitrogen or polymeric nitrogen at ambient conditions.

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.

Ab-initio study of liquid systems: Concentration dependence of electrical resistivity of binary liquid alloy Rb1-xCsx

NASA Astrophysics Data System (ADS)

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

2013-02-01

The electrical resistivity (ρL) of Rb1-XCsX binary alloys has been made calculated using Troullier Martins ab-initio pseudopotentials. The present results of the electrical resistivity (ρL) of Rb1-XCsX binary alloys have been found in good agreement with the experimental results. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys. Hence ab-initio pseudopotentials can be used instead of model pseudopotentials having problem of transferability.

Topological Semimetals Studied by Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

2018-04-01

In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.

Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

PubMed

Exner, Kai S; Over, Herbert

2017-05-16

Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a simple ab initio thermodynamics treatment. We show that ab initio thermodynamics leads to erroneous conclusions about kinetic and mechanistic aspects for the CER over RuO 2 (110), while the kinetics of the OER over RuO 2 (110) and ORR over Pt(111) are reasonably well described. Microkinetics of an electrocatalyzed reaction is largely simplified by the quasi-equilibria of the RI preceding the rate-determining step (rds) with the reactants. Therefore, in ab initio kinetics the rate of an electrocatalyzed reaction is governed by the transition state (TS) with the highest free energy G rds # , defining also the rate-determining step (rds). Ab initio thermodynamics may be even more powerful, when using the highest free energy of an reaction intermediate G max (RI) rather than the highest free energy difference between consecutive reaction intermediates, ΔG loss , as a descriptor for the kinetics.

Towards accurate ab initio predictions of the vibrational spectrum of methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.

2002-01-01

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

Evidence for a first-order liquid-liquid transition in high-pressure hydrogen from ab initio simulations

PubMed Central

Morales, Miguel A.; Pierleoni, Carlo; Schwegler, Eric; Ceperley, D. M.

2010-01-01

Using quantum simulation techniques based on either density functional theory or quantum Monte Carlo, we find clear evidence of a first-order transition in liquid hydrogen, between a low conductivity molecular state and a high conductivity atomic state. Using the temperature dependence of the discontinuity in the electronic conductivity, we estimate the critical point of the transition at temperatures near 2,000 K and pressures near 120 GPa. Furthermore, we have determined the melting curve of molecular hydrogen up to pressures of 200 GPa, finding a reentrant melting line. 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. PMID:20566888

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

PubMed

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

NASA Astrophysics Data System (ADS)

Miller, Thomas F., III; Clary, David C.

We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of the adrenaline molecule.

HPAM: Hirshfeld Partitioned Atomic Multipoles

PubMed Central

Elking, Dennis M.; Perera, Lalith; Pedersen, Lee G.

2011-01-01

An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank lmax on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from lmax = 0 (atomic charges) to lmax = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank lmax are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ lmax. In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (lmax = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used. PMID:22140274

On the incorporation of the geometric phase in general single potential energy surface dynamics: A removable approximation to ab initio data.

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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

2013-05-01

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

Mapping energetics of atom probe evaporation events through first principles calculations.

PubMed

Peralta, Joaquín; Broderick, Scott R; Rajan, Krishna

2013-09-01

The purpose of this work is to use atomistic modeling to determine accurate inputs into the atom probe tomography (APT) reconstruction process. One of these inputs is evaporation field; however, a challenge occurs because single ions and dimers have different evaporation fields. We have calculated the evaporation field of Al and Sc ions and Al-Al and Al-Sc dimers from an L1₂-Al₃Sc surface using ab initio calculations and with a high electric field applied to the surface. The evaporation field is defined as the electric field at which the energy barrier size is calculated as zero, corresponding to the minimum field that atoms from the surface can break their bonds and evaporate from the surface. The evaporation field of the surface atoms are ranked from least to greatest as: Al-Al dimer, Al ion, Sc ion, and Al-Sc dimer. The first principles results were compared with experimental data in the form of an ion evaporation map, which maps multi-ion evaporations. From the ion evaporation map of L1₂-Al₃Sc, we extract relative evaporation fields and identify that an Al-Al dimer has a lower evaporation field than an Al-Sc dimer. Additionally, comparatively an Al-Al surface dimer is more likely to evaporate as a dimer, while an Al-Sc surface dimer is more likely to evaporate as single ions. These conclusions from the experiment agree with the ab initio calculations, validating the use of this approach for modeling APT energetics. Copyright © 2013 Elsevier B.V. All rights reserved.

Structure and energetics of vinoxide and the X({sup 2}A{double{underscore}prime}) and A({sup 2}A{prime}) vinoxy radicals

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

Alconcel, L.S.; Deyerl, H.J.; Zengin, V.

1999-11-18

Enolate anions are intermediates in many organic reactions that involve carbon-carbon or carbon-oxygen food formation. They also play a key role in the development of stereoselective and stereocontrolled syntheses of complex compounds. Enolate radicals are important intermediates in combustion and photochemical smog cycles. In particular, the vinoxy radical, C{sub 2}H{sub 3}O{sup {sm{underscore}bullet}} is a major product of the reaction of odd oxygen and ethylene. The photoelectron spectrum of binoxide, C{sub 2}H{sub 3}O{sup {minus}}, at 355 nm is reported, showing photodetachment to both the X({sup 2}A{double{underscore}prime}) ground and first excited A({sup 2}A{prime}) states of the vinoxy radical. Both direct interpretations andmore » Franck-Condon simulations of the photoelectron spectrum of this simple enolate anion have been used to obtain insights into the energetics and structures of the anion and the ground and first excited state of the neutral radical. Franck-Condon simulations were generated from ab initio geometry and frequency calculations using the CASSCF method and showed good agreement with the vibrational structure visible in the experimental spectrum. The electron affinity (E.A.{sub exp} = 1.795 {+-} 0.015 eV; E.A.{sub calc} = 1.82 eV) and separation energy of the ground and first excited states (T{sub 0,exp} = 1.015 {+-} 0.015 eV; T{sub 0,calc} = 0.92 eV) obtained from the ab initio calculations are in good accord with the experimental values.« less

C 90 temperature effects on relative stabilities of the IPR isomers

NASA Astrophysics Data System (ADS)

Slanina, Zdeněk; Zhao, Xiang; Lee, Shyi-Long; Ōsawa, Eiji

1997-07-01

The complete set of 46 isolated-pentagon-rule (IPR) isomers of C 90 is treated by the SAMI quantum-chemical method (Semi-Ab-Initio Model 1), and their energetics is also checked by ab initio SCF computations (HF/3-21G, HF/4-31G) and the AM1 and PM3 semiempirical methods. All the methods point out a C2 species as the system state (with an exception at the HF/3-21G level). However, the energetics itself is not able to produce a good agreement with recent observations (one C2 v, three C2, and one C1, separeted into three HPLC fractions). The symmetries of the five SAM1 lowest-energy structures are: C2, C2 v, Cs, D5 h, C1. In order to respect temperature effects on relative stabilities, entropy contributions are also computed and significant changes are found. The symmetries of the five structures most populated in a high-temperature region are according to the SAM1 computations: two times C2, Cs, C2 v, C1. One of the recently reported HPLC fractions shows 70 lines in the 13C NMR spectrum, assigned to a C2 species (45 lines) and C2 v species (25 lines, 5 weaker). There is however an alternative interpretation of the spectrum: a Cs (46 lines, 2 weaker) and a C2 v species (24 lines, 3 weaker). The last two structures are indeed present in the SAM1 high-temperature stability set so that agreement between observations and calculations can be achieved.

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.

PubMed

Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

2003-06-06

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.

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

PubMed

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

2013-04-01

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

Design of two-photon molecular tandem architectures for solar cells by ab initio theory

DOE PAGES

Ornso, Kristian B.; Garcia-Lastra, Juan M.; De La Torre, Gema; ...

2015-03-04

An extensive database of spectroscopic properties of molecules from ab initio calculations is used to design molecular complexes for use in tandem solar cells that convert two photons into a single electron–hole pair, thereby increasing the output voltage while covering a wider spectral range. Three different architectures are considered: the first two involve a complex consisting of two dye molecules with appropriately matched frontier orbitals, connected by a molecular diode. Optimized combinations of dye molecules are determined by taking advantage of our computational database of the structural and energetic properties of several thousand porphyrin dyes. The third design is amore » molecular analogy of the intermediate band solar cell, and involves a single dye molecule with strong intersystem crossing to ensure a long lifetime of the intermediate state. Based on the calculated energy levels and molecular orbitals, energy diagrams are presented for the individual steps in the operation of such tandem solar cells. We find that theoretical open circuit voltages of up to 1.8 V can be achieved using these tandem designs. Questions about the practical implementation of prototypical devices, such as the synthesis of the tandem molecules and potential loss mechanisms, are addressed.« less

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing.

PubMed

Lee, Juyong; Lee, Jinhyuk; Sasaki, Takeshi N; Sasai, Masaki; Seok, Chaok; Lee, Jooyoung

2011-08-01

Ab initio protein structure prediction is a challenging problem that requires both an accurate energetic representation of a protein structure and an efficient conformational sampling method for successful protein modeling. In this article, we present an ab initio structure prediction method which combines a recently suggested novel way of fragment assembly, dynamic fragment assembly (DFA) and conformational space annealing (CSA) algorithm. In DFA, model structures are scored by continuous functions constructed based on short- and long-range structural restraint information from a fragment library. Here, DFA is represented by the full-atom model by CHARMM with the addition of the empirical potential of DFIRE. The relative contributions between various energy terms are optimized using linear programming. The conformational sampling was carried out with CSA algorithm, which can find low energy conformations more efficiently than simulated annealing used in the existing DFA study. The newly introduced DFA energy function and CSA sampling algorithm are implemented into CHARMM. Test results on 30 small single-domain proteins and 13 template-free modeling targets of the 8th Critical Assessment of protein Structure Prediction show that the current method provides comparable and complementary prediction results to existing top methods. Copyright © 2011 Wiley-Liss, Inc.

Accurate classical short-range forces for the study of collision cascades in Fe–Ni–Cr

DOE PAGES

Béland, Laurent Karim; Tamm, Artur; Mu, Sai; ...

2017-05-10

The predictive power of a classical molecular dynamics simulation is largely determined by the physical validity of its underlying empirical potential. In the case of high-energy collision cascades, it was recently shown that correctly modeling interactions at short distances is necessary to accurately predict primary damage production. An ab initio based framework is introduced for modifying an existing embedded-atom method FeNiCr potential to handle these short-range interactions. Density functional theory is used to calculate the energetics of two atoms approaching each other, embedded in the alloy, and to calculate the equation of state of the alloy as it is compressed.more » The pairwise terms and the embedding terms of the potential are modi ed in accordance with the ab initio results. Using this reparametrized potential, collision cascades are performed in Ni 50Fe 50, Ni 80Cr 20 and Ni 33Fe 33Cr 33. The simulations reveal that alloying Ni and NiCr to Fe reduces primary damage production, in agreement with some previous calculations. Alloying Ni and NiFe to Cr does not reduce primary damage production, in contradiction with previous calculations.« less

Ab initio multiple spawning dynamics study of dimethylnitramine and dimethylnitramine-Fe complex to model their ultrafast nonadiabatic chemistry

NASA Astrophysics Data System (ADS)

Bera, Anupam; Ghosh, Jayanta; Bhattacharya, Atanu

2017-07-01

Conical intersections are now firmly established to be the key features in the excited electronic state processes of polyatomic energetic molecules. In the present work, we have explored conical intersection-mediated nonadiabatic chemical dynamics of a simple analogue nitramine molecule, dimethylnitramine (DMNA, containing one N-NO2 energetic group), and its complex with an iron atom (DMNA-Fe). For this task, we have used the ab initio multiple spawning (AIMS) dynamics simulation at the state averaged-complete active space self-consistent field(8,5)/6-31G(d) level of theory. We have found that DMNA relaxes back to the ground (S0) state following electronic excitation to the S1 excited state [which is an (n,π*) excited state] with a time constant of approximately 40 fs. This AIMS result is in very good agreement with the previous surface hopping-result and femtosecond laser spectroscopy result. DMNA does not dissociate during this fast internal conversion from the S1 to the S0 state. DMNA-Fe also undergoes extremely fast relaxation from the upper S1 state to the S0 state; however, this relaxation pathway is dissociative in nature. DMNA-Fe undergoes initial Fe-O, N-O, and N-N bond dissociations during relaxation from the upper S1 state to the ground S0 state through the respective conical intersection. The AIMS simulation reveals the branching ratio of these three channels as N-N:Fe-O:N-O = 6:3:1 (based on 100 independent simulations). Furthermore, the AIMS simulation reveals that the Fe-O bond dissociation channel exhibits the fastest (time constant 24 fs) relaxation, while the N-N bond dissociation pathway features the slowest (time constant 128 fs) relaxation. An intermediate time constant (30 fs) is found for the N-O bond dissociation channel. This is the first nonadiabatic chemical dynamics study of metal-contained energetic molecules through conical intersections.

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

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

A note on AB INITIO semiconductor band structures

NASA Astrophysics Data System (ADS)

Fiorentini, Vincenzo

1992-09-01

We point out that only the internal features of the DFT ab initio theoretical picture of a crystal should be used in a consistent ab initio calculation of the band structure. As a consequence, we show that ground-state band structure calculations should be performed for the system in equilibrium at zero pressure, i.e. at the computed equilibrium cell volume ω th. Examples of consequences of this attitude are considered.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

Thermal Decomposition of the Solid Phase of Nitromethane: Ab Initio Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Chang, Jing; Lian, Peng; Wei, Dong-Qing; Chen, Xiang-Rong; Zhang, Qing-Ming; Gong, Zi-Zheng

2010-10-01

The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200 K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.

Ab initio modeling of point defects, self-diffusion, and incorporation of impurities in thorium

NASA Astrophysics Data System (ADS)

Daroca, D. Pérez

2017-02-01

Research on Generation-IV nuclear reactors has boosted the investigation of thorium as nuclear fuel. By means of first-principles calculations within the framework of density functional theory, structural properties and phonon dispersion curves of Th are obtained. These results agreed very well with previous ones. The stability and formation energies of vacancies, interstitial and divacancies are studied. It is found that vacancies are the energetically preferred defects. The incorporation energies of He, Xe, and Kr atoms in Th defects are analyzed. Self-diffusion, migration paths and activation energies are also calculated.

Ab initio Quantum Chemical and Experimental Reaction Kinetics Studies in the Combustion of Bipropellants

DTIC Science & Technology

2017-03-24

NUMBER (Include area code) 24 March 2017 Briefing Charts 01 March 2017 - 31 March 2017 Ab initio Quantum Chemical and Experimental Reaction Kinetics...Laboratory AFRL/RQRS 1 Ara Road Edwards AFB, CA 93524 *Email: ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical and Experimental Reaction ...Clearance 17161 Zador et al., Prog. Energ. Combust. Sci., 37 371 (2011) Why Quantum Chemical Reaction Kinetics Studies? DISTRIBUTION A: Approved for

An ab initio study of the conformational energy map of acetylcholine

NASA Astrophysics Data System (ADS)

Segall, M. D.; Payne, M. C.; Boyes, R. N.

An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans , gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.

Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet.

PubMed

Rana, Malay Kumar; Chandra, Amalendu

2013-05-28

The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.

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

PubMed

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

2017-09-05

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

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

PubMed

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

2017-11-22

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

Ab initio interatomic potentials and the thermodynamic properties of fluids

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-07-01

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

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.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-06-01

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

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

PubMed

Patil, Amol Baliram; Mahadeo Bhanage, Bhalchandra

2016-09-21

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

Bicanonical ab Initio Molecular Dynamics for Open Systems.

PubMed

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Ab initio interatomic potentials and the thermodynamic properties of fluids.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-07-14

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-06-28

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

PubMed

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.

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

PubMed Central

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 Study of Aluminium Impurity and Interstitial-Substitutional Complexes in Ge Using a Hybrid Functional (HSE)

NASA Astrophysics Data System (ADS)

Igumbor, E.; Mapasha, R. E.; Meyer, W. E.

2017-07-01

The results of an ab initio modelling of aluminium substitutional impurity ({\\hbox {Al}}_Ge), aluminium interstitial in Ge [{\\hbox {I}}_Al for the tetrahedral (T) and hexagonal (H) configurations] and aluminium interstitial-substitutional pairs in Ge ({\\hbox {I}}_Al{\\hbox {Al}}_Ge) are presented. For all calculations, the hybrid functional of Heyd, Scuseria, and Ernzerhof in the framework of density functional theory was used. Defects formation energies, charge state transition levels and minimum energy configurations of the {\\hbox {Al}}_Ge, {\\hbox {I}}_Al and {\\hbox {I}}_Al{\\hbox {Al}}_Ge were obtained for -2, -1, 0, +1 and +2 charge states. The calculated formation energy shows that for the neutral charge state, the {\\hbox {I}}_Al is energetically more favourable in the T than the H configuration. The {\\hbox {I}}_Al{\\hbox {Al}}_Ge forms with formation energies of -2.37 eV and -2.32 eV, when the interstitial atom is at the T and H sites, respectively. The {\\hbox {I}}_Al{\\hbox {Al}}_Ge is energetically more favourable when the interstitial atom is at the T site with a binding energy of 0.8 eV. The {\\hbox {I}}_Al in the T configuration, induced a deep donor (+2/+1) level at EV+0.23 eV and the {\\hbox {Al}}_Ge induced a single acceptor level (0/-1) at EV+0.14 eV in the band gap of Ge. The {\\hbox {I}}_Al{\\hbox {Al}}_Ge induced double-donor levels are at E_V+0.06 and E_V+0.12 eV, when the interstitial atom is at the T and H sites, respectively. The {\\hbox {I}}_Al and {\\hbox {I}}_Al{\\hbox {Al}}_Ge exhibit properties of charge state-controlled metastability.

Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

NASA Astrophysics Data System (ADS)

Mishra, S. B.; Nanda, B. R. K.

2017-05-01

Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

Ab initio theory and modeling of water.

PubMed

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

2017-10-10

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

Ab initio theory and modeling of water

PubMed Central

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

2017-01-01

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

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

40 CFR 92.306 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate of conformity for such engine families. The certificate of conformity may be voided ab initio for..., and the certificate may be deemed void ab initio. (3) The manufacturer or remanufacturer (as...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2010 CFR

2010-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2013 CFR

2013-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

40 CFR 86.094-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., the Administrator may deem such certificate void ab initio. (4) In any case in which certification of... fraud or other misconduct as makes the certification invalid ab initio. (6) The manufacturer may request...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2012 CFR

2012-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2011 CFR

2011-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

21 CFR 201.150 - Drugs; processing, labeling, or repacking.

Code of Federal Regulations, 2014 CFR

2014-04-01

... part thereof, from such establishment, become void ab initio if the drug comprising such shipment... ab initio with respect to the person who introduced such shipment or delivery into interstate...

Ab initio design of drug carriers for zoledronate guest molecule using phosphonated and sulfonated calix[4]arene and calix[4]resorcinarene host molecules

NASA Astrophysics Data System (ADS)

Jang, Yong-Man; Yu, Chol-Jun; Kim, Jin-Song; Kim, Song-Un

2018-04-01

Monomolecular drug carriers based on calix[n]-arenes and -resorcinarenes containing the interior cavity can enhance the affinity and specificity of the osteoporosis inhibitor drug zoledronate (ZOD). In this work we investigate the suitability of nine different calix[4]-arenes and -resorcinarenes based macrocycles as hosts for the ZOD guest molecule by conducting {\\it ab initio} density functional theory calculations for structures and energetics of eighteen different host-guest complexes. For the optimized molecular structures of the free, phosphonated, sulfonated calix[4]-arenes and -resorcinarenes, the geometric sizes of their interior cavities are measured and compared with those of the host-guest complexes in order to check the appropriateness for host-guest complex formation. Our calculations of binding energies indicate that in gaseous states some of the complexes might be unstable but in aqueous states almost all of the complexes can be formed spontaneously. Of the two different docking ways, the insertion of ZOD with the \\ce{P-C-P} branch into the cavity of host is easier than that with the nitrogen containing heterocycle of ZOD. The work will open a way for developing effective drug delivering systems for the ZOD drug and promote experimentalists to synthesize them.

Size-induced chemical and magnetic ordering in individual Fe-Au nanoparticles.

PubMed

Mukherjee, Pinaki; Manchanda, Priyanka; Kumar, Pankaj; Zhou, Lin; Kramer, Matthew J; Kashyap, Arti; Skomski, Ralph; Sellmyer, David; Shield, Jeffrey E

2014-08-26

Formation of chemically ordered compounds of Fe and Au is inhibited in bulk materials due to their limited mutual solubility. However, here we report the formation of chemically ordered L12-type Fe3Au and FeAu3 compounds in Fe-Au sub-10 nm nanoparticles, suggesting that they are equilibrium structures in size-constrained systems. The stability of these L12-ordered Fe3Au and FeAu3 compounds along with a previously discovered L10-ordered FeAu has been explained by a size-dependent equilibrium thermodynamic model. Furthermore, the spin ordering of these three compounds has been computed using ab initio first-principle calculations. All ordered compounds exhibit a substantial magnetization at room temperature. The Fe3Au had a high saturation magnetization of about 143.6 emu/g with a ferromagnetic spin structure. The FeAu3 nanoparticles displayed a low saturation magnetization of about 11 emu/g. This suggests a antiferromagnetic spin structure, with the net magnetization arising from uncompensated surface spins. First-principle calculations using the Vienna ab initio simulation package (VASP) indicate that ferromagnetic ordering is energetically most stable in Fe3Au, while antiferromagnetic order is predicted in FeAu and FeAu3, consistent with the experimental results.

Ab initio study of the O4H(+) novel species: spectroscopic fingerprints to aid its observation.

PubMed

Xavier, F George D; Hernández-Lamoneda, Rámon

2015-06-28

A detailed ab initio characterization of the structural, energetic and spectroscopic properties of the novel O4H(+) species is presented. The equilibrium structures and relative energies of all multiplet states have been determined systematically by analyzing static and dynamical correlation effects. The two and three body dissociation processes have been studied and indicate the presence of conical intersections in various states including the ground state. Comparison with available thermochemical data is very good, supporting the applied methodology. The reaction, H3(+) + O4→ O4H(+) + H2, was found to be exothermic ΔH = -19.4 kcal mol(-1) and therefore, it is proposed that the product in the singlet state could be formed in the interstellar medium (ISM) via collision processes. To aid in its laboratory or radioastronomy detection in the interstellar medium we determined spectroscopic fingerprints. It is estimated for the most stable geometry of O4H(+) dipole allowed electronic transitions in the visible region at 429 nm and 666 nm, an intense band at 1745 cm(-1) in the infrared and signals at 40.6, 81.2 and 139.2 GHz in the microwave region at 10, 50 and 150 K respectively, relevant for detection in the ISM.

SiC Schottky Diode Detectors for Measurement of Actinide Concentrations from Alpha Activities in Molten Salt Electrolyte

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

Windl, Wolfgang; Blue, Thomas

In this project, we have designed a 4H-SiC Schottky diode detector device in order to monitor actinide concentrations in extreme environments, such as present in pyroprocessing of spent fuel. For the first time, we have demonstrated high temperature operation of such a device up to 500 °C in successfully detecting alpha particles. We have used Am-241 as an alpha source for our laboratory experiments. Along with the experiments, we have developed a multiscale model to study the phenomena controlling the device behavior and to be able to predict the device performance. Our multiscale model consists of ab initio modeling tomore » understand defect energetics and their effect on electronic structure and carrier mobility in the material. Further, we have developed the basis for a damage evolution model incorporating the outputs from ab initio model in order to predict respective defect concentrations in the device material. Finally, a fully equipped TCAD-based device model has been developed to study the phenomena controlling the device behavior. Using this model, we have proven our concept that the detector is capable of performing alpha detection in a salt bath with the mixtures of actinides present in a pyroprocessing environment.« less

First-Principles Modeling of Hydrogen Storage in Metal Hydride Systems

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

J. Karl Johnson

The objective of this project is to complement experimental efforts of MHoCE partners by using state-of-the-art theory and modeling to study the structure, thermodynamics, and kinetics of hydrogen storage materials. Specific goals include prediction of the heats of formation and other thermodynamic properties of alloys from first principles methods, identification of new alloys that can be tested experimentally, calculation of surface and energetic properties of nanoparticles, and calculation of kinetics involved with hydrogenation and dehydrogenation processes. Discovery of new metal hydrides with enhanced properties compared with existing materials is a critical need for the Metal Hydride Center of Excellence. Newmore » materials discovery can be aided by the use of first principles (ab initio) computational modeling in two ways: (1) The properties, including mechanisms, of existing materials can be better elucidated through a combined modeling/experimental approach. (2) The thermodynamic properties of novel materials that have not been made can, in many cases, be quickly screened with ab initio methods. We have used state-of-the-art computational techniques to explore millions of possible reaction conditions consisting of different element spaces, compositions, and temperatures. We have identified potentially promising single- and multi-step reactions that can be explored experimentally.« less

Thermal decomposition of 1,3,3-trinitroazetidine (TNAZ): A density functional theory and ab initio study

NASA Astrophysics Data System (ADS)

Veals, Jeffrey D.; Thompson, Donald L.

2014-04-01

Density functional theory and ab initio methods are employed to investigate decomposition pathways of 1,3,3-trinitroazetidine initiated by unimolecular loss of NO2 or HONO. Geometry optimizations are performed using M06/cc-pVTZ and coupled-cluster (CC) theory with single, double, and perturbative triple excitations, CCSD(T), is used to calculate accurate single-point energies for those geometries. The CCSD(T)/cc-pVTZ energies for NO2 elimination by N-N and C-N bond fission are, including zero-point energy (ZPE) corrections, 43.21 kcal/mol and 50.46 kcal/mol, respectively. The decomposition initiated by trans-HONO elimination can occur by a concerted H-atom and nitramine NO2 group elimination or by a concerted H-atom and nitroalkyl NO2 group elimination via barriers (at the CCSD(T)/cc-pVTZ level with ZPE corrections) of 47.00 kcal/mol and 48.27 kcal/mol, respectively. Thus, at the CCSD(T)/cc-pVTZ level, the ordering of these four decomposition steps from energetically most favored to least favored is: NO2 elimination by N-N bond fission, HONO elimination involving the nitramine NO2 group, HONO elimination involving a nitroalkyl NO2 group, and finally NO2 elimination by C-N bond fission.

Ab initio study of the neutral and anionic alkali and alkaline earth hydroxides: Electronic structure and prospects for sympathetic cooling of OH−

PubMed Central

2017-01-01

We have performed a systematic ab initio study on alkali and alkaline earth hydroxide neutral (MOH) and anionic (MOH−) species where M = Li, Na, K, Rb, Cs or Be, Mg, Ca, Sr, Ba. The CCSD(T) method with extended basis sets and Dirac-Fock relativistic effective core potentials for the heavier atoms has been used to study their equilibrium geometries, interaction energies, electron affinities, electric dipole moment, and potential energy surfaces. All neutral and anionic species exhibit a linear shape with the exception of BeOH, BeOH−, and MgOH−, for which the equilibrium structure is found to be bent. Our analysis shows that the alkaline earth hydroxide anions are valence-bound whereas the alkali hydroxide anions are dipole bound. In the context of sympathetic cooling of OH− by collision with ultracold alkali and alkaline earth atoms, we investigate the 2D MOH− potential energy surfaces and the associative detachment reaction M + OH→− MOH + e−, which is the only energetically allowed reactive channel in the cold regime. We discuss the implication for the sympathetic cooling of OH− and conclude that Li and K are the best candidates for an ultracold buffer gas. PMID:28527437

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

NASA Astrophysics Data System (ADS)

Li, Yan; Kowalski, Piotr M.

2018-07-01

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

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions.

PubMed

Paton, Robert S; Goodman, Jonathan M

2009-04-01

We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol(-1) for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol(-1). For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 92.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... such certificate void ab initio. (5) In any case in which certification of a locomotive or locomotive..., except in cases of such fraud or other misconduct that makes the certification invalid ab initio. (7) The...

40 CFR 94.208 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ab initio. (5) In any case in which certification of an engine is to be withheld, denied, revoked or... makes the certification invalid ab initio. (7) The manufacturer may request, within 30 days of receiving...

Evaluating High-Throughput Ab Initio Gene Finders to Discover Proteins Encoded in Eukaryotic Pathogen Genomes Missed by Laboratory Techniques

PubMed Central

Goodswen, Stephen J.; Kennedy, Paul J.; Ellis, John T.

2012-01-01

Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. PMID:23226328

77 FR 21154 - BNSF Railway Company-Abandonment Exemption-in Oklahoma County, OK

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-09

... proceeding and reject BNSF's notice of exemption as void ab initio on the grounds that BNSF had provided... misleading information, the exemption is void ab initio. BNSF has filed a combined environmental and historic... DEPARTMENT OF TRANSPORTATION Surface Transportation Board [Docket No. AB 6 (Sub-No. 480X)] BNSF...

Thermal decomposition of the solid phase of nitromethane: ab initio molecular dynamics simulations.

PubMed

Chang, Jing; Lian, Peng; Wei, Dong-Qing; Chen, Xiang-Rong; Zhang, Qing-Ming; Gong, Zi-Zheng

2010-10-29

The Car-Parrinello molecular dynamics simulations were employed to investigate thermal decomposition of the solid nitromethane. It is found that it undergoes chemical decomposition at about 2200 K under ambient pressure. The initiation of reactions involves both proton transfer and commonly known C-N bond cleavage. About 75 species and 100 elementary reactions were observed with the final products being H2O, CO2, N2, and CNCNC. It represents the first complete simulation of solid-phase explosive reactions reported to date, which is of far-reaching implication for design and development of new energetic materials.

Stability of vacancy-type defect clusters in Ni based on first-principles and molecular dynamics simulations

DOE PAGES

Zhao, Shijun; Zhang, Yanwen; Weber, William J.

2017-10-17

Using first-principles calculations based on density-functional theory, the energetics of different vacancy-type defects, including voids, stacking fault tetrahedra (SFT) and vacancy loops, in Ni are investigated. It is found that voids are more stable than SFT at 0 K, which is also the case after taking into account the volumetric strains. By carrying out ab initio molecular dynamics simulations at temperatures up to 1000 K, direct transformations from vacancy loops and voids into SFT are observed. Our results suggest the importance of temperature effects in determining thermodynamic stability of vacancy clusters in face-centered cubic metals.

Defect charge states in Si doped hexagonal boron-nitride monolayer

NASA Astrophysics Data System (ADS)

Mapasha, R. E.; Molepo, M. P.; Andrew, R. C.; Chetty, N.

2016-02-01

We perform ab initio density functional theory calculations to investigate the energetics, electronic and magnetic properties of isolated stoichiometric and non-stoichiometric substitutional Si complexes in a hexagonal boron-nitride monolayer. The Si impurity atoms substituting the boron atom sites SiB giving non-stoichiometric complexes are found to be the most energetically favourable, and are half-metallic and order ferromagnetically in the neutral charge state. We find that the magnetic moments and magnetization energies increase monotonically when Si defects form a cluster. Partial density of states and standard Mulliken population analysis indicate that the half-metallic character and magnetic moments mainly arise from the Si 3p impurity states. The stoichiometric Si complexes are energetically unfavorable and non-magnetic. When charging the energetically favourable non-stoichiometric Si complexes, we find that the formation energies strongly depend on the impurity charge states and Fermi level position. We also find that the magnetic moments and orderings are tunable by charge state modulation q  =  -2, -1, 0, +1, +2. The induced half-metallic character is lost (retained) when charging isolated (clustered) Si defect(s). This underlines the potential of a Si doped hexagonal boron-nitride monolayer for novel spin-based applications.

DSMC study of oxygen shockwaves based on high-fidelity vibrational relaxation and dissociation models

NASA Astrophysics Data System (ADS)

Borges Sebastião, Israel; Kulakhmetov, Marat; Alexeenko, Alina

2017-01-01

This work evaluates high-fidelity vibrational-translational (VT) energy relaxation and dissociation models for pure O2 normal shockwave simulations with the direct simulation Monte Carlo (DSMC) method. The O2-O collisions are described using ab initio state-specific relaxation and dissociation models. The Macheret-Fridman (MF) dissociation model is adapted to the DSMC framework by modifying the standard implementation of the total collision energy (TCE) model. The O2-O2 dissociation is modeled with this TCE+MF approach, which is calibrated with O2-O ab initio data and experimental equilibrium dissociation rates. The O2-O2 vibrational relaxation is modeled via the Larsen-Borgnakke model, calibrated to experimental VT rates. All the present results are compared to experimental data and previous calculations available in the literature. It is found that, in general, the ab initio dissociation model is better than the TCE model at matching the shock experiments. Therefore, when available, efficient ab initio models are preferred over phenomenological models. We also show that the proposed TCE + MF formulation can be used to improve the standard TCE model results when ab initio data are not available or limited.

Multiple time step integrators in ab initio molecular dynamics.

PubMed

Luehr, Nathan; Markland, Thomas E; Martínez, Todd J

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.

21 CFR 701.9 - Exemptions from labeling requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., become void ab initio if the cosmetic comprising such shipment, delivery, or part is adulterated or... a cosmetic under paragraph (a)(2) of this section shall become void ab initio with respect to the...

Near infrared overtone (vOH = 2 ← 0) spectroscopy of Ne-H2O clusters

NASA Astrophysics Data System (ADS)

Ziemkiewicz, Michael P.; Pluetzer, Christian; Wojcik, Michael; Loreau, Jérôme; van der Avoird, Ad; Nesbitt, David J.

2017-03-01

Vibrationally state selective overtone spectroscopy and dynamics of weakly bound Ne-H2O complexes (D0(para) = 31.67 cm-1, D0(ortho) = 34.66 cm-1) are reported for the first time, based on near infrared excitation of van der Waals cluster bands correlating with vOH = 2 ← 0 overtone transitions (|02-⟩←|00+⟩ and |02+⟩ ←|00+⟩ ) out of the ortho (101) and para (000) internal rotor states of the H2O moiety. Quantum theoretical calculations for nuclear motion on a high level ab initio potential energy surface (CCSD(T)/VnZ-f12 (n = 3,4), corrected for basis set superposition error and extrapolated to the complete basis set limit) are employed for assignment of Σ ←Σ ,Π ←Σ , and Σ ←Π infrared bands in the overtone spectra, where Σ ( K = 0) and Π (K = 1) represent approximate projections (K) of the body angular momentum along the Ne-H2O internuclear axis. End-over-end tumbling of the ortho Ne-H2O cluster is evident via rotational band contours observed, with band origins and rotational progressions in excellent agreement with ab initio frequency and intensity predictions. A clear Q branch in the corresponding |02+⟩fΠ (111) ←eΣ (000) para Ne-H2O spectrum provides evidence for a novel e/f parity-dependent metastability in these weakly bound clusters, in agreement with ab initio bound state calculations and attributable to the symmetry blocking of an energetically allowed channel for internal rotor predissociation. Finally, Boltzmann analysis of the rotational spectra reveals anomalously low jet temperatures (Trot ≈ 4(1) K), which are attributed to "evaporative cooling" of weakly bound Ne-H2O clusters and provide support for similar cooling dynamics in rare gas-tagging studies.

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2010 CFR

2010-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

40 CFR 86.442-78 - Denial, revocation, or suspension of certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... ab initio. (d) In any case in which certification of a vehicle is proposed to be withheld, denied... fraud or other misconduct as makes the certification invalid ab initio. (f) The manufacturer may request...

21 CFR 501.100 - Animal food; exemptions from labeling.

Code of Federal Regulations, 2014 CFR

2014-04-01

... become void ab initio if the food comprising such shipment, delivery, or part is adulterated or... a food under paragraph (d)(2) of this section shall become void ab initio with respect to the person...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2014 CFR

2014-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2011 CFR

2011-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2012 CFR

2012-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

21 CFR 801.150 - Medical devices; processing, labeling, or repacking.

Code of Federal Regulations, 2013 CFR

2013-04-01

... such shipment or delivery, or any part thereof, from such establishment, become void ab initio if the...)(2) of this section shall become void ab initio with respect to the person who introduced such...

Many-body optimization using an ab initio monte carlo method.

PubMed

Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

2003-01-01

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Surface energetics and protein-protein interactions: analysis and mechanistic implications

PubMed Central

Peri, Claudio; Morra, Giulia; Colombo, Giorgio

2016-01-01

Understanding protein-protein interactions (PPI) at the molecular level is a fundamental task in the design of new drugs, the prediction of protein function and the clarification of the mechanisms of (dis)regulation of biochemical pathways. In this study, we use a novel computational approach to investigate the energetics of aminoacid networks located on the surface of proteins, isolated and in complex with their respective partners. Interestingly, the analysis of individual proteins identifies patches of surface residues that, when mapped on the structure of their respective complexes, reveal regions of residue-pair couplings that extend across the binding interfaces, forming continuous motifs. An enhanced effect is visible across the proteins of the dataset forming larger quaternary assemblies. The method indicates the presence of energetic signatures in the isolated proteins that are retained in the bound form, which we hypothesize to determine binding orientation upon complex formation. We propose our method, BLUEPRINT, as a complement to different approaches ranging from the ab-initio characterization of PPIs, to protein-protein docking algorithms, for the physico-chemical and functional investigation of protein-protein interactions. PMID:27050828

InP and InAs nanowires hetero- and homojunctions: energetic stability and electronic properties.

PubMed

Dionízio Moreira, M; Venezuela, P; Miwa, R H

2010-07-16

We performed an ab initio total energy investigation, within the density functional theory, of the energetic stability and the electronic properties of hydrogenated InAs/InP nanowire (NW) heterojunctions, as well as InAs and InP homojunctions composed of different structural arrangements, zinc-blend (zb) and wurtzite (w). For InAs/InP NW heterojunctions our results indicate that w and zb NW heterojunctions are quite similar, energetically, for thin NWs. We also examined the robustness of the abrupt interface through an atomic <--> swap at the InAs/InP interface. Our results support the formation of abrupt (non-abrupt) interfaces in w (zb) InAs/InP heterojunctions. Concerning InAs/InP NW-SLs, our results indicate a type-I band alignment, with the energy barrier at the InP layers, in accordance with experimental works. For InAs or InP zb/w homojunctions, we also found a type-I band alignment for thin NWs, however, on increasing the NW diameter both InAs and InP homojunctions exhibit a type-II band alignment.

Dispersion Corrected Structural Properties and Quasiparticle Band Gaps of Several Organic Energetic Solids.

PubMed

Appalakondaiah, S; Vaitheeswaran, G; Lebègue, S

2015-06-18

We have performed ab initio calculations for a series of energetic solids to explore their structural and electronic properties. To evaluate the ground state volume of these molecular solids, different dispersion correction methods were accounted in DFT, namely the Tkatchenko-Scheffler method (with and without self-consistent screening), Grimme's methods (D2, D3(BJ)), and the vdW-DF method. Our results reveal that dispersion correction methods are essential in understanding these complex structures with van der Waals interactions and hydrogen bonding. The calculated ground state volumes and bulk moduli show that the performance of each method is not unique, and therefore a careful examination is mandatory for interpreting theoretical predictions. This work also emphasizes the importance of quasiparticle calculations in predicting the band gap, which is obtained here with the GW approximation. We find that the obtained band gaps are ranging from 4 to 7 eV for the different compounds, indicating their insulating nature. In addition, we show the essential role of quasiparticle band structure calculations to correlate the gap with the energetic properties.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory.

PubMed

Marsalek, Ondrej; Markland, Thomas E

2016-02-07

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.

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)

Concentration dependence of electrical resistivity of binary liquid alloy HgZn: Ab-initio study

NASA Astrophysics Data System (ADS)

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

2013-06-01

The electrical resistivity of HgZn liquid alloy has been made calculated using Troullier and Martins ab-initio pseudopotential as a function of concentration. Hard sphere diameters of Hg and Zn are obtained through the inter-ionic pair potential have been used to calculate partial structure factors. Considering the liquid alloy to be a ternary mixture Ziman's formula for calculating the resistivity of binary liquid alloys, modified for complex formation, has been used. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys.

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.

Accurate ab initio quartic force fields for borane and BeH2

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.

1992-01-01

The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

PubMed

Sumner, Isaiah; Iyengar, Srinivasan S

2007-10-18

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

PubMed Central

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian

2017-01-01

Abstract Motivation: Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. Results: We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Availability and Implementation: Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. Contact: deane@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28453681

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

PubMed Central

Zhang, Yang

2014-01-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. PMID:23760925

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

PubMed

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

2017-05-01

Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

PubMed

Zhang, Yang

2014-02-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials

NASA Astrophysics Data System (ADS)

Prahl, Ulrich; Bleck, Wolfgang; Saeed-Akbari, Alireza

This contribution reports the results of the collaborative research unit SFB 761 "Steel — ab initio", a cooperative project between RWTH Aachen University and the Max-Planck-Institute for Iron Research in Düsseldorf (MPIE) financed by the German Research Foundation (DFG). For the first time, it is exploited how ab initio approaches may lead to a detailed understanding and thus to a specific improvement of material development. The challenge lies in the combination of abstract natural science theories with rather engineering-like established concepts. Aiming at the technological target of the development of a new type of structural materials based on Fe-Mn-C alloys, the combination of ab initio and engineering methods is new, but could be followed quite successfully. Three major topics are treated in this research unit: a) development of a new method for material- and process-development based on ab initio calculations; b) design of a new class of structural materials with extraordinary property combinations; c) acceleration of development time and reduction of experimental efforts and complexity for material- and process-development. In the present work, an overview of the results of the first five years as well as an outlook for the upcoming three-year period is given.

Ab initio DNA synthesis by Bst polymerase in the presence of nicking endonucleases Nt.AlwI, Nb.BbvCI, and Nb.BsmI.

PubMed

Antipova, Valeriya N; Zheleznaya, Lyudmila A; Zyrina, Nadezhda V

2014-08-01

In the absence of added DNA, thermophilic DNA polymerases synthesize double-stranded DNA from free dNTPs, which consist of numerous repetitive units (ab initio DNA synthesis). The addition of thermophilic restriction endonuclease (REase), or nicking endonuclease (NEase), effectively stimulates ab initio DNA synthesis and determines the nucleotide sequence of reaction products. We have found that NEases Nt.AlwI, Nb.BbvCI, and Nb.BsmI with non-palindromic recognition sites stimulate the synthesis of sequences organized mainly as palindromes. Moreover, the nucleotide sequence of the palindromes appeared to be dependent on NEase recognition/cleavage modes. Thus, the heterodimeric Nb.BbvCI stimulated the synthesis of palindromes composed of two recognition sites of this NEase, which were separated by AT-reach sequences or (A)n (T)m spacers. Palindromic DNA sequences obtained in the ab initio DNA synthesis with the monomeric NEases Nb.BsmI and Nt.AlwI contained, along with the sites of these NEases, randomly synthesized sequences consisted of blocks of short repeats. These findings could help investigation of the potential abilities of highly productive ab initio DNA synthesis for the creation of DNA molecules with desirable sequence. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

2014-07-14

The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.

Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.

PubMed

Kramer, Christian; Gedeck, Peter; Meuwly, Markus

2013-03-12

Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol).

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

PubMed

Timko, Jeff; Kuyucak, Serdar

2012-11-28

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

Ab initio molecular dynamics with nuclear quantum effects at classical cost: Ring polymer contraction for density functional theory

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

Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu

Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding asmore » a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.« less

Dangling bond defects in SiC: An ab initio study

NASA Astrophysics Data System (ADS)

Tuttle, Blair R.

2018-01-01

We report first-principles microscopic calculations of the properties of defects with dangling bonds in crystalline 3 C -SiC. Specifically, we focus on hydrogenated Si and C vacancies, divacancies, and multivacancies. The latter is a generic model for an isolated dangling bond within a bulk SiC matrix. Hydrogen serves to passivate electrically active defects to allow the isolation of a single dangling-bond defect. We used hybrid density-functional methods to determine energetics and electrical activity. The present results are compared to previous 3 C -SiC calculations and experiments. Finally, we identify homopolar carbon dangling-bond defects as the leakage causing defects in nanoporous SiC alloys.

Controlling Magnetic and Ferroelectric Order Through Geometry: Synthesis, Ab Initio Theory, Characterization of New Multi-Ferric Fluoride Materials

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

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.

7Be(p,gamma)8B S-factor from Ab Initio Wave Functions

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

Navratil, P; Bertulani, C A; Caurier, E

2006-10-12

There has been a significant progress in ab initio approaches to the structure of light nuclei. Starting from realistic two- and three-nucleon interactions the ab initio no-core shell model (NCSM) predicts low-lying levels in p-shell nuclei. It is a challenging task to extend ab initio methods to describe nuclear reactions. We present here a brief overview of the first steps taken toward nuclear reaction applications. In particular, we discuss our calculation of the {sup 7}Be(p,{gamma}){sup 8}B S-factor. We also present our first results of the {sup 3}He({alpha},{gamma}){sup 7}Be S-factor and of the S-factor of the mirror reaction {sup 3}H({alpha},{gamma}){sup 7}Li.more » The {sup 7}Be(p,{gamma}){sup 8}B and {sup 3}He({alpha},{gamma}){sup 7}Be reactions correspond to the most important uncertainties in solar model predictions of neutrino fluxes.« less

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

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

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

2014-09-01

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

Ab initio Studies of Magnetism in the Iron Chalcogenides FeTe and FeSe

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Misawa, Takahiro; Miyake, Takashi; Imada, Masatoshi

2015-09-01

The iron chalcogenides FeTe and FeSe belong to the family of iron-based superconductors. We study the magnetism in these compounds in the normal state using the ab initio downfolding scheme developed for strongly correlated electron systems. In deriving ab initio low-energy effective models, we employ the constrained GW method to eliminate the double counting of electron correlations originating from the exchange correlations already taken into account in the density functional theory. By solving the derived ab initio effective models, we reveal that the elimination of the double counting is important in reproducing the bicollinear antiferromagnetic order in FeTe, as is observed in experiments. We also show that the elimination of the double counting induces a unique degeneracy of several magnetic orders in FeSe, which may explain the absence of the magnetic ordering. We discuss the relationship between the degeneracy and the recently found puzzling phenomena in FeSe as well as the magnetic ordering found under pressure.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

Materials Screening for the Discovery of New Half-Heuslers: Machine Learning versus ab Initio Methods.

PubMed

Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio

2018-01-18

Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

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

PubMed

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

2016-11-01

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

Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction.

PubMed

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.

Resolution of ab initio shapes determined from small-angle scattering

PubMed Central

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

2016-01-01

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

A coupled channel study of HN2 unimolecular decay based on a global ab initio potential surface

NASA Technical Reports Server (NTRS)

Koizumi, Hiroyasu; Schatz, George C.; Walch, Stephen P.

1991-01-01

The unimolecular decay lifetimes of several vibrational states of HN2 are determined on the basis of an accurate coupled channel dynamics study using a global analytical potential surface. The surface reproduces the ab initio points with an rms error of 0.08 kcal/mol for energies below 20 kcal/mol. Modifications to the potential that describe the effect of improving the basis set in the ab initio calculations are provided. Converged coupled channel calculations are performed for the ground rotational state of HN2 to determine the lifetimes of the lowest ten vibrational states. Only the ground vibrational state (000) and first excited bend (001) are found to have lifetimes longer than 1 ps. The lifetimes of these states are estimated at 3 x 10 to the -9th and 2 x 10 to the -10th s, respectively. Variation of these results with quality of the ab initio calculations is not more than a factor of 5.

A highly accurate ab initio potential energy surface for methane.

PubMed

Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

2016-09-14

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 (12)CH4 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.

Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions

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

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 tomore » 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.« less

Ab Initio Kinetics of Hydrogen Abstraction from Methyl Acetate by Hydrogen, Methyl, Oxygen, Hydroxyl, and Hydroperoxy Radicals.

PubMed

Tan, Ting; Yang, Xueliang; Krauter, Caroline M; Ju, Yiguang; Carter, Emily A

2015-06-18

The kinetics of hydrogen abstraction by five radicals (H, O((3)P), OH, CH3, and HO2) from methyl acetate (MA) is investigated theoretically in order to gain further understanding of certain aspects of the combustion chemistry of biodiesels, such as the effect of the ester moiety. We employ ab initio quantum chemistry methods, coupled cluster singles and doubles with perturbative triples correction (CCSD(T)) and multireference averaged coupled pair functional theory (MRACPF2), to predict chemically accurate reaction energetics. Overall, MRACPF2 predicts slightly higher barrier heights than CCSD(T) for MA + H/CH3/O/OH, but slightly lower barrier heights for hydrogen abstraction by HO2. Based on the obtained reaction energies, we also report high-pressure-limit rate constants using transition state theory (TST) in conjunction with the separable-hindered-rotor approximation, the variable reaction coordinate TST, and the multi-structure all-structure approach. The fitted modified Arrhenius expressions are provided over a temperature range of 250 to 2000 K. The predictions are in good agreement with available experimental results. Abstractions from both of the methyl groups in MA are expected to contribute to consumption of the fuel as they exhibit similar rate coefficients. The reactions involving the OH radical are predicted to have the highest rates among the five abstracting radicals, while those initiated by HO2 are expected to be the lowest.

Molecular electrostatic potential and "atoms-in-molecules" analyses of the interplay between π-hole and lone pair···π/X-H···π/metal···π interactions.

PubMed

Bauzá, Antonio; Seth, Saikat Kumar; Frontera, Antonio

2018-04-05

Using ab initio calculations, we analyze the interplay between π-hole interactions involving the nitro group of 1,4-dinitrobenzene and lone pair···π (lp···π), C-H···π or metal(M)···π noncovalent interactions. Moreover, we have also used 1,4-phenylenebis(phosphine dioxide) for comparison purposes. Interesting cooperativity effects are found when π-hole (F···N,P) and lp···π/C-H···π/M···π interactions coexist in the same supramolecular assembly. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods (RI-MP2/def2-TZVP). A charge density analysis using the Bader's theory of "atoms in molecules" is carried out to characterize the interactions and to analyze their strengthening or weakening depending on the variation of charge density at critical points. The importance of electrostatic effects on the mutual influence of the interaction is studied by means of molecular electrostatic potential calculations. By taking advantage of these computational tools, the present study examines interplay of these interactions. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Design of two-photon molecular tandem architectures for solar cells by ab initio theory† †Electronic supplementary information (ESI) available: Visualizations of molecular orbitals, one-particle mechanisms and a table with Kohn–Sham eigenvalues. See DOI: 10.1039/c4sc03835e

PubMed Central

Garcia-Lastra, Juan M.; De La Torre, Gema; Himpsel, F. J.; Rubio, Angel

2015-01-01

An extensive database of spectroscopic properties of molecules from ab initio calculations is used to design molecular complexes for use in tandem solar cells that convert two photons into a single electron–hole pair, thereby increasing the output voltage while covering a wider spectral range. Three different architectures are considered: the first two involve a complex consisting of two dye molecules with appropriately matched frontier orbitals, connected by a molecular diode. Optimized combinations of dye molecules are determined by taking advantage of our computational database of the structural and energetic properties of several thousand porphyrin dyes. The third design is a molecular analogy of the intermediate band solar cell, and involves a single dye molecule with strong intersystem crossing to ensure a long lifetime of the intermediate state. Based on the calculated energy levels and molecular orbitals, energy diagrams are presented for the individual steps in the operation of such tandem solar cells. We find that theoretical open circuit voltages of up to 1.8 V can be achieved using these tandem designs. Questions about the practical implementation of prototypical devices, such as the synthesis of the tandem molecules and potential loss mechanisms, are addressed. PMID:29142685

Semiempirical prediction of protein folds

NASA Astrophysics Data System (ADS)

Fernández, Ariel; Colubri, Andrés; Appignanesi, Gustavo

2001-08-01

We introduce a semiempirical approach to predict ab initio expeditious pathways and native backbone geometries of proteins that fold under in vitro renaturation conditions. The algorithm is engineered to incorporate a discrete codification of local steric hindrances that constrain the movements of the peptide backbone throughout the folding process. Thus, the torsional state of the chain is assumed to be conditioned by the fact that hopping from one basin of attraction to another in the Ramachandran map (local potential energy surface) of each residue is energetically more costly than the search for a specific (Φ, Ψ) torsional state within a single basin. A combinatorial procedure is introduced to evaluate coarsely defined torsional states of the chain defined ``modulo basins'' and translate them into meaningful patterns of long range interactions. Thus, an algorithm for structure prediction is designed based on the fact that local contributions to the potential energy may be subsumed into time-evolving conformational constraints defining sets of restricted backbone geometries whereupon the patterns of nonbonded interactions are constructed. The predictive power of the algorithm is assessed by (a) computing ab initio folding pathways for mammalian ubiquitin that ultimately yield a stable structural pattern reproducing all of its native features, (b) determining the nucleating event that triggers the hydrophobic collapse of the chain, and (c) comparing coarse predictions of the stable folds of moderately large proteins (N~100) with structural information extracted from the protein data bank.

Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

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.

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

Sano, Yukio; Sano, Tomokazu

A quadratic equation for the temperature-independent Grueneisen coefficient {gamma} was derived by a method in which the Walsh-Christian and Mie-Grueneisen equations are combined. Some previously existing ab initio temperature Hugoniots for hexagonal close-packed solid Fe are inaccurate because the constant-volume specific heats on the Hugoniots CVH, which are related uniquely to the solutions of the quadratic equation, have values that are too small. A CVH distribution in the solid phase range was demonstrated to agree approximately with a previous ab initio distribution. In contrast, the corresponding {gamma} distribution was significantly different from the ab initio distribution in the lower pressuremore » region. The causes of these disagreements are clarified.« less

Ab initio study of collective excitations in a disparate mass molten salt.

PubMed

Bryk, Taras; Klevets, Ivan

2012-12-14

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

PubMed

Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

2015-02-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

NASA Astrophysics Data System (ADS)

Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

2018-06-01

We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

NASA Astrophysics Data System (ADS)

Saieswari, A.; Kumar, Sanjay

2007-12-01

An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

Ab initio calculation of one-nucleon halo states

NASA Astrophysics Data System (ADS)

Rodkin, D. M.; Tchuvil'sky, Yu M.

2018-02-01

We develop an approach to microscopic and ab initio description of clustered systems, states with halo nucleon and one-nucleon resonances. For these purposes a basis combining ordinary shell-model components and cluster-channel terms is built up. The transformation of clustered wave functions to the uniform Slater-determinant type is performed using the concept of cluster coefficients. The resulting basis of orthonormalized wave functions is used for calculating the eigenvalues and the eigenvectors of Hamiltonians built in the framework of ab initio approaches. Calculations of resonance and halo states of 5He, 9Be and 9B nuclei demonstrate that the approach is workable and labor-saving.

40 CFR 86.096-7 - Maintenance of records; submittal of information; right of entry.

Code of Federal Regulations, 2010 CFR

2010-07-01

...] (ii) EPA may void ab initio a certificate for a 1994 or 1995 model year light-duty vehicle or light... Administrator upon request. (iii) Any voiding ab initio of a certificate under § 86.091-7(c)(6) and paragraph (h...

40 CFR 80.607 - What are the requirements for obtaining an exemption for diesel fuel or ECA marine fuel used for...

Code of Federal Regulations, 2010 CFR

2010-07-01

... section, will cause the exemption to be void ab initio. (6) If any information required under paragraph (c... void ab initio, and may make the party liable for a violation of this subpart. (f) Effects of exemption...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

The Band Structure of Polymers: Its Calculation and Interpretation. Part 2. Calculation.

ERIC Educational Resources Information Center

Duke, B. J.; O'Leary, Brian

1988-01-01

Details ab initio crystal orbital calculations using all-trans-polyethylene as a model. Describes calculations based on various forms of translational symmetry. Compares these calculations with ab initio molecular orbital calculations discussed in a preceding article. Discusses three major approximations made in the crystal case. (CW)

Ab initio calculations of the lattice dynamics of silver halides

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2011 CFR

2011-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

40 CFR 90.108 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... the certificate may be determined to be void ab initio. (2) The manufacturer shall bear the burden of... certificates that failure to meet these conditions may result in suspension or revocation or the voiding ab initio of the certificate. [60 FR 34598, July 3, 1995, as amended at 64 FR 15238, Mar. 30, 1999] ...

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

PubMed

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 CF3X-B that involve one trifluorohalomethane CF3X (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 (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). 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.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

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

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw

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-pairmore » (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.« less

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).

Ab initio calculation of the shear viscosity of neon in the liquid and hypercritical state over a wide pressure and temperature range

NASA Astrophysics Data System (ADS)

Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc

1992-08-01

The shear viscosity is calculated ab initio for the liquid and hypercritical state, i.e. a previously published potential for Ne 2, obtained from ab initio calculations including electron correlation, is used in classical equilibrium molecular dynamics simulations to obtain the shear viscosity from a Green-Kubo integral. The quality of the results is quite uniform over a large pressure range up to 1000 MPa and a wide temperature range from 26 to 600 K. In most cases the calculated shear viscosity deviates by less than 10% from the experimental value, in general the error being only a few percent.

Ab initio determination of mode coupling in HSSH - The torsional splitting in the first excited S-S stretching state

NASA Technical Reports Server (NTRS)

Herbst, Eric; Winnewisser, G.; Yamada, K. M. T.; Defrees, D. J.; Mclean, A. D.

1989-01-01

A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.

Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations

NASA Astrophysics Data System (ADS)

Fujimori, Mitsuki; Sogawa, Haruki; Ota, Shintaro; Karpov, Pavel; Shulga, Sergey; Blume, Yaroslav; Kurita, Noriyuki

2018-01-01

Filamentous temperature-sensitive Z (FtsZ) protein plays essential role in bacteria cell division, and its inhibition prevents Mycobacteria reproduction. Here we adopted curcumin derivatives as candidates of novel inhibitors and investigated their specific interactions with FtsZ, using ab initio molecular simulations based on protein-ligand docking, classical molecular mechanics and ab initio fragment molecular orbital (FMO) calculations. Based on FMO calculations, we specified the most preferable site of curcumin binding to FtsZ and highlighted the key amino acid residues for curcumin binding at an electronic level. The result will be useful for proposing novel inhibitors against FtsZ based on curcumin derivatives.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

PubMed Central

Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

2015-01-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744

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

PubMed

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

2017-12-01

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

AB INITIO Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions

NASA Astrophysics Data System (ADS)

Goldman, Nir; Fried, Laurence E.; Mundy, Christopher J.; Kuo, I.-F. William; Curioni, Alessandro; Reed, Evan J.

2007-12-01

We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.

One Size Fits All? Learning Conditions and Working Memory Capacity in "Ab Initio" Language Development

ERIC Educational Resources Information Center

Sanz, Cristina; Lin, Hui-Ju; Lado, Beatriz; Stafford, Catherine A.; Bowden, Harriet W.

2016-01-01

The article summarizes results from two experimental studies (N = 23, N = 21) investigating the extent to which working memory capacity (WMC) intervenes in "ab initio" language development under two pedagogical conditions [± grammar lesson + input-based practice + explicit feedback]. The linguistic target is the use of morphosyntax to…

Ab initio theory of noble gas atoms in bcc transition metals

DOE PAGES

Jiang, Chao; Zhang, Yongfeng; Gao, Yipeng; ...

2018-01-01

Systematic ab initio calculations based on density functional theory have been performed to gain fundamental understanding of the interactions between noble gas atoms (He, Ne, Ar and Kr) and bcc transition metals in groups 5B (V, Nb and Ta), 6B (Cr, Mo and W) and 8B (Fe).

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…

Infrared Emission Spectrum of the Hydroxyl Radical: A Novel Experiment in Molecular Spectroscopy.

ERIC Educational Resources Information Center

Henderson, Giles; And Others

1982-01-01

Describes an experiment in which parameters from an "ab-initio" potential are used to calculate vibrational-rotational energy levels and construct a "stick spectrum" for the overtone emission of the hydroxyl radical. Provides background information on ab-initio spectrum, experimental procedures, and analysis of data. (Author/JN)

Vibrational modes in thymine molecule from an ab initio MO calculation

NASA Astrophysics Data System (ADS)

Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ueda, Toyotoshi; Ushizawa, Koichi; Ito, Gen; Kumakura, Akiko; Tsuboi, Masamichi

1997-03-01

Ab initio self-consistent field molecular orbital (SCF MO) calculations have been made of the thymine molecule for the equilibrium geometry, harmonic force constants, vibrational frequencies, vibrational modes, infrared intensities, and Raman intensities. The results have been correlated with the observed Raman and infrared spectra of thymine crystalline powder.

NSSEFF COMPUTATIONAL AND THEORETICAL DESIGN OF PHOTO AND MECHANORESPONSIVE MOLECULAR DEVICES

DTIC Science & Technology

2016-11-10

R. McGibbon, F. Liu, V.S. Pande and T.J. Martinez, "Discovering Chemistry with an Ab Initio Nanoreactor," Nature Chem. 6, 1044 (2014...Pande and T.J. Martinez, "Discovering Chemistry with an Ab Initio Nanoreactor," Nature Chem. 6, 1044 (2014). New discoveries, inventions, or patent

Ab initio calculations for industrial materials engineering: successes and challenges.

PubMed

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.

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.

Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

2002-01-01

The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

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

PubMed Central

Xu, Dong; Zhang, Yang

2013-01-01

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

Ab initio parameterization of a charge optimized many-body forcefield for Si-SiO2: Validation and thermal transport in nanostructures.

PubMed

France-Lanord, Arthur; Soukiassian, Patrick; Glattli, Christian; Wimmer, Erich

2016-03-14

In an effort to extend the reach of current ab initio calculations to simulations requiring millions of configurations for complex systems such as heterostructures, we have parameterized the third-generation Charge Optimized Many-Body (COMB3) potential using solely ab initio total energies, forces, and stress tensors as input. The quality and the predictive power of the new forcefield are assessed by computing properties including the cohesive energy and density of SiO2 polymorphs, surface energies of alpha-quartz, and phonon densities of states of crystalline and amorphous phases of SiO2. Comparison with data from experiments, ab initio calculations, and molecular dynamics simulations using published forcefields including BKS (van Beest, Kramer, and van Santen), ReaxFF, and COMB2 demonstrates an overall improvement of the new parameterization. The computed temperature dependence of the thermal conductivity of crystalline alpha-quartz and the Kapitza resistance of the interface between crystalline Si(001) and amorphous silica is in excellent agreement with experiment, setting the stage for simulations of complex nanoscale heterostructures.

An ab-initio study of the energetics and geometry of sulfide, sulfite and sulfate incorporation into apatite: The thermodynamic basis for using this system as an oxybarometer

NASA Astrophysics Data System (ADS)

Kim, Y.; Konecke, B.; Fiege, A.; Simon, A. C.; Becker, U.

2017-12-01

We use ab-initio calculations to investigate the energetics and geometry of incorporation of S with its oxidation states S6+, S4+, and S2- into the apatite end-members fluor-, chlor-, and hydroxylapatite, [Ca10(PO4)6(F,Cl,OH)2]. The reaction energy of the balanced equation indicates the stability of the modeled S-incorporated apatite relative to the host apatite, the source, and sink phases. One possible coupled substitution mechanism involves the replacement of La3+ + PO43- ↔ Ca2+ + SO42-. Our results show that the incorporation of SO42- into La- and Na-bearing apatite, Ca8NaLa(PO4)6(F,Cl,OH)2, is energetically favored over the incorporation into La- and Si-bearing apatite, Ca9La(PO4)5(SiO4)(F,Cl,OH)2. Co-incorporation of SO42- and SO32- is energetically favored when the lone pair electrons of SO32- face towards the anion column site, compared to facing away from it. Full or partial incorporation of S2- is favored on the column anion site in the form of [Ca10(PO4)6S] and [Ca20(PO4)12SX2)], where X = F, Cl, or OH. Upon full incorporation (i.e., replacing all column ions by sulfide ions), S2- is positioned in the anion column at z = 0.5 (half way between the mirror planes at z = 1/4 and z = 3/4) in the energy-optimized structure. The calculated energies for partial incorporation of S2- demonstrate that in an energy-optimized structure, S2- is displaced from the mirror plane at z = 1/4 or 3/4, by 1.0 to 1.6 Å, depending on the surrounding species (F-, Cl- or OH-); however, the probability for S2- to be incorporated into the apatite structure is highest for chlorapatite end-members. Our results describe energetically feasible incorporation mechanisms for all three oxidations states of S (S6+, S4+, S2-) in apatite, along with structural distortion and concurring electronic structure changes. These observations are consistent with recently published experimental results (Konecke et al. 2017) that demonstrate S6+, S4+ and S2- incorporation into apatite, where the ratio of S6+/∑S in apatite is controlled by oxygen fugacity (fO2). The new computational results coupled with published experimental data provide the basis for using S in apatite as a geochemical proxy to trace variations in oxygen fugacity of magmatic and magmatic-hydrothermal systems.

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

PubMed

Qu, Chen; Bowman, Joel M

2018-05-17

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH) 2 and (DCOOH) 2 , using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm -1 . Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm -1 . In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

Ab Initio and Improved Empirical Potentials for the Calculation of the Anharmonic Vibrational States and Intramolecular Mode Coupling of N-Methylacetamide

NASA Technical Reports Server (NTRS)

Gregurick, Susan K.; Chaban, Galina M.; Gerber, R. Benny; Kwak, Dochou (Technical Monitor)

2001-01-01

The second-order Moller-Plesset ab initio electronic structure method is used to compute points for the anharmonic mode-coupled potential energy surface of N-methylacetamide (NMA) in the trans(sub ct) configuration, including all degrees of freedom. The vibrational states and the spectroscopy are directly computed from this potential surface using the Correlation Corrected Vibrational Self-Consistent Field (CC-VSCF) method. The results are compared with CC-VSCF calculations using both the standard and improved empirical Amber-like force fields and available low temperature experimental matrix data. Analysis of our calculated spectroscopic results show that: (1) The excellent agreement between the ab initio CC-VSCF calculated frequencies and the experimental data suggest that the computed anharmonic potentials for N-methylacetamide are of a very high quality; (2) For most transitions, the vibrational frequencies obtained from the ab initio CC-VSCF method are superior to those obtained using the empirical CC-VSCF methods, when compared with experimental data. However, the improved empirical force field yields better agreement with the experimental frequencies as compared with a standard AMBER-type force field; (3) The empirical force field in particular overestimates anharmonic couplings for the amide-2 mode, the methyl asymmetric bending modes, the out-of-plane methyl bending modes, and the methyl distortions; (4) Disagreement between the ab initio and empirical anharmonic couplings is greater than the disagreement between the frequencies, and thus the anharmonic part of the empirical potential seems to be less accurate than the harmonic contribution;and (5) Both the empirical and ab initio CC-VSCF calculations predict a negligible anharmonic coupling between the amide-1 and other internal modes. The implication of this is that the intramolecular energy flow between the amide-1 and the other internal modes may be smaller than anticipated. These results may have important implications for the anharmonic force fields of peptides, for which N-methylacetamide is a model.

Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands.

PubMed

Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A

2017-02-14

Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16 O 3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV 3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μm range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν 3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm -1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

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

PubMed

Kawashima, Yukio; Tachikawa, Masanori

2014-01-14

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

Serious Gaming for Test & Evaluation of Clean-Slate (Ab Initio) National Airspace System (NAS) Designs

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 contains the system and other systems evolves with the CAS as well. The effects of the emerging adaptation and co-evolution are difficult to capture with only combined mathematical and computational experimentation. Therefore, an ab initio flight simulation environment must accommodate individual vehicles, groups of self-organizing vehicles, and large-scale infrastructure behavior. Inspired by Massively Multiplayer Online Role Playing Games (MMORPG) and Serious Gaming, the proposed ab initio simulation environment is similar to online gaming environments in which player participants interact with each other, affect their environment, and expect the simulation to persist and change regardless of any individual player's active participation.

Ab initio modeling of zincblende AlN layer in Al-AlN-TiN multilayers

DOE PAGES

Yadav, S. K.; Wang, J.; Liu, X. -Y.

2016-06-13

An unusual growth mechanism of metastable zincblende AlN thin film by diffusion of nitrogen atoms into Al lattice is established. Using first-principles density functional theory, we studied the possibility of thermodynamic stability of AlN as a zincblende phase due to epitaxial strains and interface effect, which fails to explain the formation of zincblende AlN. We then compared the formation energetics of rocksalt and zincblende AlN in fcc Al through direct diffusion of nitrogen atoms to Al octahedral and tetrahedral interstitials. Furthermore, the formation of a zincblende AlN thin film is determined to be a kinetically driven process, not a thermodynamicallymore » driven process.« less

Theoretical Investigation of the NO3 Radical Addition to Double Bonds of Limonene

PubMed Central

Jiang, Lei; Wang, Wei; Xu, Yi-Sheng

2009-01-01

The addition reactions of NO3 to limonene have been investigated using ab initio methods. Six different possibilities for NO3 addition to the double bonds, which correspond to the two C–C double bonds (endocyclic or exocyclic) have been considered. The negative activation energies for the addition of NO3 to limonene are calculated and the energies of NO3-limonene radical adducts are found to be 14.55 to 20.17 kcal mol-1 more stable than the separated NO3 and limonene at the CCSD(T)/6–31G(d) + CF level. The results also indicate that the endocyclic addition reaction is more energetically favorable than the exocyclic one. PMID:19865516

Pressure Induced Phase Transition and Electronic Properties of 1d ZnO Nanocrystal: AN AB INITIO Study

NASA Astrophysics Data System (ADS)

Srivastava, Anurag; Tyagi, Neha

2012-10-01

We have analyzed the one-dimensional (1D) ZnO nanocrystals in its wurtzite (B4); zinc-blende (B3) and rocksalt (B1) type phases, by means of density functional theory (DFT) calculations. The energetic stability of nanocrystal has been analyzed using Revised Perdew-Burke-Ernzerhof (revPBE) type parameterized GGA potential. The B3 type phase is most stable amongst other phases of nanocrystals. The computation of ground state properties for all the phases of ZnO nanocrystals finds that the bulk modulus are smaller than their bulk counterpart, in turn softening the material at reduced dimensions. The electronic band structure analysis confirms the semiconducting nature of B4 type phase whereas other two are metallic.

Correlation study of sodium-atom chemisorption on the GaAs(110) surface

NASA Astrophysics Data System (ADS)

Song, K. M.; Khan, D. C.; Ray, A. K.

1994-01-01

Different possible adsorption sites of sodium atoms on a gallium arsenide surface have been investigated using ab initio self-consistent unrestricted Hartree-Fock total-energy cluster calculations with Hay-Wadt effective core potentials. The effects of electron correlation have been included by invoking the concepts of many-body perturbation theory and are found to be highly significant. We find that the Na-atom adsorption at a site modeled with an NaGa5As4H12 cluster is most favored energetically followed by Na adsorption at the site modeled with the NaGa4As5H12 cluster. The effects of charge transfer from Na to the GaAs surface as also possibilities of metallization are also analyzed and discussed.

Full-dimensional analytical potential energy surface describing the gas-phase Cl + C2H6 reaction and kinetics study of rate constants and kinetic isotope effects.

PubMed

Rangel, Cipriano; Espinosa-Garcia, Joaquin

2018-02-07

Within the Born-Oppenheimer approximation a full-dimensional analytical potential energy surface, PES-2017, was developed for the gas-phase hydrogen abstraction reaction between the chlorine atom and ethane, which is a nine body system. This surface presents a valence-bond/molecular mechanics functional form dependent on 60 parameters and is fitted to high-level ab initio calculations. This reaction presents little exothermicity, -2.30 kcal mol -1 , with a low height barrier, 2.44 kcal mol -1 , and intermediate complexes in the entrance and exit channels. We found that the energetic description was strongly dependent on the ab initio level used and it presented a very flat topology in the entrance channel, which represents a theoretical challenge in the fitting process. In general, PES-2017 reproduces the ab initio information used as input, which is merely a test of self-consistency. As a first test of the quality of the PES-2017, a theoretical kinetics study was performed in the temperature range 200-1400 K using two approaches, i.e. the variational transition-state theory and quasi-classical trajectory calculations, with spin-orbit effects. The rate constants show reasonable agreement with experiments in the whole temperature range, with the largest differences at the lowest temperatures, and this behaviour agrees with previous theoretical studies, thus indicating the inherent difficulties in the theoretical simulation of the kinetics of the title reaction. Different sources of error were analysed, such as the limitations of the PES and theoretical methods, recrossing effects, and the tunnelling effect, which is negligible in this reaction, and the manner in which the spin-orbit effects were included in this non-relativistic study. We found that the variation of spin-orbit coupling along the reaction path, and the influence of the reactivity of the excited Cl( 2 P 1/2 ) state, have relative importance, but do not explain the whole discrepancy. Finally, the activation energy and the kinetics isotope effects reproduce the experimental information.

Vacuum Ultraviolet Laser Probe of Chemical Dynamics of Aerospace Relevance

DTIC Science & Technology

2012-09-12

carbide cation”, J. Phys. Chem. A (invited), 113, 4242 (2009). 5. Kai-Chung Lau , Yih-Chung Chang, Chow-Sheng Lam , and C. Y. Ng, “High-level ab...Chem. A (invited), 113, 14321 (2009). 6. Kai-Chung Lau , Yih-Chung Chang, Chow-Sheng Lam , and C. Y. Ng, “High-level ab initio predictions of the...VI. Selected scientific findings 1. Kai-Chung Lau , Yih-Chung Chang, Xiaoyu Shi, and C. Y. Ng, “High-level ab initio predictions of the ionization

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.

{bold {ital Ab initio}} studies of the structural and electronic properties of solid cubane

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

Richardson, S.L.; Martins, J.L.

1998-12-01

In this paper, we report {ital ab initio} calculation of the structural and electronic properties of solid cubane (s-C{sub 8}H{sub 8}) in the local-density approximation. By using an {ital ab initio} constant pressure extended molecular dynamics method with variable cell shape proposed by Wentzcovitch, Martins, and Price, we compute a lattice parameter {ital a} and a bond angle {alpha} for the rhombohedral Bravais lattice and compare it with experimental x-ray data. We obtain bond lengths for the mononuclear C{sub 8}H{sub 8} unit of basis atoms, as well as a density of states and heat of formation. {copyright} {ital 1998} {italmore » The American Physical Society}« less

Einstein coefficients and oscillator strengths for low lying state of CO molecules

NASA Astrophysics Data System (ADS)

Swer, S.; Syiemiong, A.; Ram, M.; Jha, A. K.; Saxena, A.

2018-04-01

Einstein Coefficients and Oscillator Strengths for different state of CO molecule have been calculated using LEROY'S LEVEL program and MOLCAS ab initio code. Using the wave function derived from Morse potential and transition dipole moment obtained from ab initio calculation, The potential energy functions were computed for these states using the spectroscopic constants. The Morse potential of these states and electronic transition dipole moment of the transition calculated in a recent ab initio study have been used in LEVEL program to produce transition dipole matrix element for a large number of bands. Einstein Coefficients have also been used to compute the radiative lifetimes of several vibrational levels and the calculated values are compared with other theoretical results and experimental values.

A first-principles comparative study of lithium, sodium, and magnesium storage in pure and gallium-doped germanium: Competition between interstitial and substitutional sites

NASA Astrophysics Data System (ADS)

Legrain, Fleur; Manzhos, Sergei

2017-01-01

Thermodynamics and kinetics of Li, Na, and Mg storage in Ge are studied ab initio. The most stable configurations can consist of tetrahedral, substitutional, or a combination of the two types of sites. In the dilute limit, Li and Na prefer interstitial, while Mg prefers substitutional sites. At higher concentrations of Li, Na, and Mg, there is a combination of interstitial and substitutional sites. This is an important finding, as most previous ab initio studies of alloying type electrode materials ignored substitutional sites. Insertion energies computed at dilute concentration (x = 1/64) show that Na and Mg insertion are not thermodynamically favored in Ge vs. the formation of bulk Na and Mg, as opposed to Li insertion which is favored. We investigate the effect of p-doping of Ge (with Ga) on the thermodynamics and find that it considerably lowers the defect formation energies associated with the insertion of Li/Na/Mg at tetrahedral sites. On the other hand, the energetics associated with Li/Na/Mg insertion at substitutional sites are not significantly affected. In addition, we compute the migration energy barriers for Li/Na/Mg diffusion between two tetrahedral sites (0.38/0.79/0.66 eV), between two substitutional sites (0.77/0.93/1.83 eV), and between two sites of different types (2.15/1.75/0.85 eV).

A first-principles comparative study of lithium, sodium, and magnesium storage in pure and gallium-doped germanium: Competition between interstitial and substitutional sites.

PubMed

Legrain, Fleur; Manzhos, Sergei

2017-01-21

Thermodynamics and kinetics of Li, Na, and Mg storage in Ge are studied ab initio. The most stable configurations can consist of tetrahedral, substitutional, or a combination of the two types of sites. In the dilute limit, Li and Na prefer interstitial, while Mg prefers substitutional sites. At higher concentrations of Li, Na, and Mg, there is a combination of interstitial and substitutional sites. This is an important finding, as most previous ab initio studies of alloying type electrode materials ignored substitutional sites. Insertion energies computed at dilute concentration (x = 1/64) show that Na and Mg insertion are not thermodynamically favored in Ge vs. the formation of bulk Na and Mg, as opposed to Li insertion which is favored. We investigate the effect of p-doping of Ge (with Ga) on the thermodynamics and find that it considerably lowers the defect formation energies associated with the insertion of Li/Na/Mg at tetrahedral sites. On the other hand, the energetics associated with Li/Na/Mg insertion at substitutional sites are not significantly affected. In addition, we compute the migration energy barriers for Li/Na/Mg diffusion between two tetrahedral sites (0.38/0.79/0.66 eV), between two substitutional sites (0.77/0.93/1.83 eV), and between two sites of different types (2.15/1.75/0.85 eV).

Ab initio theory of noble gas atoms in bcc transition metals.

PubMed

Jiang, Chao; Zhang, Yongfeng; Gao, Yipeng; Gan, Jian

2018-06-18

Systematic ab initio calculations based on density functional theory have been performed to gain fundamental understanding of the interactions between noble gas atoms (He, Ne, Ar and Kr) and bcc transition metals in groups 5B (V, Nb and Ta), 6B (Cr, Mo and W) and 8B (Fe). Our charge density analysis indicates that the strong polarization of nearest-neighbor metal atoms by noble gas interstitials is the electronic origin of their high formation energies. Such polarization becomes more significant with an increasing gas atom size and interstitial charge density in the host bcc metal, which explains the similar trend followed by the unrelaxed formation energies of noble gas interstitials. Upon allowing for local relaxation, nearby metal atoms move farther away from gas interstitials in order to decrease polarization, albeit at the expense of increasing the elastic strain energy. Such atomic relaxation is found to play an important role in governing both the energetics and site preference of noble gas atoms in bcc metals. Our most notable finding is that the fully relaxed formation energies of noble gas interstitials are strongly correlated with the elastic shear modulus of the bcc metal, and the physical origin of this unexpected correlation has been elucidated by our theoretical analysis based on the effective-medium theory. The kinetic behavior of noble gas atoms and their interaction with pre-existing vacancies in bcc transition metals have also been discussed in this work.

Real-time ab initio simulations of excited-state dynamics in nanostructures

NASA Astrophysics Data System (ADS)

Tomanek, David

2007-03-01

Combining time-dependent ab initio density functional calculations for electrons with molecular dynamics simulations for ions, we investigate the effect of excited-state dynamics in nanostructures. In carbon nanotubes, we find electronic excitations to last for a large fraction of a picosecond. The de-excitation process is dominated by coupling to other electronic degrees of freedom during the first few hundred femtoseconds. Later, the de-excitation process becomes dominated by coupling to ionic motion. The onset point and damping rate in that regime change with initial ion velocities, a manifestation of temperature dependent electron-phonon coupling. Considering the fact that the force field in the electronically excited state differs significantly from the ground state, as reflected in the Franck-Condon effect, atomic bonds can easily be broken or restored during the relatively long lifetime of electronic excitations. This effect can be utilized in a ``photo-surgery" of nanotubes, causing structural self-healing at vacancy sites or selective de-oxidation processes induced by photo-absorption. Also, electronic excitations are a key ingredient for the understanding of sputtering processes in nanostructures, induced by energetic collisions with ions. Yoshiyuki Miyamoto, Angel Rubio, and David Tomanek, Phys. Rev. Lett. 97, 126104 (2006). Yoshiyuki Miyamoto, Savas Berber, Mina Yoon, Angel Rubio, and David Tomanek, Chem. Phys. Lett. 392, 209 (2004). Yoshiyuki Miyamoto, Noboru Jinbo, Hisashi Nakamura, Angel Rubio, and David Tomanek, Phys. Rev. B 70, 233408 (2004). Yoshiyuki Miyamoto, Arkady Krasheninnikov, and David Tomanek (in preparation).

Molecular dynamics modeling of atomic displacement cascades in 3C-SiC: Comparison of interatomic potentials

NASA Astrophysics Data System (ADS)

Samolyuk, G. D.; Osetsky, Y. N.; Stoller, R. E.

2015-10-01

We used molecular dynamics modeling of atomic displacement cascades to characterize the nature of primary radiation damage in 3C-SiC. We demonstrated that the most commonly used interatomic potentials are inconsistent with ab initio calculations of defect energetics. Both the Tersoff potential used in this work and a modified embedded-atom method potential reveal a barrier to recombination of the carbon interstitial and carbon vacancy which is much higher than the density functional theory (DFT) results. The barrier obtained with a newer potential by Gao and Weber is closer to the DFT result. This difference results in significant differences in the cascade production of point defects. We have completed both 10 keV and 50 keV cascade simulations in 3C-SiC at a range of temperatures. In contrast to the Tersoff potential, the Gao-Weber potential produces almost twice as many C vacancies and interstitials at the time of maximum disorder (∼0.2 ps) but only about 25% more stable defects at the end of the simulation. Only about 20% of the carbon defects produced with the Tersoff potential recombine during the in-cascade annealing phase, while about 60% recombine with the Gao-Weber potential. The Gao-Weber potential appears to give a more realistic description of cascade dynamics in SiC, but still has some shortcomings when the defect migration barriers are compared to the ab initio results.

Determination of Structures and Energetics of Small- and Medium-Sized One-Carbon-Bridged Twisted Amides using ab Initio Molecular Orbital Methods: Implications for Amidic Resonance along the C-N Rotational Pathway.

PubMed

Szostak, Roman; Aubé, Jeffrey; Szostak, Michal

2015-08-21

Twisted amides containing nitrogen at the bridgehead position are attractive practical prototypes for the investigation of the electronic and structural properties of nonplanar amide linkages. Changes that occur during rotation around the N-C(O) axis in one-carbon-bridged twisted amides have been studied using ab initio molecular orbital methods. Calculations at the MP2/6-311++G(d,p) level performed on a set of one-carbon-bridged lactams, including 20 distinct scaffolds ranging from [2.2.1] to [6.3.1] ring systems, with the C═O bond on the shortest bridge indicate significant variations in structures, resonance energies, proton affinities, core ionization energies, frontier molecular orbitals, atomic charges, and infrared frequencies that reflect structural changes corresponding to the extent of resonance stabilization during rotation along the N-C(O) axis. The results are discussed in the context of resonance theory and activation of amides toward N-protonation (N-activation) by distortion. This study demonstrates that one-carbon-bridged lactams-a class of readily available, hydrolytically robust twisted amides-are ideally suited to span the whole spectrum of the amide bond distortion energy surface. Notably, this study provides a blueprint for the rational design and application of nonplanar amides in organic synthesis. The presented findings strongly support the classical amide bond resonance model in predicting the properties of nonplanar amides.

Ab initio calculation of 1H, 17O, 27Al and 29Si NMR parameters, vibrational frequencies and bonding energetics in hydrous silica and Na-aluminosilicate glasses

NASA Astrophysics Data System (ADS)

Kubicki, J. D.; Sykes, D. G.

2004-10-01

Ab initio, molecular orbital (MO) calculations were performed on model systems of SiO 2, NaAlSi 3O 8 (albite), H 2O-SiO 2 and H 2O-NaAlSi 3O 8 glasses. Model nuclear magnetic resonance (NMR) isotropic chemical shifts (δ iso) for 1H, 17O, 27Al and 29Si are consistent with experimental data for the SiO 2, NaAlSi 3O 8, H 2O-SiO 2 systems where structural interpretations of the NMR peak assignments are accepted. For H 2O-NaSi 3AlO 8 glass, controversy has surrounded the interpretation of NMR and infrared (IR) spectra. Calculated δ iso1H, δ iso17O, δ iso27Al and δ iso29Si are consistent with the interpretation of Kohn et al. (1992) that Si-(OH)-Al linkages are responsible for the observed peaks in hydrous Na-aluminosilicate glasses. In addition, a theoretical vibrational frequency associated with the Kohn et al. (1992) model agrees well with the observed shoulder near 900 cm -1 in the IR and Raman spectra of hydrous albite glasses. MO calculations suggest that breaking this Si-(OH)-Al linkage requires ˜+56 to +82 kJ/mol which is comparable to the activation energies for viscous flow in hydrous aluminosilicate melts.

Penning ionization and ion fragmentation of formamide HCONH2 by He∗, Ne∗, and Ar∗ in molecular beams

NASA Astrophysics Data System (ADS)

Madison, Tamika A.; Siska, P. E.

2009-10-01

Mass spectra from Penning ionization by metastable atom bombardment (MAB) in the title system at kinetic energies near 1 kcal/mol are reported. The experiments employ a supersonic excited noble gas beam crossing an effusive beam of formamide vapor. Product ions are extracted perpendicular to the plane of the beams, analyzed by a quadrupole mass filter, and counted by a scintillation-type ion counter. Relative to 70 eV electron impact, the He∗ and Ne∗ spectra show more extensive breakage of C-N and C-H bonds despite the smaller available energy, while the Ar∗ spectrum shows only the molecular ion (m /z 45), H atom elimination (44), and the decarbonylation products CO+NH3+ (17). Fragmentation in the latter system has been analyzed using a combination of ab initio calculations and Rice-Ramsperger-Kassel-Marcus theory with tunneling correction; good agreement with the experimental 45/44/17 intensity ratio 100/6.8±0.7/6.2±1.7 is obtained. 15% of m/z 17 and 50% of m /z 44 is attributed to tunneling. The ab initio decarbonylation reaction path yields a hydrogen bonded H2N-HCO+ transition state, which transfers a proton while proceeding downhill to the observed products, while both the path and the energetics support the earlier conclusion that the lowest lying electronically excited state of the ion (2π or 2a″) crosses the ground state early along the reaction path, thereby dominating the dynamics of decarbonylation.

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies.

PubMed

Zeng, Lu; Kortschak, R Daniel; Raison, Joy M; Bertozzi, Terry; Adelson, David L

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package.

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

PubMed

Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

Superior ab initio identification, annotation and characterisation of TEs and segmental duplications from genome assemblies

PubMed Central

Zeng, Lu; Kortschak, R. Daniel; Raison, Joy M.

2018-01-01

Transposable Elements (TEs) are mobile DNA sequences that make up significant fractions of amniote genomes. However, they are difficult to detect and annotate ab initio because of their variable features, lengths and clade-specific variants. We have addressed this problem by refining and developing a Comprehensive ab initio Repeat Pipeline (CARP) to identify and cluster TEs and other repetitive sequences in genome assemblies. The pipeline begins with a pairwise alignment using krishna, a custom aligner. Single linkage clustering is then carried out to produce families of repetitive elements. Consensus sequences are then filtered for protein coding genes and then annotated using Repbase and a custom library of retrovirus and reverse transcriptase sequences. This process yields three types of family: fully annotated, partially annotated and unannotated. Fully annotated families reflect recently diverged/young known TEs present in Repbase. The remaining two types of families contain a mixture of novel TEs and segmental duplications. These can be resolved by aligning these consensus sequences back to the genome to assess copy number vs. length distribution. Our pipeline has three significant advantages compared to other methods for ab initio repeat identification: 1) we generate not only consensus sequences, but keep the genomic intervals for the original aligned sequences, allowing straightforward analysis of evolutionary dynamics, 2) consensus sequences represent low-divergence, recently/currently active TE families, 3) segmental duplications are annotated as a useful by-product. We have compared our ab initio repeat annotations for 7 genome assemblies to other methods and demonstrate that CARP compares favourably with RepeatModeler, the most widely used repeat annotation package. PMID:29538441

Strategic L2 Lexical Innovation: Case Study of a University-Level Ab Initio Learner of German.

ERIC Educational Resources Information Center

Ridley, Jennifer; Singleton, David

1995-01-01

This article presents a case study of one English-speaking ab initio learner of German. It found that in target language production tasks performed over a two-year period, the subject exhibited a particular tendency toward lexical innovation as a strategy to cope with the lack of target language lexical knowledge. (38 references) (MDM)

Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

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

Xie, Binbin; Liu, Lihong; Cui, Ganglong

2015-11-21

In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as themore » final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.« less

Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

NASA Astrophysics Data System (ADS)

Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

Common lines modeling for reference free Ab-initio reconstruction in cryo-EM.

PubMed

Greenberg, Ido; Shkolnisky, Yoel

2017-11-01

We consider the problem of estimating an unbiased and reference-free ab initio model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all images. The contribution of each common line to the estimated orientations is weighted according to a statistical model for common lines' detection errors. The key property of the proposed algorithm is that it finds the global optimum for the orientations given the common lines. In particular, any local optima in the common lines energy landscape do not affect the proposed algorithm. As a result, it is applicable to thousands of images at once, very robust to noise, completely reference free, and not biased towards any initial model. A byproduct of the algorithm is a set of measures that allow to asses the reliability of the obtained ab initio model. We demonstrate the algorithm using class averages from two experimental data sets, resulting in ab initio models with resolutions of 20Å or better, even from class averages consisting of as few as three raw images per class. Copyright © 2017 Elsevier Inc. All rights reserved.

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

PubMed

Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

2017-03-14

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.

PubMed

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.

Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation

PubMed Central

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

Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.

PubMed

Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim

2016-10-26

For CO and N 2 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.

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.

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.

Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations.

PubMed

Hagiwara, Yohsuke; Tateno, Masaru

2010-10-20

We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems. © 2010 IOP Publishing Ltd

Ab initio NMR parameters of BrCH3 and ICH3 with relativistic and vibrational corrections

NASA Astrophysics Data System (ADS)

Uhlíková, Tereza; Urban, Štěpán

2018-05-01

This study is focused on two effects identified when NMR parameters are calculated based on first principles. These effects are 1. vibrational correction of properties when using ab initio optimized equilibrium geometry; 2. relativistic effects and limits of using the Flygare equation. These effects have been investigated and determined for nuclear spin-rotation constants and nuclear magnetic shieldings for the CH3Br and CH3I molecules. The most significant result is the difference between chemical shieldings determined based on the ab initio relativistic four-component Dirac-Coulomb Hamiltonian and chemical shieldings calculated using experimental values and the Flygare equation. This difference is approximately 320 ppm and 1290 ppm for 79Br and 127I in the CH3X molecule, respectively.

An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

NASA Astrophysics Data System (ADS)

Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

2018-04-01

The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

PubMed

Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

2016-07-15

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

PubMed

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study.

PubMed

Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate

2015-04-21

Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems.

Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

PubMed

Shen, Lin; Yang, Weitao

2018-03-13

Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of reaction dynamics, which provides a useful tool to study chemical or biochemical systems in solution or enzymes.

Energetics of intrinsic defects in NiO and the consequences for its resistive random access memory performance

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

Dawson, J. A., E-mail: jad95@cam.ac.uk; Guo, Y.; Robertson, J.

2015-09-21

Energetics for a variety of intrinsic defects in NiO are calculated using state-of-the-art ab initio hybrid density functional theory calculations. At the O-rich limit, Ni vacancies are the lowest cost defect for all Fermi energies within the gap, in agreement with the well-known p-type behaviour of NiO. However, the ability of the metal electrode in a resistive random access memory metal-oxide-metal setup to shift the oxygen chemical potential towards the O-poor limit results in unusual NiO behaviour and O vacancies dominating at lower Fermi energy levels. Calculated band diagrams show that O vacancies in NiO are positively charged at themore » operating Fermi energy giving it the advantage of not requiring a scavenger metal layer to maximise drift. Ni and O interstitials are generally found to be higher in energy than the respective vacancies suggesting that significant recombination of O vacancies and interstitials does not take place as proposed in some models of switching behaviour.« less

Influence of an external electric field on the potential-energy surface of alkali-metal-decorated C60

NASA Astrophysics Data System (ADS)

De, Deb Sankar; Saha, Santanu; Genovese, Luigi; Goedecker, Stefan

2018-06-01

We present a fully ab initio, unbiased structure search of the configurational space of decorated C60 fullerenes in the presence of an electric field. We observed that the potential-energy surface is significantly perturbed by an external electric field and that the energetic ordering of low-energy isomers differs with and without electric field. We identify the energetically lowest configuration for a varying number of decorating atoms (1 ≤n ≤12 ) for Li and (1 ≤n ≤6 ) for K on the C60 surface at different electric-field strengths. Using the correct geometric ground state in the electric field for the calculation of the dipole we obtain better agreement with the experimentally measured values than previous calculations based on the ground state in absence of an electric field. Since the lowest-energy structures are typically nearly degenerate in energy, a combination of different structures is expected to be found at room temperature. The experimentally measured dipole is therefore also expected to contain significant contributions from several low-energy structures.

Structural and configurational properties of nanoconfined monolayer ice from first principles

PubMed Central

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations. PMID:26728125

Structural and configurational properties of nanoconfined monolayer ice from first principles

NASA Astrophysics Data System (ADS)

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations.

Ab Initio Modeling of the Electronic Absorption Spectrum of Previtamin D in Solution

NASA Astrophysics Data System (ADS)

Zhu, Tianyang

To study the solvent effects of water on the previtamin D absorption spectrum, we use the quantum mechanics (QM)/molecular mechanics (MM) method combined with replica-exchange molecular dynamics (REMD). The QM method is applied for the previtamin D molecule and the MM method is used for the water molecules. To enhance conformational sampling of the flexible previtamin D molecule we apply REMD. Based on the REMD structures, we calculate the macroscopic ensemble of the absorption spectrum in solution by time-dependent density functional theory (TDDFT). Comparison between the calculated spectrum in the gas phase and in the solution reveals minor influences of the solvent on the absorption spectrum. In the conventional molecule dynamics simulation, the previtamin D molecule can be trapped by local minimum and cannot overcome energetics barriers when it is calculated at the room temperature. In addition, the higher temperature calculation for the molecule in REMD allows to overcome energetics barriers and to change the structure to other rotational isomers, then switch to the lower temperature and gives a more complete result in the configuration space for the lower temperature.

Adequacy of damped dynamics to represent the electron-phonon interaction in solids

DOE PAGES

Caro, A.; Correa, A. A.; Tamm, A.; ...

2015-10-16

Time-dependent density functional theory and Ehrenfest dynamics are used to calculate the electronic excitations produced by a moving Ni ion in a Ni crystal in the case of energetic MeV range (electronic stopping power regime), as well as thermal energy meV range (electron-phonon interaction regime). Results at high energy compare well to experimental databases of stopping power, and at low energy the electron-phonon interaction strength determined in this way is very similar to the linear response calculation and experimental measurements. This approach to electron-phonon interaction as an electronic stopping process provides the basis for a unified framework to perform classicalmore » molecular dynamics of ion-solid interaction with ab initio type nonadiabatic terms in a wide range of energies.« less

A Novel Intrinsic Interface State Controlled by Atomic Stacking Sequence at Interfaces of SiC/SiO2.

PubMed

Matsushita, Yu-Ichiro; Oshiyama, Atsushi

2017-10-11

On the basis of ab initio total-energy electronic-structure calculations, we find that electron states localized at the SiC/SiO 2 interface emerge in the energy region between 0.3 eV below and 1.2 eV above the bulk conduction-band minimum (CBM) of SiC, being sensitive to the sequence of atomic bilayers in SiC near the interface. These new interface states unrecognized in the past are due to the peculiar characteristics of the CBM states that are distributed along the crystallographic channels. We also find that the electron doping modifies the energetics among the different stacking structures. Implication for performance of electron devices fabricated on different SiC surfaces is discussed.

A density functional global optimisation study of neutral 8-atom Cu-Ag and Cu-Au clusters

NASA Astrophysics Data System (ADS)

Heard, Christopher J.; Johnston, Roy L.

2013-02-01

The effect of doping on the energetics and dimensionality of eight atom coinage metal subnanometre particles is fully resolved using a genetic algorithm in tandem with on the fly density functional theory calculations to determine the global minima (GM) for Cu n Ag(8- n) and Cu n Au(8- n) clusters. Comparisons are made to previous ab initio work on mono- and bimetallic clusters, with excellent agreement found. Charge transfer and geometric arguments are considered to rationalise the stability of the particular permutational isomers found. An interesting transition between three dimensional and two dimensional GM structures is observed for copper-gold clusters, which is sharper and appears earlier in the doping series than is known for gold-silver particles.

On the theory of Carriers's Electrostatic Interaction near an Interface

NASA Astrophysics Data System (ADS)

Waters, Michael; Hashemi, Hossein; Kieffer, John

2015-03-01

Heterojunction interfaces are common in non-traditional photovoltaic device designs, such as those based small molecules, polymers, and perovskites. We have examined a number of the effects of the heterojunction interface region on carrier/exciton energetics using a mixture of both semi-classical and quantum electrostatic methods, ab initio methods, and statistical mechanics. Our theoretical analysis has yielded several useful relationships and numerical recipes that should be considered in device design regardless of the particular materials system. As a demonstration, we highlight these formalisms as applied to carriers and polaron pairs near a C60/subphthalocyanine interface. On the regularly ordered areas of the heterojunction, the effect of the interface is a significant set of corrections to the carrier energies, which in turn directly affects device performance.

Closed-edged bilayer phosphorene nanoribbons producing from collapsing armchair phosphorene nanotubes.

PubMed

Liao, Xiangbiao; Xiao, Hang; Lu, Xiaobo; Chen, Youlong; Shi, Xiaoyang; Chen, Xi

2018-02-23

A new phosphorous allotrope, closed-edged bilayer phosphorene nanoribbon, is proposed via radially deforming armchair phosphorene nanotubes. Using molecular dynamics simulations, the transformation pathway from round PNTs falls into two types of collapsed structures: arc-like and sigmoidal bilayer nanoribbons, dependent on the number of phosphorene unit cells. The fabricated nanoribbions are energetically more stable than their parent nanotubes. It is also found via ab initio calculations that the band structure along tube axis substantially changes with the structural transformation. The direct-to-indirect transition of band gap is highlighted when collapsing into the arc-like nanoribbons but not the sigmoidal ones. Furthermore, the band gaps of these two types of nanoribbons show significant size-dependence of the nanoribbon width, indicative of wider tunability of their electrical properties.

Ab Initio Study of Structural and Electronic Properties of (ZnO) n "Magical" Nanoclusters n = (34, 60)

NASA Astrophysics Data System (ADS)

Bovhyra, Rostyslav; Popovych, Dmytro; Bovgyra, Oleg; Serednytski, Andrew

2017-01-01

Density functional theory studies of the structural and electronic properties of nanoclusters (ZnO) n ( n = 34, 60) in different geometric configurations were conducted. For each cluster, an optimization (relaxation) of structure geometry was performed, and the basic properties of the band structure were investigated. It was established that for the (ZnO)34 nanoclusters, the most stable are fullerene-like hollow structures that satisfy the rule of six isolated quadrangles. For the (ZnO)60 nanoclusters, different types of isomers, including hollow structures and sodalite-like structures composed from (ZnO)12 nanoclusters, were investigated. It was determined that the most energetically favorable structure was sodalite-type structure composed of seven (ZnO)12 clusters with common quadrangle edges.

A theoretical study of the reaction of Ti+ with ethane

NASA Astrophysics Data System (ADS)

Moc, Jerzy; Fedorov, Dmitri G.; Gordon, Mark S.

2000-06-01

The doublet and quartet potential energy surfaces for the Ti++C2H6→TiC2H4++H2 and Ti++C2H6→TiCH2++CH4 reactions are studied using density functional theory (DFT) with the B3LYP functional and ab initio coupled cluster CCSD(T) methods with high quality basis sets. Structures have been optimized at the DFT level and the minima connected to each transition state (TS) by following the intrinsic reaction coordinate (IRC). Relative energies are calculated both at the DFT and coupled-cluster levels of theory. The relevant parts of the potential energy surface, especially key transition states, are also studied using multireference wave functions with the final energetics obtained with multireference second-order perturbation theory.

Ab initio SCF study of the barrier to internal rotation in simple amides. Part 3. Thioamides

NASA Astrophysics Data System (ADS)

Vassilev, Nikolay G.; Dimitrov, Valentin S.

2003-06-01

The free energies of activation for rotation about the thiocarbonyl C-N bond in X-C(S)N(CH 3) 2 (X=H, F, Cl, CH 3, CF 3) were calculated at the MP2(fc)/6-31+G*//6-31G* and MP2(fc)/6-311++G**//6-311++G** levels and compared with literature NMR gas-phase data. The results of calculations indicate that the nonbonded interactions in ground state (GS) are mainly responsible for the differences in the rotational barriers. For X=H, CH 3 and CF 3, the anti transition state (TS) is more stable; for the case X=Cl, the syn TS is more stable, while for the X=F, the two TS are energetically almost equivalent.

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

DOE PAGES

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan; ...

2017-11-27

Here, diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et~al. in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VOmore » $$_2$$, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development.« less

Accuracy of ab initio electron correlation and electron densities in vanadium dioxide

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

Kylänpää, Ilkka; Balachandran, Janakiraman; Ganesh, Panchapakesan

Here, diffusion quantum Monte Carlo results are used as a reference to analyze properties related to phase stability and magnetism in vanadium dioxide computed with various formulations of density functional theory. We introduce metrics related to energetics, electron densities and spin densities that give us insight on both local and global variations in the antiferromagnetic M1 and R phases. Importantly, these metrics can address contributions arising from the challenging description of the 3d orbital physics in this material. We observe that the best description of energetics between the structural phases does not correspond to the best accuracy in the charge density, which is consistent with observations made recently by Medvedev et~al. in the context of isolated atoms. However, we do find evidence that an accurate spin density connects to correct energetic ordering of different magnetic states in VOmore » $$_2$$, although local, semilocal, and meta-GGA functionals tend to erroneously favor demagnetization of the vanadium sites. The recently developed SCAN functional stands out as remaining nearly balanced in terms of magnetization across the M1-R transition and correctly predicting the ground state crystal structure. In addition to ranking current density functionals, our reference energies and densities serve as important benchmarks for future functional development.« less

Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

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

Wang, Yimin, E-mail: yimin.wang@emory.edu; Bowman, Joel M., E-mail: jmbowma@emory.edu; Kamarchik, Eugene, E-mail: eugene.kamarchik@gmail.com

2016-03-21

We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na{sup +}H{sub 2}O, F{sup −}H{sub 2}O, and Cl{sup −}H{sub 2}O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H{sub 2}O potentials are permutationally invariant fits to roughly 20 000more » coupled cluster CCSD(T) energies (awCVTZ basis for Na{sup +} and aVTZ basis for Cl{sup −} and F{sup −}), over a large range of distances and H{sub 2}O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.« less

Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

PubMed

Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro

2016-12-15

MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.

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

PubMed

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

2016-07-01

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

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

PubMed

Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

2015-09-28

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

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

PubMed Central

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

2016-01-01

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

Ab initio study of the electron energy loss function in a graphene-sapphire-graphene composite system

NASA Astrophysics Data System (ADS)

Despoja, Vito; Djordjević, Tijana; Karbunar, Lazar; Radović, Ivan; Mišković, Zoran L.

2017-08-01

The propagator of a dynamically screened Coulomb interaction W in a sandwichlike structure consisting of two graphene layers separated by a slab of Al2O3 (or vacuum) is derived from single-layer graphene response functions and by using a local dielectric function for the bulk Al2O3 . The response function of graphene is obtained using two approaches within the random phase approximation (RPA): an ab initio method that includes all electronic bands in graphene and a computationally less demanding method based on the massless Dirac fermion (MDF) approximation for the low-energy excitations of electrons in the π bands. The propagator W is used to derive an expression for the effective dielectric function of our sandwich structure, which is relevant for the reflection electron energy loss spectroscopy of its surface. Focusing on the range of frequencies from THz to mid-infrared, special attention is paid to finding an accurate optical limit in the ab initio method, where the response function is expressed in terms of a frequency-dependent conductivity of graphene. It was shown that the optical limit suffices for describing hybridization between the Dirac plasmons in graphene layers and the Fuchs-Kliewer phonons in both surfaces of the Al2O3 slab, and that the spectra obtained from both the ab initio method and the MDF approximation in the optical limit agree perfectly well for wave numbers up to about 0.1 nm-1. Going beyond the optical limit, the agreement between the full ab initio method and the MDF approximation was found to extend to wave numbers up to about 0.3 nm-1 for doped graphene layers with the Fermi energy of 0.2 eV.

Ab initio potential-energy surfaces for complex, multichannel systems using modified novelty sampling and feedforward neural networks

NASA Astrophysics Data System (ADS)

Raff, L. M.; Malshe, M.; Hagan, M.; Doughan, D. I.; Rockley, M. G.; Komanduri, R.

2005-02-01

A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.

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

NASA Astrophysics Data System (ADS)

Enrique, Raúl A.; Van der Ven, Anton

2017-10-01

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

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.

Towards ab initio Calculations with the Dynamical Vertex Approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Kaufmann, Josef; Gunacker, Patrik; Pickem, Matthias; Thunström, Patrik; Tomczak, Jan M.; Held, Karsten

2018-04-01

While key effects of the many-body problem — such as Kondo and Mott physics — can be understood in terms of on-site correlations, non-local fluctuations of charge, spin, and pairing amplitudes are at the heart of the most fascinating and unresolved phenomena in condensed matter physics. Here, we review recent progress in diagrammatic extensions to dynamical mean-field theory for ab initio materials calculations. We first recapitulate the quantum field theoretical background behind the two-particle vertex. Next we discuss latest algorithmic advances in quantum Monte Carlo simulations for calculating such two-particle quantities using worm sampling and vertex asymptotics, before giving an introduction to the ab initio dynamical vertex approximation (AbinitioDΓA). Finally, we highlight the potential of AbinitioDΓA by detailing results for the prototypical correlated metal SrVO3.

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

NASA Astrophysics Data System (ADS)

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

2011-04-01

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

Determination of NMR chemical shifts for cholesterol crystals from first-principles

NASA Astrophysics Data System (ADS)

Kucukbenli, Emine; de Gironcoli, Stefano

2011-03-01

Solid State Nuclear Magnetic Resonance (NMR) is a powerful tool in crystallography when combined with theoretical predictions. So far, empirical calculations of spectra have been employed for an unambiguous identification. However, many complex systems are outside the scope of these methods. Our implementation of ultrasoft and projector augmented wave pseudopotentials within ab initio gauge including projector augmented plane wave (GIPAW) method in Quantum Espresso simulation package allows affordable calculations of NMR spectra for systems of thousands of electrons. We report here the first ab initio determination of NMR spectra for several crystal structures of cholesterol. Cholesterol crystals, the main component of human gallstones, are of interest to medical research as their structural properties can shed light on the pathologies of gallbladder. With our application we show that ab initio calculations can be employed to aid NMR crystallography.

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Ab initio structures and polarizabilities of sodium clusters

NASA Astrophysics Data System (ADS)

Kronik, Leeor; Vasiliev, Igor; Jain, Manish; Chelikowsky, James R.

2001-09-01

We present quantitative ab initio calculations for Na cluster structures and polarizabilities, for all cluster sizes up to 20 atoms. Our calculations are performed by combining an ab initio core-corrected pseudopotential and a gradient-corrected density functional within a real space approach. We find the cluster bonding to be very floppy and catalog a host of low-energy quasi-degenerate isomers for all second-decade clusters. The existence of these isomers results in a band of polarizability values for each cluster size even at zero temperature. This eliminates any finer structure in the polarizability curve. We further show that the experimental polarizability values are consistently underestimated by calculations at zero temperature. By computing the effects of structure expansion and distortion due to a finite temperature we arrive at a quantitative agreement between theory and experiment.

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

NASA Astrophysics Data System (ADS)

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

2000-08-01

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

Exploring the Nature of the H[subscript 2] Bond. 2. Using Ab Initio Molecular Orbital Calculations to Obtain the Molecular Constants

ERIC Educational Resources Information Center

Halpern, Arthur M.; Glendening, Eric D.

2013-01-01

A project for students in an upper-level course in quantum or computational chemistry is described in which they are introduced to the concepts and applications of a high quality, ab initio treatment of the ground-state potential energy curve (PEC) for H[subscript 2] and D[subscript 2]. Using a commercial computational chemistry application and a…

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

DTIC Science & Technology

1999-12-07

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

An ab initio mechanism for efficient population of triplet states in cytotoxic sulfur substituted DNA bases: the case of 6-thioguanine.

PubMed

Martínez-Fernández, Lara; González, Leticia; Corral, Inés

2012-02-18

The deactivation mechanism of the cytotoxic 6-thioguanine, the 6-sulfur-substituted analogue of the canonical DNA base, is unveiled by ab initio calculations. Oxygen-by-sulfur substitution leads to efficient population of triplet states-the first step for generating singlet oxygen-which is responsible for its cytotoxicity. This journal is © The Royal Society of Chemistry 2012

Ab initio optical potentials and nucleon scattering on medium mass nuclei

NASA Astrophysics Data System (ADS)

Idini, A.; Barbieri, C.; Navrátil, P.

2018-03-01

We show first results for the elastic scattering of neutrons off oxygen and calcium isotopes obtained from ab initio optical potentials. The potential is derived using self-consistent Green’s function theory (SCGF) with the saturating chiral interaction NNLOsat. Calculations are compared to available scattering data and show that it is possible to reproduce low energy scattering observables in medium mass nuclei from first principles.

The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Huo, Winifred (Technical Monitor)

1998-01-01

We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions,

The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Huo, Winifred (Technical Monitor)

1998-01-01

We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions.

State of the art for ab initio vs empirical potentials for HeH+ (2e-), BeH+ (4e-), BeH (5e-), Li2 (6e-) and BH (6e-)

NASA Astrophysics Data System (ADS)

Dattani, Nike

For large internuclear distances, the potential energy between two atoms is known analytically, based on constants that are calculated from atomic ab initio rather than molecular ab initio. This analytic form can be built into models for molecular potentials that are fitted to spectroscopic data. Such empirical potentials constitute the most accurate molecular potentials known. For HeH+, and BeH+, the long-range form of the potential is based only on the polarizabilities for He and H respectively, for which we have included up to 4th order QED corrections. For BeH, the best ab initio potential matches all but one observed vibrational spacing to < 1 cm- accuracy, and for Li2 the discrepancy in the spacings is < 0.08 cm-1 for all vibrational levels. But experimental methods such as photoassociation require the absolute energies, not spacings, and these are still several in several cm-1 disagreement. So empirical potentials are still the only reliable way to predict energies for few-electron systems. We also give predictions for various unobserved ''halo nucleonic molecules'' containing the ''halo'' isotopes: 6,8He, 11Li, 11,14Be and 8 , 17 , 19B.

Ab Initio Crystal Field for Lanthanides.

PubMed

Ungur, Liviu; Chibotaru, Liviu F

2017-03-13

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

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

PubMed

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

2018-06-07

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

A Complete and Accurate Ab Initio Repeat Finding Algorithm.

PubMed

Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua

2016-03-01

It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy.

Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

NASA Astrophysics Data System (ADS)

Zaharieva, Roussislava; Hanagud, Sathya

2009-06-01

Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

Energetic studies and phase diagram of thioxanthene.

PubMed

Freitas, Vera L S; Monte, Manuel J S; Santos, Luís M N B F; Gomes, José R B; Ribeiro da Silva, Maria D M C

2009-11-19

The molecular stability of thioxanthene, a key species from which very important compounds with industrial relevance are derived, has been studied by a combination of several experimental techniques and computational approaches. The standard (p degrees = 0.1 MPa) molar enthalpy of formation of crystalline thioxanthene (117.4 +/- 4.1 kJ x mol(-1)) was determined from the experimental standard molar energy of combustion, in oxygen, measured by rotating-bomb combustion calorimetry at T = 298.15 K. The enthalpy of sublimation was determined by a direct method, using the vacuum drop microcalorimetric technique, and also by an indirect method, using a static apparatus, where the vapor pressures at different temperatures were measured. The latter technique was used for both crystalline and undercooled liquid samples, and the phase diagram of thioxanthene near the triple point was obtained (triple point coordinates T = 402.71 K and p = 144.7 Pa). From the two methods, a mean value for the standard (p degrees = 0.1 MPa) molar enthalpy of sublimation, at T = 298.15 K (101.3 +/- 0.8 kJ x mol(-1)), was derived. From the latter value and from the enthalpy of formation of the solid, the standard (p degrees = 0.1 MPa) enthalpy of formation of gaseous thioxanthene was calculated as 218.7 +/- 4.2 kJ x mol(-1). Standard ab initio molecular orbital calculations were performed using the G3(MP2)//B3LYP composite procedure and several homodesmotic reactions in order to derive the standard molar enthalpy of formation of thioxanthene. The ab initio results are in excellent agreement with the experimental data.

Ab initio chemical kinetics for the ClOO + NO reaction: Effects of temperature and pressure on product branching formation

NASA Astrophysics Data System (ADS)

Raghunath, P.; Lin, M. C.

2012-07-01

The kinetics and mechanism for the reaction of ClOO with NO have been investigated by ab initio molecular orbital theory calculations based on the CCSD(T)/6-311+G(3df)//PW91PW91/6-311+G(3df) method, employed to evaluate the energetics for the construction of potential energy surfaces and prediction of reaction rate constants. The results show that the reaction can produce two key low energy products ClNO + 3O2 via the direct triplet abstraction path and ClO + NO2 via the association and decomposition mechanism through long-lived singlet pc-ClOONO and ClONO2 intermediates. The yield of ClNO + O2 (1△) from any of the singlet intermediates was found to be negligible because of their high barriers and tight transition states. As both key reactions initially occur barrierlessly, their rate constants were evaluated with a canonical variational approach in our transition state theory and Rice-Ramspergen-Kassel-Marcus/master equation calculations. The rate constants for ClNO + 3O2 and ClO + NO2 production from ClOO + NO can be given by 2.66 × 10-16 T1.91 exp(341/T) (200-700 K) and 1.48 × 10-24 T3.99 exp(1711/T) (200-600 K), respectively, independent of pressure below atmospheric pressure. The predicted total rate constant and the yields of ClNO and NO2 in the temperature range of 200-700 K at 10-760 Torr pressure are in close agreement with available experimental results.

Efficient conformational space exploration in ab initio protein folding simulation.

PubMed

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.

Structure models: From shell model to ab initio methods. A brief introduction to microscopic theories for exotic nuclei

NASA Astrophysics Data System (ADS)

Bacca, Sonia

2016-04-01

A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.

Vibrational spectra for uric acid and its D- and 15N-substituted analogues. Assignments for its normal modes from ab initio 3-21G force field.

NASA Astrophysics Data System (ADS)

Majoube, M.; Vergoten, G.

1993-03-01

FTR, Raman, FTIR spectra are obtained for polycrystalline uric acid and seven of its D-and 15N-substituted analogues. Assignments are given from a normal coordinate analysis carried out using a 3-21G ab initio force field. These are discussed by considering observed and calculated frequencies and D- and 15N-isotopic shifts.

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

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

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

2015-05-15

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factormore » shows the presence of liquid state in the considered alloys.« less

Kubo–Greenwood approach to conductivity in dense plasmas with average atom models

DOE PAGES

Starrett, C. E.

2016-04-13

In this study, a new formulation of the Kubo–Greenwood conductivity for average atom models is given. The new formulation improves upon previous treatments by explicitly including the ionic-structure factor. Calculations based on this new expression lead to much improved agreement with ab initio results for DC conductivity of warm dense hydrogen and beryllium, and for thermal conductivity of hydrogen. We also give and test a slightly modified Ziman–Evans formula for the resistivity that includes a non-free electron density of states, thus removing an ambiguity in the original Ziman–Evans formula. Again, results based on this expression are in good agreement withmore » ab initio simulations for warm dense beryllium and hydrogen. However, for both these expressions, calculations of the electrical conductivity of warm dense aluminum lead to poor agreement at low temperatures compared to ab initio simulations.« less

Ab initio study of the electrostatic multipole nature of torsional potentials in CH3SSCH3, CH3SSH, and HOOH

NASA Technical Reports Server (NTRS)

Sokalski, W. A.; Lai, J.; Luo, N.; Sun, S.; Shibata, M.; Ornstein, R.; Rein, R.

1991-01-01

The origin of torsional potentials in H3CSSCH3, H3CSSH, and HOOH and the anisotropy of the local charge distribution has been analyzed in terms of atomic multipoles calculated from the ab initio LCAO-MO-SCF wave function in the 6-31G* basis set. The results indicate that for longer -S-S-bonds the major contribution to these torsional barriers are electrostatic interactions of the atomic multipoles located on two atoms forming the rotated bond. This finding demonstrates the important role of electrostatic 1-2 interatomic interactions, usually neglected in conformational studies. It also opens the possibility to derive directly from accurate ab initio wave functions a simple nonempirical torsional potential involving atomic multipoles of two bonded atoms defining the torsional angle. For shorter -O-O- bonds, use of more precise models and inclusion of 1-3 interactions seems to be necessary.

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

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.

Symplectic no-core configuration interaction framework for ab initio nuclear structure. II. Structure of rotational states

NASA Astrophysics Data System (ADS)

Caprio, Mark A.; McCoy, Anna E.; Dytrych, Tomas

2017-09-01

Rotational band structure is readily apparent as an emergent phenomenon in ab initio nuclear many-body calculations of light nuclei, despite the incompletely converged nature of most such calculations at present. Nuclear rotation in light nuclei can be analyzed in terms of approximate dynamical symmetries of the nuclear many-body problem: in particular, Elliott's SU (3) symmetry of the three-dimensional harmonic oscillator and the symplectic Sp (3 , R) symmetry of three-dimensional phase space. Calculations for rotational band members in the ab initio symplectic no-core configuration interaction (SpNCCI) framework allow us to directly examine the SU (3) and Sp (3 , R) nature of rotational states. We present results for rotational bands in p-shell nuclei. Supported by the US DOE under Award No. DE-FG02-95ER-40934 and the Czech Science Foundation under Grant No. 16-16772S.

Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

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

Sharma, Nalini, E-mail: nalini-2808@yahoo.co.in; Ahluwalia, P. K.; Thakur, Anil

2016-05-23

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 (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}Pb{sub 10}) 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 localmore » arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.« less

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

PubMed

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

2018-05-15

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

Atomic defects in monolayer WSe2 tunneling FETs studied by systematic ab initio calculations

NASA Astrophysics Data System (ADS)

Wu, Jixuan; Fan, Zhiqiang; Chen, Jiezhi; Jiang, Xiangwei

2018-05-01

Atomic defects in monolayer WSe2 tunneling FETs (TFETs) are studied through systematic ab initio calculations aiming at performance predictions and enhancements. The effects of various defect positions and different passivation atoms are characterized in WSe2 TFETs by rigorous ab initio quantum transport simulations. It is suggested that the Se vacancy (VSe) defect located in the gate-controlled channel region tends to increase the OFF current (I off), whereas it can be well suppressed by oxygen passivation. It is demonstrated that chlorine (Cl) passivation at the source-side tunneling region can largely suppress I off, leading to an impressively improved on–off ratio (I on/I off) compared with that without any defect. However, it is also observed that randomly positioned atomic defects tend to induce significant fluctuation of the TFET output. Further discussions are made with focus on the performance-variability trade-off for robust circuit design.

Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

DOE PAGES

Dytrych, T.; Maris, P.; Launey, K. D.; ...

2016-06-22

We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU3-selected subspaces. We demonstrate LSU3shell’s strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and significant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis affords memory savings in calculations of states withmore » a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

NASA Astrophysics Data System (ADS)

Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

2015-03-01

Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

Ab initio results for intermediate-mass, open-shell nuclei

NASA Astrophysics Data System (ADS)

Baker, Robert B.; Dytrych, Tomas; Launey, Kristina D.; Draayer, Jerry P.

2017-01-01

A theoretical understanding of nuclei in the intermediate-mass region is vital to astrophysical models, especially for nucleosynthesis. Here, we employ the ab initio symmetry-adapted no-core shell model (SA-NCSM) in an effort to push first-principle calculations across the sd-shell region. The ab initio SA-NCSM's advantages come from its ability to control the growth of model spaces by including only physically relevant subspaces, which allows us to explore ultra-large model spaces beyond the reach of other methods. We report on calculations for 19Ne and 20Ne up through 13 harmonic oscillator shells using realistic interactions and discuss the underlying structure as well as implications for various astrophysical reactions. This work was supported by the U.S. NSF (OCI-0904874 and ACI -1516338) and the U.S. DOE (DE-SC0005248), and also benefitted from the Blue Waters sustained-petascale computing project and high performance computing resources provided by LSU.

Ab initio theoretical calculations of the electronic excitation energies of small water clusters.

PubMed

Tachikawa, Hiroto; Yabushita, Akihiro; Kawasaki, Masahiro

2011-12-14

A direct ab initio molecular dynamics method has been applied to a water monomer and water clusters (H(2)O)(n) (n = 1-3) to elucidate the effects of zero-point energy (ZPE) vibration on the absorption spectra of water clusters. Static ab initio calculations without ZPE showed that the first electronic transitions of (H(2)O)(n), (1)B(1)←(1)A(1), are blue-shifted as a function of cluster size (n): 7.38 eV (n = 1), 7.58 eV (n = 2) and 8.01 eV (n = 3). The inclusion of the ZPE vibration strongly affects the excitation energies of a water dimer, and a long red-tail appears in the range of 6.42-6.90 eV due to the structural flexibility of a water dimer. The ultraviolet photodissociation of water clusters and water ice surfaces is relevant to these results.

General Rule of Negative Effective Ueff System & Materials Design of High-Tc Superconductors by ab initio Calculations

NASA Astrophysics Data System (ADS)

Katayama-Yoshida, Hiroshi; Nakanishi, Akitaka; Uede, Hiroki; Takawashi, Yuki; Fukushima, Tetsuya; Sato, Kazunori

2014-03-01

Based upon ab initio electronic structure calculation, I will discuss the general rule of negative effective U system by (1) exchange-correlation-induced negative effective U caused by the stability of the exchange-correlation energy in Hund's rule with high-spin ground states of d5 configuration, and (2) charge-excitation-induced negative effective U caused by the stability of chemical bond in the closed-shell of s2, p6, and d10 configurations. I will show the calculated results of negative effective U systems such as hole-doped CuAlO2 and CuFeS2. Based on the total energy calculations of antiferromagnetic and ferromagnetic states, I will discuss the magnetic phase diagram and superconductivity upon hole doping. I also discuss the computational materials design method of high-Tc superconductors by ab initio calculation to go beyond LDA and multi-scale simulations.

A global ab initio potential for HCN/HNC, exact vibrational energies, and comparison to experiment

NASA Technical Reports Server (NTRS)

Bentley, Joseph A.; Bowman, Joel M.; Gazdy, Bela; Lee, Timothy J.; Dateo, Christopher E.

1992-01-01

An ab initio (i.e., from first principles) calculation of vibrational energies of HCN and HNC is reported. The vibrational calculations were done with a new potential derived from a fit to 1124 ab initio electronic energies which were calculated using the highly accurate CCSD(T) coupled-cluster method in conjunction with a large atomic natural orbital basis set. The properties of this potential are presented, and the vibrational calculations are compared to experiment for 54 vibrational transitions, 39 of which are for zero total angular momentum, J = 0, and 15 of which are for J = 1. The level of agreement with experiment is unprecedented for a triatomic with two nonhydrogen atoms, and demonstrates the capability of the latest computational methods to give reliable predictions on a strongly bound triatomic molecule at very high levels of vibrational excitation.

Linear free-energy relationships between a single gas-phase ab initio equilibrium bond length and experimental pKa values in aqueous solution.

PubMed

Alkorta, Ibon; Popelier, Paul L A

2015-02-02

Remarkably simple yet effective linear free energy relationships were discovered between a single ab initio computed bond length in the gas phase and experimental pKa values in aqueous solution. The formation of these relationships is driven by chemical features such as functional groups, meta/para substitution and tautomerism. The high structural content of the ab initio bond length makes a given data set essentially divide itself into high correlation subsets (HCSs). Surprisingly, all molecules in a given high correlation subset share the same conformation in the gas phase. Here we show that accurate pKa values can be predicted from such HCSs. This is achieved within an accuracy of 0.2 pKa units for 5 drug molecules. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectroscopic and Ab Initio Determination of the Ring-Twisting Potential Energy Function for 1,3-Cyclohexadiene

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.

Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)

NASA Astrophysics Data System (ADS)

Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik

2018-04-01

The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.

Ab initio study of MF2 (M=Mn, Fe, Co, Ni) rutile-type compounds using the periodic unrestricted Hartree-Fock approach

NASA Astrophysics Data System (ADS)

de P. R. Moreira, Ibério; Dovesi, Roberto; Roetti, Carla; Saunders, Victor R.; Orlando, Roberto

2000-09-01

The ab initio periodic unrestricted Hartree-Fock method has been applied in the investigation of the ground-state structural, electronic, and magnetic properties of the rutile-type compounds MF2 (M=Mn, Fe, Co, and Ni). All electron Gaussian basis sets have been used. The systems turn out to be large band-gap antiferromagnetic insulators; the optimized geometrical parameters are in good agreement with experiment. The calculated most stable electronic state shows an antiferromagnetic order in agreement with that resulting from neutron scattering experiments. The magnetic coupling constants between nearest-neighbor magnetic ions along the [001], [111], and [100] (or [010]) directions have been calculated using several supercells. The resulting ab initio magnetic coupling constants are reasonably satisfactory when compared with available experimental data. The importance of the Jahn-Teller effect in FeF2 and CoF2 is also discussed.

Nuclear shielding constants by density functional theory with gauge including atomic orbitals

NASA Astrophysics Data System (ADS)

Helgaker, Trygve; Wilson, Philip J.; Amos, Roger D.; Handy, Nicholas C.

2000-08-01

Recently, we introduced a new density-functional theory (DFT) approach for the calculation of NMR shielding constants. First, a hybrid DFT calculation (using 5% exact exchange) is performed on the molecule to determine Kohn-Sham orbitals and their energies; second, the constants are determined as in nonhybrid DFT theory, that is, the paramagnetic contribution to the constants is calculated from a noniterative, uncoupled sum-over-states expression. The initial results suggested that this semiempirical DFT approach gives shielding constants in good agreement with the best ab initio and experimental data; in this paper, we further validate this procedure, using London orbitals in the theory, having implemented DFT into the ab initio code DALTON. Calculations on a number of small and medium-sized molecules confirm that our approach produces shieldings in excellent agreement with experiment and the best ab initio results available, demonstrating its potential for the study of shielding constants of large systems.

Ab-initio calculations on melting of thorium

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

Mukherjee, D., E-mail: debojyoti@barc.gov.in; Sahoo, B. D.; Joshi, K. D.

2016-05-23

Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a{sub 0}){sup 3} and (1.02a{sub 0}){sup 3} and (1.04a{sub 0}){sup 3} increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a{sub 0} = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures asmore » melting point. The melting point of 2100 K is close to the experimental value of 2023 K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.« less

Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

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

Dytrych, T.; Maris, Pieter; Launey, K. D.

2016-06-09

We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations ofmore » states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.« less

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

NASA Astrophysics Data System (ADS)

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

2007-04-01

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

Ab initio study of the ground and excited electronic states of the methyl radical

PubMed Central

Zanchet, A.; Bañares, L.; Senent, M. L.; García-Vela, A.

2016-01-01

The ground and some excited electronic states of the methyl radical have been characterized by means of highly correlated ab intio techniques. The specific excited states investigated are those involved in the dissociation of the radical, namely the 3s and 3pz Rydberg states, and the A1 and B1 valence states crossing them, respectively. The C-H dissociative coordinate and the HCH bending angle were considered in order to generate the first two-dimensional ab initio representation of the potential surfaces of the above electronic states of CH3, along with the nonadiabatic couplings between them. Spectroscopic constants and frequencies calculated for the ground and bound excited states agree well with most of the available experimental data. Implications of the shape of the excited potential surfaces and couplings for the dissociation pathways of CH3 are discussed in the light of recent experimental results for dissociation from low-lying vibrational states of CH3. Based on the ab initio data some predictions are made regarding methyl photodissociation from higher initial vibrational states. PMID:27892569

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

PubMed

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

2012-06-07

Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1) region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH(2)F(2) as a prototype molecule to test ab initio calculations and theoretical models.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm-1 studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations

NASA Astrophysics Data System (ADS)

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Charmet, Andrea Pietropolli; Gambi, Alberto

2012-06-01

Difluoromethane (CH2F2, HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm-1. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm-1 while intensities are predicted within few km mol-1 from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν1⟩, |2ν8⟩, |2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm-1 region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.

Investigations of Reactive Processes at Temperatures Relevant to the Hypersonic Flight Regime

DTIC Science & Technology

2014-10-31

molecule is constructed based on high- level ab-initio calculations and interpolated using the reproducible kernel Hilbert space (RKHS) method and...a potential energy surface (PES) for the ground state of the NO2 molecule is constructed based on high- level ab initio calculations and interpolated...between O(3P) and NO(2Π) at higher temperatures relevant to the hypersonic flight regime of reentering space- crafts. At a more fundamental level , we

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 the elastic properties of magnesium under pressure

NASA Astrophysics Data System (ADS)

Sin'Ko, G. V.; Smirnov, N. A.

2009-09-01

Results of ab initio calculations of the elastic constants for the hcp, bcc, double hcp (dhcp), and fcc magnesium in a wide range of pressures are presented. The calculated elastic constants are compared with available experimental and theoretical data. We discuss the effect of the electron topological transition that occurs when the hcp structure is compressed on results of calculations and consider possibility of observing the hcp→dhcp transition on the magnesium Hugoniot.

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

DOE PAGES

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

2017-04-26

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

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

Geng, Hua Y., E-mail: huay.geng@gmail.com; Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate ismore » about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.« less

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

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

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Experimental and Ab Initio Studies of the HDO Absorption Spectrum in the 13165-13500 1/cm Spectral Region

NASA Technical Reports Server (NTRS)

Schwenke, David; Naumenko, Olga; Bertseva, Elena; Campargue, Alain; Arnold, James O. (Technical Monitor)

2000-01-01

The HDO absorption spectrum has been recorded in the 13165 - 13500 cm(exp-1) spectral region by Intracavity Laser Absorption Spectroscopy. The spectrum (615 lines), dominated by the 2n2 + 3n3 and n1+3n3 bands was assigned and modeled leading to the derivation of 196 accurate energy levels of the (103) and (023) vibrational states. Finally, 150 of these levels have been reproduced by an effective Hamiltonian involving two vibrational dark states interacting with the (023) and ( 103) bright states. The rms deviation achieved by variation of 28 parameters is 0.05-1 cm, compared to an averaged experimental uncertainty of 0.007-1 cm, indicating the limit of validity of the effective Hamiltonian approach for HDO at high vibrational excitation. The predictions of previous ab initio calculations of the HDO spectrum were extensively used in the assignment process. The particular spectral region under consideration has been used to test and discuss the improvements of new ab initio calculations recently performed on the basis of the same potential energy surface but with an improved dipole moment surface. The improvements concern both the energy levels and the line intensities. In particular, the strong hybrid character of the n1+3n3 band is very well accounted for by the the new ab initio calculations.

Magnetic Excitations in Polyoxotungstate-Supported Lanthanoid Single-Molecule Magnets: An Inelastic Neutron Scattering and ab Initio Study.

PubMed

Vonci, Michele; Giansiracusa, Marcus J; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

2017-01-03

Inelastic neutron scattering (INS) has been used to investigate the crystal field (CF) magnetic excitations of the analogs of the most representative lanthanoid-polyoxometalate single-molecule magnet family: Na 9 [Ln(W 5 O 18 ) 2 ] (Ln = Nd, Tb, Ho, Er). Ab initio complete active space self-consistent field/restricted active space state interaction calculations, extended also to the Dy analog, show good agreement with the experimentally determined low-lying CF levels, with accuracy better in most cases than that reported for approaches based only on simultaneous fitting to CF models of magnetic or spectroscopic data for isostructural Ln families. In this work we demonstrate the power of a combined spectroscopic and computational approach. Inelastic neutron scattering has provided direct access to CF levels, which together with the magnetometry data, were employed to benchmark the ab initio results. The ab initio determined wave functions corresponding to the CF levels were in turn employed to assign the INS transitions allowed by selection rules and interpret the observed relative intensities of the INS peaks. Ultimately, we have been able to establish the relationship between the wave function composition of the CF split Ln III ground multiplets and the experimentally measured magnetic and spectroscopic properties for the various analogs of the Na 9 [Ln(W 5 O 18 ) 2 ] family.

Pressure-induced cation-cation bonding in V 2 O 3

DOE PAGES

Bai, Ligang; Li, Quan; Corr, Serena A.; ...

2015-10-09

A pressure-induced phase transition, associated with the formation of cation-cation bonding, occurs in V 2O 3 by combining synchroton x-ray diffraction in a diamond anvil cell and ab initio evolutionary calculations. The high-pressure phase has a monoclinic structure with a C2/c space group, and it is both energetically and dynamically stable at pressures above 47 GPa to at least 105 GPa. this phase transition can be viewed as a two-dimensional Peierls-like distortion, where the cation-cation dimer chains are connected along the c axis of the monoclinic cell. In conclusion, this finding provides insights into the interplay of electron correlation andmore » lattice distortion in V 2O 3, and it may also help to understand novel properties of other early transition-metal oxides.« less

Ni2C surface carbide to catalyze low-temperature graphene growth

NASA Astrophysics Data System (ADS)

Martinez-Gordillo, Rafael; Varvenne, Céline; Amara, Hakim; Bichara, Christophe

2018-05-01

The possibility to grow a graphene layer using the chemical-vapor-deposition technique over a Ni2C /Ni (111 ) substrate has been identified experimentally, with the advantage of having a lower processing temperature (T <500 ∘C ), compared to standard growth over a Ni (111 ) surface. To understand the role of the metal carbide/metal catalyst, we first perform a static study of the Ni2C /Ni (111 ) structure and of the binding and removal of a carbon atom at the surface, using both a tight-binding (TB) energetic model and ab initio calculations. Grand-canonical Monte Carlo TB simulations then allow us (i) to determine the thermodynamic conditions to grow graphene and (ii) to separate key reaction steps in the growth mechanism explaining how the Ni2C /Ni (111 ) substrate catalyzes graphene formation at low temperature.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

PubMed

Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

2010-01-21

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

Spin-orbit coupled potential energy surfaces and properties using effective relativistic coupling by asymptotic representation.

PubMed

Ndome, Hameth; Eisfeld, Wolfgang

2012-08-14

A new method has been reported recently [H. Ndome, R. Welsch, and W. Eisfeld, J. Chem. Phys. 136, 034103 (2012)] that allows the efficient generation of fully coupled potential energy surfaces (PESs) including derivative and spin-orbit (SO) coupling. The method is based on the diabatic asymptotic representation of the molecular fine structure states and an effective relativistic coupling operator and therefore is called effective relativistic coupling by asymptotic representation (ERCAR). The resulting diabatic spin-orbit coupling matrix is constant and the geometry dependence of the coupling between the eigenstates is accounted for by the diabatization. This approach allows to generate an analytical model for the fully coupled PESs without performing any ab initio SO calculations (except perhaps for the atoms) and thus is very efficient. In the present work, we study the performance of this new method for the example of hydrogen iodide as a well-established test case. Details of the diabatization and the accuracy of the results are investigated in comparison to reference ab initio calculations. The energies of the adiabatic fine structure states are reproduced in excellent agreement with reference ab initio data. It is shown that the accuracy of the ERCAR approach mainly depends on the quality of the underlying ab initio data. This is also the case for dissociation and vibrational level energies, which are influenced by the SO coupling. A method is presented how one-electron operators and the corresponding properties can be evaluated in the framework of the ERCAR approach. This allows the computation of dipole and transition moments of the fine structure states in good agreement with ab initio data. The new method is shown to be very promising for the construction of fully coupled PESs for more complex polyatomic systems to be used in quantum dynamics studies.

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

DOE PAGES

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr; ...

2016-05-10

Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. Asmore » a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d,p) 8Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7Li and p– 8Li particle-decay channels determines some features of the 9Be spectrum above the d+ 7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, a quantitative description of the 7Li(d,p) 8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.« less

An ensemble approach to protein fold classification by integration of template-based assignment and support vector machine classifier.

PubMed

Xia, Jiaqi; Peng, Zhenling; Qi, Dawei; Mu, Hongbo; Yang, Jianyi

2017-03-15

Protein fold classification is a critical step in protein structure prediction. There are two possible ways to classify protein folds. One is through template-based fold assignment and the other is ab-initio prediction using machine learning algorithms. Combination of both solutions to improve the prediction accuracy was never explored before. We developed two algorithms, HH-fold and SVM-fold for protein fold classification. HH-fold is a template-based fold assignment algorithm using the HHsearch program. SVM-fold is a support vector machine-based ab-initio classification algorithm, in which a comprehensive set of features are extracted from three complementary sequence profiles. These two algorithms are then combined, resulting to the ensemble approach TA-fold. We performed a comprehensive assessment for the proposed methods by comparing with ab-initio methods and template-based threading methods on six benchmark datasets. An accuracy of 0.799 was achieved by TA-fold on the DD dataset that consists of proteins from 27 folds. This represents improvement of 5.4-11.7% over ab-initio methods. After updating this dataset to include more proteins in the same folds, the accuracy increased to 0.971. In addition, TA-fold achieved >0.9 accuracy on a large dataset consisting of 6451 proteins from 184 folds. Experiments on the LE dataset show that TA-fold consistently outperforms other threading methods at the family, superfamily and fold levels. The success of TA-fold is attributed to the combination of template-based fold assignment and ab-initio classification using features from complementary sequence profiles that contain rich evolution information. http://yanglab.nankai.edu.cn/TA-fold/. yangjy@nankai.edu.cn or mhb-506@163.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

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

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr

Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. Asmore » a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d,p) 8Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7Li and p– 8Li particle-decay channels determines some features of the 9Be spectrum above the d+ 7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, a quantitative description of the 7Li(d,p) 8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.« less

Curved-line search algorithm for ab initio atomic structure relaxation

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

2017-09-01

Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

Kinetic study on the H + SiH4 abstraction reaction using an ab initio potential energy surface.

PubMed

Cao, Jianwei; Zhang, Zhijun; Zhang, Chunfang; Bian, Wensheng; Guo, Yin

2011-01-14

Variational transition state theory calculations with the correction of multidimensional tunneling are performed on a 12-dimensional ab initio potential energy surface for the H + SiH(4) abstraction reaction. The surface is constructed using a dual-level strategy. For the temperature range 200-1600 K, thermal rate constants are calculated and kinetic isotope effects for various isotopic species of the title reaction are investigated. The results are in very good agreement with available experimental data.

Ab initio theory of the N2V defect in diamond for quantum memory implementation

NASA Astrophysics Data System (ADS)

Udvarhelyi, Péter; Thiering, Gergő; Londero, Elisa; Gali, Adam

2017-10-01

The N2V defect in diamond is characterized by means of ab initio methods relying on density functional theory calculated parameters of a Hubbard model Hamiltonian. It is shown that this approach appropriately describes the energy levels of correlated excited states induced by this defect. By determining its critical magneto-optical parameters, we propose to realize a long-living quantum memory by N2V defect, i.e., H 3 color center in diamond.

Ab initio calculations of potential energy curves of Hg/sub 2/ and TlHg

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

Celestino, K.C.; Ermler, W.C.

1984-08-15

Potential energy curves for electronic states of Hg/sub 2/ and TlHg are presented and analyzed. They are derived using large scale configuration interaction procedures for the valence electrons, with the core electrons represented by ab initio relativistic effective potentials. The effect of spin-orbit coupling are investigated for the low-lying excimer states. It is determined that neither system possesses strongly bound electronic states for which transitions to the repulsive ground states are optically allowed.

Development and Application of New Algorithms for the Simulation of Viscous Compressible Flows with Moving Bodies in Three Dimensions.

DTIC Science & Technology

1996-12-01

ranging from academic to industrial demonstrated the utility of the developed procedure for ab initio surface meshing from discrete data, such as...academic to industrial demonstrate the utility of the pro- hypersonic reentry problems, where ray-tracing based on posed procedure for ab initio surface...data input within industrial simulations. The origi- nal CAD dataset had over 500 surface patches, many All of the surface grids shown were obtained

Ab initio SCF calculations on the potential energy surface of potassium cyanide (KCN)

NASA Astrophysics Data System (ADS)

Wormer, Paul E. S.; Tennyson, Jonathan

1981-08-01

The potential energy surface of KCN has been generated by ab initio SCF calculations in the region of equilibrium bond distances. An analytic representation of the surface is presented. The calculations show that the bonding between K and CN is ionic, and that the structure of KCN is triangular, which confirms recent experimental findings. The computed geometry is &KCN = 62.4°, rCK = 5.492a0, and rCN = 2.186a0.

Determination of the electronic energy levels of colloidal nanocrystals using field-effect transistors and Ab-initio calculations.

PubMed

Bisri, Satria Zulkarnaen; Degoli, Elena; Spallanzani, Nicola; Krishnan, Gopi; Kooi, Bart Jan; Ghica, Corneliu; Yarema, Maksym; Heiss, Wolfgang; Pulci, Olivia; Ossicini, Stefano; Loi, Maria Antonietta

2014-08-27

Colloidal nanocrystals electronic energy levels are determined by strong size-dependent quantum confinement. Understanding the configuration of the energy levels of nanocrystal superlattices is vital in order to use them in heterostructures with other materials. A powerful method is reported to determine the energy levels of PbS nanocrystal assemblies by combining the utilization of electric-double-layer-gated transistors and advanced ab-initio theory. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab-initio study of pressure evolution of structural, mechanical and magnetic properties of cementite (Fe3C) phase

NASA Astrophysics Data System (ADS)

Gorai, S.; Ghosh, P. S.; Bhattacharya, C.; Arya, A.

2018-04-01

The pressure evolution of phase stability, structural and mechanical properties of Fe3C in ferro-magnetic (FM) and high pressure non magnetic (NM) phase is investigated from first principle calculations. The 2nd order FM to NM phase transition of Fe3C is identified around 60 GPa. Pressure (or density) variation of sound velocities from our ab-initio calculated single crystal elastic constants are determined to predict these parameters at Earth's outer core pressure.

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.

Data files for ab initio calculations of the lattice parameter and elastic stiffness coefficients of bcc Fe with solutes

DOE PAGES

Fellinger, Michael R.; Hector, Jr., Louis G.; Trinkle, Dallas R.

2016-11-29

Here, we present computed datasets on changes in the lattice parameter and elastic stiffness coefficients of BCC Fe due to substitutional Al, B, Cu, Mn, and Si solutes, and octahedral interstitial C and N solutes. The data is calculated using the methodology based on density functional theory (DFT). All the DFT calculations were performed using the Vienna Ab initio Simulations Package (VASP). The data is stored in the NIST dSpace repository.

Ab initio tensile experiment on a model of an intergranular glassy film in β-Si3N4 with prismatic surfaces

NASA Astrophysics Data System (ADS)

Ching, W. Y.; Rulis, Paul; Ouyang, Lizhi; Misra, A.

2009-02-01

We report the results of a large-scale ab initio simulation of an intergranular glassy film (IGF) model in β-Si3N4. It is shown that the stress-strain behavior under uniaxial load in the model with prismatic surfaces and few defective bonds is very different from an earlier IGF model with basal planes. The results are explained by the fundamental electronic structure of the model.

Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications

PubMed Central

2015-01-01

We report the parametrization of the approximate density functional theory, DFTB3, for magnesium and zinc for chemical and biological applications. The parametrization strategy follows that established in previous work that parametrized several key main group elements (O, N, C, H, P, and S). This 3OB set of parameters can thus be used to study many chemical and biochemical systems. The parameters are benchmarked using both gas-phase and condensed-phase systems. The gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization (MIO). The results indicate that DFTB3/3OB is particularly successful at predicting structures, including rather complex dinuclear metalloenzyme active sites, while being semiquantitative (with a typical mean absolute deviation (MAD) of ∼3–5 kcal/mol) for energetics. Single-point calculations with high-level quantum mechanics (QM) methods generally lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic properties. DFTB3/MM simulations for solution and two enzyme systems also lead to encouraging structural and energetic properties in comparison to available experimental data. The remaining limitations of DFTB3, such as the treatment of interaction between metal ions and highly charged/polarizable ligands, are also discussed. PMID:25178644

Polymer amide as an early topology.

PubMed

McGeoch, Julie E M; McGeoch, Malcolm W

2014-01-01

Hydrophobic polymer amide (HPA) could have been one of the first normal density materials to accrete in space. We present ab initio calculations of the energetics of amino acid polymerization via gas phase collisions. The initial hydrogen-bonded di-peptide is sufficiently stable to proceed in many cases via a transition state into a di-peptide with an associated bound water molecule of condensation. The energetics of polymerization are only favorable when the water remains bound. Further polymerization leads to a hydrophobic surface that is phase-separated from, but hydrogen bonded to, a small bulk water complex. The kinetics of the collision and subsequent polymerization are discussed for the low-density conditions of a molecular cloud. This polymer in the gas phase has the properties to make a topology, viz. hydrophobicity allowing phase separation from bulk water, capability to withstand large temperature ranges, versatility of form and charge separation. Its flexible tetrahedral carbon atoms that alternate with more rigid amide groups allow it to deform and reform in hazardous conditions and its density of hydrogen bonds provides adhesion that would support accretion to it of silicon and metal elements to form a stellar dust material.

Understanding the Mechanism of SiC Plasma-Enhanced Chemical Vapor Deposition (PECVD) and Developing Routes toward SiC Atomic Layer Deposition (ALD) with Density Functional Theory.

PubMed

Filatova, Ekaterina A; Hausmann, Dennis; Elliott, Simon D

2018-05-02

Understanding the mechanism of SiC chemical vapor deposition (CVD) is an important step in investigating the routes toward future atomic layer deposition (ALD) of SiC. The energetics of various silicon and carbon precursors reacting with bare and H-terminated 3C-SiC (011) are analyzed using ab initio density functional theory (DFT). Bare SiC is found to be reactive to silicon and carbon precursors, while H-terminated SiC is found to be not reactive with these precursors at 0 K. Furthermore, the reaction pathways of silane plasma fragments SiH 3 and SiH 2 are calculated along with the energetics for the methane plasma fragments CH 3 and CH 2 . SiH 3 and SiH 2 fragments follow different mechanisms toward Si growth, of which the SiH 3 mechanism is found to be more thermodynamically favorable. Moreover, both of the fragments were found to show selectivity toward the Si-H bond and not C-H bond of the surface. On the basis of this, a selective Si deposition process is suggested for silicon versus carbon-doped silicon oxide surfaces.

Linking molecular level chemistry to macroscopic combustion behavior for nano-energetic materials with halogen containing oxides.

PubMed

Farley, Cory W; Pantoya, Michelle L; Losada, Martin; Chaudhuri, Santanu

2013-08-21

Coupling molecular scale reaction kinetics with macroscopic combustion behavior is critical to understanding the influences of intermediate chemistry on energy propagation, yet bridging this multi-scale gap is challenging. This study integrates ab initio quantum chemical calculations and condensed phase density functional theory to elucidate factors contributing to experimentally measured high flame speeds (i.e., >900 m∕s) associated with halogen based energetic composites, such as aluminum (Al) and iodine pentoxide (I2O5). Experiments show a direct correlation between apparent activation energy and flame speed suggesting that flame speed is directly influenced by chemical kinetics. Toward this end, the first principle simulations resolve key exothermic surface and intermediate chemistries contributing toward the kinetics that promote high flame speeds. Linking molecular level exothermicity to macroscopic experimental investigations provides insight into the unique role of the alumina oxide shell passivating aluminum particles. In the case of Al reacting with I2O5, the alumina shell promotes exothermic surface chemistries that reduce activation energy and increase flame speed. This finding is in contrast to Al reaction with metal oxides that show the alumina shell does not participate exothermically in the reaction.

Isomers and conformational barriers of gas phase nicotine, nornicotine and their protonated forms

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

Yoshida, Tomoki; Farone, William A.; Xantheas, Sotiris S.

We report extensive conformational searches of the neutral nicotine, nornicotine and their protonated analogs that are based on ab-initio second order Møller-Plesset perturbation (MP2) electronic structure calculations. Initial searches were performed with the 6-31G(d,p) and the energetics of the most important structures were further refined from geometry optimizations with the aug-cc-pVTZ basis set. Based on the calculated free energies at T=298 K for the gas phase molecules, neutral nicotine has two dominant trans conformers, whereas neutral nornicotine is a mixture of several conformers. For nicotine, the protonation on both the pyridine and the pyrrolidine sites is energetically competitive, whereas nornicotinemore » prefers protonation on the pyridine nitrogen. The protonated form of nicotine is mainly a mixture of two pyridine-protonated trans conformers and two pyrrolidine-protonated trans conformers, whereas the protonated form of nornicotine is a mixture of four pyridine-protonated trans conformers. Nornicotine is conformationally more flexible than nicotine, however it is less protonated at the biologically important pyrrolidine nitrogen site. The lowest energy isomers for each case were found to interconvert via low (< 6 kcal/mol) rotational barriers around the pyridine-pyrrolidine bond.« less

Importance of many-body dispersion and temperature effects on gas-phase gold cluster (meta)stability

NASA Astrophysics Data System (ADS)

Goldsmith, Bryan R.; Gruene, Philipp; Lyon, Jonathan T.; Rayner, David M.; Fielicke, André; Scheffler, Matthias; Ghiringhelli, Luca M.

Gold clusters in the gas phase exhibit many structural isomers that are shown to intercovert frequently, even at room temperature. We performed ab initio replica-exchange molecular dynamics (REMD) calculations on gold clusters (of sizes 5-14 atoms) to identify metastable states and their relative populations at finite temperature, as well as to examine the importance of temperature and van der Waals (vdW) on their isomer energetic ordering. Free energies of the gold cluster isomers are optimally estimated using the Multistate Bennett Acceptance Ratio. The distribution of bond coordination numbers and radius of gyration are used to address the challenge of discriminating isomers along their dynamical trajectories. Dispersion effects are important for stabilizing three-dimensional structures relative to planar structures and brings isomer energetic predictions to closer quantitative agreement compared with RPA@PBE calculations. We find that higher temperatures typically stabilize metastable three-dimensional structures relative to planar/quasiplanar structures. Computed IR spectra of low free energy Au9, Au10, and Au12 isomers are in agreement with experimental spectra obtained by far-IR multiple photon dissociation in a molecular beam at 100 K.

Structure, energetics and vibrational spectra of dimers, trimers, and tetramers of HX (X = Cl, Br, I)

NASA Astrophysics Data System (ADS)

Latajka, Zdzislaw; Scheiner, Steve

1997-03-01

The title complexes are studied by correlated ab initio methods using a pseudopotential double-ζ basis set, augmented by diffuse sp and two sets of polarization functions. The binding energies of the complexes decrease in the order HCl > HBr > HI. In the mixed HX…HX' dimers, the nature of the proton-donor molecule is more important than is the proton-acceptor with respect to the strength of the interaction. Only one minimum is found on the potential energy surface of the trimers and tetramers, which corresponds to the C nh cyclic structure. Enlargement of the complex leads to progressively greater individual H-bond energy and HX bond stretch, coupled with reduced intermolecular separation and smaller nonlinearity of each H-bond. Electron correlation makes a larger contribution as the atomic number of X increases. The highest degree of cooperativity is noted for oligomers of HCl and HBr, as compared to HI. The nonadditivity is dominated by terms present at the SCF level. The vibrational frequencies exhibit trends that generally parallel the energetics and geometry patterns, particularly the red shifts of the HX stretches and the intermolecular modes.

The Pariser-Parr-Pople model for trans-polyenes. I. Ab initio and semiempirical study of the bond alternation in trans-butadiene

NASA Astrophysics Data System (ADS)

Förner, Wolfgang

1992-03-01

Ab initio investigations of the bond alternation in butadiene are presented. The atomic basis sets applied range from minimal to split valence plus polarization quality. With the latter one the Hartree-Fock limit for the bond alternation is reached. Correlation is considered on Møller-Plesset many-body perturbation theory of second order (MP2), linear coupled cluster doubles (L-CCD) and coupled cluster doubles (CCD) level. For the smaller basis sets it is shown that for the bond alternation π-π correlations are essential while the effects of σ-σ and σ-π correlations are, though large, nearly independent of bond alternation. On MP2 level the variation of σ-π correlation with bond alternation is surprisingly large. This is discussed as an artefact of MP2. Comparative Su-Schrieffer-Heeger (SSH) and Pariser-Parr-Pople (PPP) calculations show that these models in their usual parametrizations cannot reproduce the ab initio results.

Operator evolution for ab initio electric dipole transitions of 4He

DOE PAGES

Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; ...

2015-07-24

A goal of nuclear theory is to make quantitative predictions of low-energy nuclear observables starting from accurate microscopic internucleon forces. A major element of such an effort is applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence of ab initio calculations as a function of the model space size. The consistent simultaneous transformation of external operators, however, has been overlooked in applications of the theory, particularly for nonscalar transitions. We study the evolution of the electric dipole operator in the framework of the similarity renormalization group method and apply the renormalized matrix elements to the calculationmore » of the 4He total photoabsorption cross section and electric dipole polarizability. All observables are calculated within the ab initio no-core shell model. Furthermore, we find that, although seemingly small, the effects of evolved operators on the photoabsorption cross section are comparable in magnitude to the correction produced by including the chiral three-nucleon force and cannot be neglected.« less

Three-cluster dynamics within an ab initio framework

DOE PAGES

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 calculations of the concentration dependent band gap reduction in dilute nitrides

NASA Astrophysics Data System (ADS)

Rosenow, Phil; Bannow, Lars C.; Fischer, Eric W.; Stolz, Wolfgang; Volz, Kerstin; Koch, Stephan W.; Tonner, Ralf

2018-02-01

While being of persistent interest for the integration of lattice-matched laser devices with silicon circuits, the electronic structure of dilute nitride III/V-semiconductors has presented a challenge to ab initio computational approaches. The origin of the computational problems is the strong distortion exerted by the N atoms on most host materials. Here, these issues are resolved by combining density functional theory calculations based on the meta-GGA functional presented by Tran and Blaha (TB09) with a supercell approach for the dilute nitride Ga(NAs). Exploring the requirements posed to supercells, it is shown that the distortion field of a single N atom must be allowed to decrease so far that it does not overlap with its periodic images. This also prevents spurious electronic interactions between translational symmetric atoms, allowing us to compute band gaps in very good agreement with experimentally derived reference values. In addition to existing approaches, these results offer a promising ab initio avenue to the electronic structure of dilute nitride semiconductor compounds.

Ab Initio Classical Dynamics Simulations of CO_2 Line-Mixing Effects in Infrared Bands

NASA Astrophysics Data System (ADS)

Lamouroux, Julien; Hartmann, Jean-Michel; Tran, Ha; Snels, Marcel; Stefani, Stefania; Piccioni, Giuseppe

2013-06-01

Ab initio calculations of line-mixing effects in CO_2 infrared bands are presented and compared with experiments. The predictions were carried using requantized Classical Dynamics Molecular Simulations (rCDMS) based on an approach previously developed and successfully tested for CO_2 isolated line shapes. Using classical dynamics equations, the force and torque applied to each molecule by the surrounding molecules (described by an ab initio intermolecular potential) are computed at each time step. This enables, using a requantization procedure, to predict dipole and isotropic polarizability auto-correlation functions whose Fourier-Laplace transforms yield the spectra. The quality of the rCDMS calculations is demonstrated by comparisons with measured spectra in the spectral regions of the 3ν_3 and 2ν_1+2ν_2+ν_3 Infrared bands. J.-M. Hartmann, H. Tran, N. H. Ngo, et al., Phys. Rev. Lett. A {87} (2013), 013403. H. Tran, C. Boulet, M. Snels, S. Stefani, J. Quant. Spectrosc. Radiat. Transfer {112} (2011), 925-936.

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.

Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

PubMed

Hoy, Erik P; Mazziotti, David A

2015-08-14

Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

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

NASA Astrophysics Data System (ADS)

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

2012-09-01

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

Towards an ab-initio treatment of nonlocal electronic correlations with dynamical vertex approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Gunacker, Patrik; Tomczak, Jan; Thunström, Patrik; Held, Karsten

Recently, approaches such as the dynamical vertex approximation (D ΓA) or the dual-fermion method have been developed. These diagrammatic approaches are going beyond dynamical mean field theory (DMFT) by including nonlocal electronic correlations on all length scales as well as the local DMFT correlations. Here we present our efforts to extend the D ΓA methodology to ab-initio materials calculations (ab-initio D ΓA). Our approach is a unifying framework which includes both GW and DMFT-type of diagrams, but also important nonlocal correlations beyond, e.g. nonlocal spin fluctuations. In our multi-band implementation we are using a worm sampling technique within continuous-time quantum Monte Carlo in the hybridization expansion to obtain the DMFT vertex, from which we construct the reducible vertex function using the two particle-hole ladders. As a first application we show results for transition metal oxides. Support by the ERC project AbinitioDGA (306447) is acknowledged.

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

PubMed

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

2014-08-28

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

Multiscale modeling of current-induced switching in magnetic tunnel junctions using ab initio spin-transfer torques

NASA Astrophysics Data System (ADS)

Ellis, Matthew O. A.; Stamenova, Maria; Sanvito, Stefano

2017-12-01

There exists a significant challenge in developing efficient magnetic tunnel junctions with low write currents for nonvolatile memory devices. With the aim of analyzing potential materials for efficient current-operated magnetic junctions, we have developed a multi-scale methodology combining ab initio calculations of spin-transfer torque with large-scale time-dependent simulations using atomistic spin dynamics. In this work we introduce our multiscale approach, including a discussion on a number of possible schemes for mapping the ab initio spin torques into the spin dynamics. We demonstrate this methodology on a prototype Co/MgO/Co/Cu tunnel junction showing that the spin torques are primarily acting at the interface between the Co free layer and MgO. Using spin dynamics we then calculate the reversal switching times for the free layer and the critical voltages and currents required for such switching. Our work provides an efficient, accurate, and versatile framework for designing novel current-operated magnetic devices, where all the materials details are taken into account.

Ab initio Computations of the Electronic, Mechanical, and Thermal Properties of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2

NASA Technical Reports Server (NTRS)

Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray

2011-01-01

Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.

Phenolic Polymer Solvation in Water and Ethylene Glycol, II: Ab Initio Computations.

PubMed

Bauschlicher, Charles W; Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Lawson, John W

2017-04-06

Ab initio techniques are used to study the interaction of ethylene glycol and water with a phenolic polymer. The water bonds more strongly with the phenolic OH than with the ring. The phenolic OH groups can form hydrogen bonds between themselves. For more than one water molecule, there is a competition between water-water and water-phenolic interactions. Ethylene glycol shows the same effects as those of water, but the potential energy surface is further complicated by CH 2 -phenolic interactions, different conformers of ethylene glycol, and two OH groups on each molecule. Thus, the ethylene glycol-phenolic potential is more complicated than the water-phenolic potential. The results of the ab initio calculations are compared to those obtained using a force field. These calibration studies show that the water system is easier to describe than the ethylene glycol system. The calibration studies confirm the reliability of force fields used in our companion molecular dynamics study of a phenolic polymer in water and ethylene solutions.

Multiple emissions of benzil at room temperature and 77 K and their assignments from ab initio quantum chemical calculations

NASA Astrophysics Data System (ADS)

Bhattacharya, Bhaswati; Jana, Barnali; Bose, Debosreeta; Chattopadhyay, Nitin

2011-01-01

Multiple emissions have been observed from benzil under different conditions in solutions at room temperature as well as in low temperature glass matrices at 77 K. Low temperature emission has been monitored in rigid matrices frozen under different conditions of illumination. Steady state and time-resolved results together with the ab initio quantum chemical calculations provide, for the first time, the assignments of the different fluorescence bands to the different geometries and/or electronic states of the fluorophore molecule. It is revealed that the skew form of benzil emits from the first (S1) as well as the second excited singlet (S2) states depending on the excitation wavelength, while the relaxed transplanar conformer fluoresces only from the S1 state. The yet unexplored emission band peaking at around 360 nm has been assigned to originate from the S2 state. Ab initio calculations using the density functional theory at B3LYP/6-31G** level corroborate well with the experimental observations.

Multiple emissions of benzil at room temperature and 77 K and their assignments from ab initio quantum chemical calculations.

PubMed

Bhattacharya, Bhaswati; Jana, Barnali; Bose, Debosreeta; Chattopadhyay, Nitin

2011-01-28

Multiple emissions have been observed from benzil under different conditions in solutions at room temperature as well as in low temperature glass matrices at 77 K. Low temperature emission has been monitored in rigid matrices frozen under different conditions of illumination. Steady state and time-resolved results together with the ab initio quantum chemical calculations provide, for the first time, the assignments of the different fluorescence bands to the different geometries and∕or electronic states of the fluorophore molecule. It is revealed that the skew form of benzil emits from the first (S(1)) as well as the second excited singlet (S(2)) states depending on the excitation wavelength, while the relaxed transplanar conformer fluoresces only from the S(1) state. The yet unexplored emission band peaking at around 360 nm has been assigned to originate from the S(2) state. Ab initio calculations using the density functional theory at B3LYP∕6-31G∗∗ level corroborate well with the experimental observations.

Vibrational inelastic and charge transfer processes in H++H2 system: An ab initio study

NASA Astrophysics Data System (ADS)

Amaran, Saieswari; Kumar, Sanjay

2007-12-01

State-resolved differential cross sections, total and integral cross sections, average vibrational energy transfer, and the relative probabilities are computed for the H++H2 system using the newly obtained ab initio potential energy surfaces at the full CI/cc-pVQZ level of accuracy which allow for both the direct vibrational inelastic and the charge transfer processes. The quantum dynamics is treated within the vibrational close-coupling infinite-order-sudden approximation approach using the two ab initio quasidiabatic potential energy surfaces. The computed collision attributes for both the processes are compared with the available state-to-state scattering experiments at Ec.m.=20eV. The results are in overall good agreement with most of the observed scattering features such as rainbow positions, integral cross sections, and relative vibrational energy transfers. A comparison with the earlier theoretical study carried out on the semiempirical surfaces (diatomics in molecules) is also made to illustrate the reliability of the potential energy surfaces used in the present work.

Nonconventional screening of the Coulomb interaction in FexOy clusters: An ab initio study

NASA Astrophysics Data System (ADS)

Peters, L.; Şaşıoǧlu, E.; Rossen, S.; Friedrich, C.; Blügel, S.; Katsnelson, M. I.

2017-04-01

From microscopic point-dipole model calculations of the screening of the Coulomb interaction in nonpolar systems by polarizable atoms, it is known that screening strongly depends on dimensionality. For example, in one-dimensional systems, the short-range interaction is screened, while the long-range interaction is antiscreened. This antiscreening is also observed in some zero-dimensional structures, i.e., molecular systems. By means of ab initio calculations in conjunction with the random-phase approximation (RPA) within the FLAPW method, we study screening of the Coulomb interaction in FexOy clusters. For completeness, these results are compared with their bulk counterpart magnetite. It appears that the on-site Coulomb interaction is very well screened both in the clusters and bulk. On the other hand, for the intersite Coulomb interaction, the important observation is made that it is almost constant throughout the clusters, while for the bulk it is almost completely screened. More precisely and interestingly, in the clusters antiscreening is observed by means of ab initio calculations.

A permutationally invariant full-dimensional ab initio potential energy surface for the abstraction and exchange channels of the H + CH{sub 4} system

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

Li, Jun, E-mail: jli15@cqu.edu.cn, E-mail: zhangdh@dicp.ac.cn; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131; Chen, Jun

2015-05-28

We report a permutationally invariant global potential energy surface (PES) for the H + CH{sub 4} system based on ∼63 000 data points calculated at a high ab initio level (UCCSD(T)-F12a/AVTZ) using the recently proposed permutation invariant polynomial-neural network method. The small fitting error (5.1 meV) indicates a faithful representation of the ab initio points over a large configuration space. The rate coefficients calculated on the PES using tunneling corrected transition-state theory and quasi-classical trajectory are found to agree well with the available experimental and previous quantum dynamical results. The calculated total reaction probabilities (J{sub tot} = 0) including themore » abstraction and exchange channels using the new potential by a reduced dimensional quantum dynamic method are essentially the same as those on the Xu-Chen-Zhang PES [Chin. J. Chem. Phys. 27, 373 (2014)].« less

Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory

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.

Ab initio study of the structural properties of acetonitrile-water mixtures

NASA Astrophysics Data System (ADS)

Chen, Jinfan; Sit, Patrick H.-L.

2015-08-01

Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.

Using Ab-Initio Calculations to Appraise Stm-Based - and Kink-Formation Energies

NASA Astrophysics Data System (ADS)

Feibelman, Peter J.

2001-03-01

Ab-initio total energies can and should be used to test the typically model-dependent results of interpreting STM morphologies. The benefits of such tests are illustrated here by ab-initio energies of step- and kink-formation on Pb and Pt(111) which show that the STM-based values of the kink energies must be revised. On Pt(111), the computed kink-energies for (100)- and (111)-microfacet steps are about 0.25 and 0.18 eV. These results imply a specific ratio of formation energies for the two step types, namely 1.14, in excellent agreement with experiment. If kink-formation actually cost the same energy on the two step types, an inference drawn from scanning probe observations of step wandering,(M. Giesen et al., Surf. Sci. 366, 229(1996).) this ratio ought to be 1. In the case of Pb(111), though computed energies to form (100)- and (111)-microfacet steps agree with measurement, the ab-initio kink-formation energies for the two step types, 41 and 60 meV, are 40-50% below experimental values drawn from STM images.(K. Arenhold et al., Surf. Sci. 424, 271(1999).) The discrepancy results from interpreting the images with a step-stiffness vs. kink-energy relation appropriate to (100) but not (111) surfaces. Good agreement is found when proper account of the trigonal symmetry of Pb(111) is taken in reinterpreting the step-stiffness data.

Summary of Research/Publications

NASA Technical Reports Server (NTRS)

1997-01-01

Summary of research/publications include:(1) Comment on broadening of water microwave lines by collisions with helium atoms; (2) Calculations of ion-molecule deuterium fractionation reactions involving HD; (3) Ab initio predictions on the rotational spectra of carbon-chain carbene molecules; (4) Theoretical IR spectra of ionized naphthalene; (5) Improved collisional excitation rates for interstellar water; (6) Calculations on the competition between association and reaction for C3H+ + H2; (7) Theoretical infrared spectra of some model polycyclic aromatic hydrocarbons: effect of ionization; (8) Calculations concerning interstellar isomeric abundance ratios for C3H and C3H2; (9) New calculations on the ion-molecule processes C2H2+ + H2 C2H3+ + H and C2H2+ + H2 C2H4+; (10) Anisotropic rigid rotor potential energy function for H2O-H2; (11) A correlated ab initio study of linear carbon-chain radicals CnH (n=2-7); (12) Ab initio characterization of MgCCH, MgCCH+, and MgC2 and pathways to their formation in the interstellar medium; (13) Why HOC+ is detectable in interstellar clouds: The rate of the reaction between HOC+ and H2; (14) A correlated ab initio study of the X 2A 1 and A 2E states of MgCH3; (15) On the stability of interstellar carbon clusters: The rate of the reaction between C3 and O; and (16) The rate of the reaction between CN and C2H2 at interstellar temperatures.

Interaction of single-walled carbon nanotubes and saxitoxin: Ab initio simulations and biological responses in hippocampal cell line HT-22.

PubMed

Ramos, Patrícia; Schmitz, Marcos; Filgueira, Daza; Votto, Ana Paula; Durruthy, Michael; Gelesky, Marcos; Ruas, Caroline; Yunes, João; Tonel, Mariana; Fagan, Solange; Monserrat, José

2017-07-01

Saxitoxins (STXs) are potent neurotoxins that also induce cytotoxicity through the generation of reactive oxygen species. Carbon nanotubes (CNTs) are nanomaterials that can promote a Trojan horse effect, facilitating the entry of toxic molecules to cells when adsorbed to nanomaterials. The interaction of pristine single-walled (SW)CNTs and carboxylated (SWCNT-COOH) nanotubes with STX was evaluated by ab initio simulation and bioassays using the cell line HT-22. Cells (5 × 10 4  cells/mL) were exposed to SWCNT and SWCNT-COOH (5 μg mL -1 ), STX (200 μg L -1 ), SWCNT+STX, and SWCNT-COOH+STX for 30 min or 24 h. Results of ab initio simulation showed that the interaction between SWCNT and SWCNT-COOH with STX occurs in a physisorption. The interaction of SWCNT+STX induced a decrease in cell viability. Cell proliferation was not affected in any treatment after 30 min or 24 h of exposure (p > 0.05). Treatment with SWCNT-COOH induced high reactive oxygen species levels, an effect attenuated in SWCNT-COOH+STX treatment. In terms of cellular oxygen consumption, both CNTs when coexposed with STX antagonize the toxin effect. Based on these results, it can be concluded that the results obtained in vitro corroborate the semiempirical evidence found using density functional theory ab initio simulation. Environ Toxicol Chem 2017;36:1728-1737. © 2016 SETAC. © 2016 SETAC.

A Model for Predicting Thermoelectric Properties of Bi2Te3

NASA Technical Reports Server (NTRS)

Lee, Seungwon; VonAllmen, Paul

2009-01-01

A parameterized orthogonal tight-binding mathematical model of the quantum electronic structure of the bismuth telluride molecule has been devised for use in conjunction with a semiclassical transport model in predicting the thermoelectric properties of doped bismuth telluride. This model is expected to be useful in designing and analyzing Bi2Te3 thermoelectric devices, including ones that contain such nano - structures as quantum wells and wires. In addition, the understanding gained in the use of this model can be expected to lead to the development of better models that could be useful for developing other thermoelectric materials and devices having enhanced thermoelectric properties. Bi2Te3 is one of the best bulk thermoelectric materials and is widely used in commercial thermoelectric devices. Most prior theoretical studies of the thermoelectric properties of Bi2Te3 have involved either continuum models or ab-initio models. Continuum models are computationally very efficient, but do not account for atomic-level effects. Ab-initio models are atomistic by definition, but do not scale well in that computation times increase excessively with increasing numbers of atoms. The present tight-binding model bridges the gap between the well-scalable but non-atomistic continuum models and the atomistic but poorly scalable ab-initio models: The present tight-binding model is atomistic, yet also computationally efficient because of the reduced (relative to an ab-initio model) number of basis orbitals and flexible parameterization of the Hamiltonian.

Acceleration of saddle-point searches with machine learning.

PubMed

Peterson, Andrew A

2016-08-21

In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the number of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

Acceleration of saddle-point searches with machine learning

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

Peterson, Andrew A., E-mail: andrew-peterson@brown.edu

In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the numbermore » of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.« less

Computational study of collisions between O({sup 3}P) and NO({sup 2}Π) at temperatures relevant to the hypersonic flight regime

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

Castro-Palacio, Juan Carlos; Nagy, Tibor; Meuwly, Markus, E-mail: m.meuwly@unibas.ch

2014-10-28

Reactions involving N and O atoms dominate the energetics of the reactive air flow around spacecraft when reentering the atmosphere in the hypersonic flight regime. For this reason, the thermal rate coefficients for reactive processes involving O({sup 3}P) and NO({sup 2}Π) are relevant over a wide range of temperatures. For this purpose, a potential energy surface (PES) for the ground state of the NO{sub 2} molecule is constructed based on high-level ab initio calculations. These ab initio energies are represented using the reproducible kernel Hilbert space method and Legendre polynomials. The global PES of NO{sub 2} in the ground statemore » is constructed by smoothly connecting the surfaces of the grids of various channels around the equilibrium NO{sub 2} geometry by a distance-dependent weighting function. The rate coefficients were calculated using Monte Carlo integration. The results indicate that at high temperatures only the lowest A-symmetry PES is relevant. At the highest temperatures investigated (20 000 K), the rate coefficient for the “O1O2+N” channel becomes comparable (to within a factor of around three) to the rate coefficient of the oxygen exchange reaction. A state resolved analysis shows that the smaller the vibrational quantum number of NO in the reactants, the higher the relative translational energy required to open it and conversely with higher vibrational quantum number, less translational energy is required. This is in accordance with Polanyi's rules. However, the oxygen exchange channel (NO2+O1) is accessible at any collision energy. Finally, this work introduces an efficient computational protocol for the investigation of three-atom collisions in general.« less

Computational study of collisions between O(3P) and NO(2Π) at temperatures relevant to the hypersonic flight regime.

PubMed

Castro-Palacio, Juan Carlos; Nagy, Tibor; Bemish, Raymond J; Meuwly, Markus

2014-10-28

Reactions involving N and O atoms dominate the energetics of the reactive air flow around spacecraft when reentering the atmosphere in the hypersonic flight regime. For this reason, the thermal rate coefficients for reactive processes involving O((3)P) and NO((2)Π) are relevant over a wide range of temperatures. For this purpose, a potential energy surface (PES) for the ground state of the NO2 molecule is constructed based on high-level ab initio calculations. These ab initio energies are represented using the reproducible kernel Hilbert space method and Legendre polynomials. The global PES of NO2 in the ground state is constructed by smoothly connecting the surfaces of the grids of various channels around the equilibrium NO2 geometry by a distance-dependent weighting function. The rate coefficients were calculated using Monte Carlo integration. The results indicate that at high temperatures only the lowest A-symmetry PES is relevant. At the highest temperatures investigated (20,000 K), the rate coefficient for the "O1O2+N" channel becomes comparable (to within a factor of around three) to the rate coefficient of the oxygen exchange reaction. A state resolved analysis shows that the smaller the vibrational quantum number of NO in the reactants, the higher the relative translational energy required to open it and conversely with higher vibrational quantum number, less translational energy is required. This is in accordance with Polanyi's rules. However, the oxygen exchange channel (NO2+O1) is accessible at any collision energy. Finally, this work introduces an efficient computational protocol for the investigation of three-atom collisions in general.

Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study.

PubMed

Dong, Minghui; Liu, Haiyan

2008-08-21

The Escherichia coli peptide deformylase (PDF) and Bacillus thermoproteolyticus thermolysin (TLN) are two representative metal-requiring peptidases having remarkably similar active centers but distinctively different metal preferences. Zinc is a competent catalytic cofactor for TLN but not for PDF. Reaction pathways and the associated energetics for both enzymes were determined using combined semiempirical and ab initio quantum mechanical/molecular mechanical modeling, without presuming reaction coordinates. The results confirmed that both enzymes catalyze via the same chemical steps, and reproduced their different preferences for zinc or iron as competent cofactors. Further analyses indicated that different feasibility of the nucleophilic attack step leads to different metal preferences of the two enzymes. In TLN, the substrate is strongly activated and can serve as the fifth coordination ligand of zinc prior to the chemical steps. In PDF, the substrate carbonyl is activated by the chemical step itself, and becomes the fifth coordination partner of zinc only in a later stage of the nucleophilic attack. These leads to a much more difficult nucleophilic attack in PDF than in TLN. Different from some earlier suggestions, zinc has no difficulty in accepting an activated substrate as the fifth ligand to switch from tetra- to penta-coordination in either PDF or TLN. When iron replaces zinc, its stronger interaction with the hydroxide ligand may lead to higher activation barrier in TLN. In PDF, the stronger interactions of iron with ligands allow iron-substrate coordination to take place either before or at a very early stage of the chemical step, leading to effective catalysis. Our calculations also show combined semiempirical and ab initio quantum mechanical modeling can be efficient approaches to explore complicated reaction pathways in enzyme systems.

Adsorption and dissociation of H2O on the (001) surface of uranium mononitride: energetics and mechanism from first-principles investigation.

PubMed

Bo, Tao; Lan, Jian-Hui; Zhang, Yu-Juan; Zhao, Yao-Lin; He, Chao-Hui; Chai, Zhi-Fang; Shi, Wei-Qun

2016-05-21

The interfacial interaction of uranium mononitride (UN) with water from the environment unavoidably leads to corrosion of nuclear fuels, which affects a lot of processes in the nuclear fuel cycle. In this work, the microscopic adsorption behaviors of water on the UN(001) surface as well as water dissociation and accompanying H2 formation mechanisms have been investigated on the basis of DFT+U calculations and ab initio atomistic thermodynamics. For adsorption of one H2O monomer, the predicted adsorption energies are -0.88, -2.07, and -2.07 eV for the most stable molecular, partially dissociative, and completely dissociative adsorption, respectively. According to our calculations, a water molecule dissociates into OH and H species via three pathways with small energy barriers of 0.78, 0.72, and 0.85 eV, respectively. With the aid of the neighboring H atom, H2 formation through the reaction of H* + OH* can easily occur via two pathways with energy barriers of 0.61 and 0.36 eV, respectively. The molecular adsorption of water shows a slight coverage dependence on the surface while this dependence becomes obvious for partially dissociative adsorption as the water coverage increases from 1/4 to 1 ML. In addition, based on the "ab initio atomistic thermodynamic" simulations, increasing H2O partial pressure will enhance the stability of the adsorbed system and water coverage, while increasing temperature will decrease the H2O coverage. We found that the UN(001) surface reacts easily with H2O at room temperature, leading to dissolution and corrosion of the UN fuel materials.

Gas-Phase Molecular Structure of Nopinone and its Water Complexes Studied by Microwave Fourier Transform Spectroscopy and Quantum Chemical Calculations

NASA Astrophysics Data System (ADS)

Neeman, Elias M.; Aviles Moreno, Juan-Ramon; Huet, T. R.

2016-06-01

Several monoterpenes and terpenoids are biogenic volatile organic compounds which are emitted in the atmosphere, where they react with OH, O_3 and NO_x etc. to give rise to several oxidation and degradation products. Their decomposition products are a major source of secondray organic aerosol (SOA). Spectroscopic information on these atmospheric species is still very scarce. The rotational spectrum of nopinone (C_9H14O) one of the major oxidation products of β-pinene, and of its water complexes were recorded in a supersonic jet expansion with a Fourier transform microwave spectrometer over the range 2-20 GHz. The structure of the unique stable conformer of the nopinone was optimized using density functional theory and ab initio calculations. Signals from the parent species and from the 13C and 18O isotopomers were observed in natural abundance. A magnetic hyperfine structure associated with the pairs of hydrogen nuclei in the methylene groups was observed and modeled. The structures of several conformers of the nopinone-water complexes with up to three molecules of water were optimized using density functional theory and ab initio calculations. The energetically most stable of calculated conformers were observed and anlyzed. The rotational and centrifugal distortion parameters were fitted to a Watson's Hamiltonian in the A-reduction. The present work provides the first spectroscopic characterization of nopinone and its water complexes in the gas phase. A. Calogirou, B.R. Larsen, and D. Kotzias, Atmospheric Environment, 33, 1423-1439, (1999) P. Paasonen et al., Nat. Geosci., 6, 438-442 (2013) D. Zhang and R. Zhang The Journal of Chemical Physics, 122, 114308, (2005) R. Winterhalter et al. Journal of Atmospheric Chemistry, 35, 165-197, (2000)

On the elimination of the electronic structure bottleneck in on the fly nonadiabatic dynamics for small to moderate sized (10-15 atom) molecules using fit diabatic representations based solely on ab initio electronic structure data: The photodissociation of phenol

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

Zhu, Xiaolei, E-mail: virtualzx@gmail.com; Yarkony, David R., E-mail: yarkony@jhu.edu

2016-01-14

In this work, we demonstrate that for moderate sized systems, here a system with 13 atoms, global coupled potential energy surfaces defined for several electronic states over a wide energy range and for distinct regions of nuclear coordinate space characterized by distinct electron configurations, can be constructed with precise energetics and an excellent description of non-adiabatic interactions in all regions. This is accomplished using a recently reported algorithm for constructing quasi-diabatic representations, H{sup d}, of adiabatic electronic states coupled by conical intersections. In this work, the algorithm is used to construct an H{sup d} to describe the photodissociation of phenolmore » from its first and second excited electronic states. The representation treats all 33 internal degrees of freedom in an even handed manner. The ab initio adiabatic electronic structure data used to construct the fit are obtained exclusively from multireference configuration interaction with single and double excitation wave functions comprised of 88 × 10{sup 6} configuration state functions, at geometries determined by quasi-classical trajectories. Since the algorithm uses energy gradients and derivative couplings in addition to electronic energies to construct H{sup d}, data at only 7379 nuclear configurations are required to construct a representation, which describes all nuclear configurations involved in H atom photodissociation to produce the phenoxyl radical in its ground or first excited electronic state, with a mean unsigned energy error of 202.9 cm{sup −1} for electronic energies <60 000 cm{sup −1}.« less

Ab Initio Ligand Field Molecular Mechanics and the Nature of Metal-Ligand π-Bonding in Fe(II) 2,6-di(pyrazol-1-yl)pyridine Spin Crossover Complexes.

PubMed

Deeth, Robert J; Halcrow, Malcolm A; Kershaw Cook, Laurence J; Raithby, Paul R

2018-04-06

A ligand field molecular mechanics (LFMM) force field has been constructed for the spin states of [Fe(bpp) 2 ] 2+ (bpp=2,6-di(pyrazol-1-yl)pyridine) and related complexes. A new charge scheme is employed which interpolates between partial charges for neutral bpp and protonated [H 3 bpp] 3+ to achieve a target metal charge. The LFMM angular overlap model (AOM) parameters are fitted to fully ab initio d orbital energies. However, several AOM parameter sets are possible. The ambiguity is resolved by calculating the Jahn-Teller distortion mode for high spin, which indicates that in [Fe(bpp) 2 ] 2+ pyridine is a π-acceptor and pyrazole a weak π-donor. The alternative fit, assumed previously, where both ligands act as π-donors leads to an inconsistent distortion. LFMM optimisations in the presence of [BF 4 ] - or [PF 6 ] - anions are in good agreement with experiment and the model also correctly predicts the spin state energetics for 3-pyrazolyl substituents where the interactions are mainly steric. However, for 4-pyridyl or 4-pyrazolyl substituents, LFMM only treats the electrostatic contribution which, for the pyridyl substituents, generates a fair correlation with the spin crossover transition temperatures, T 1/2 , but in the reverse sense to the dominant electronic effect. Thus, LFMM generates its smallest spin state energy difference for the substituent with the highest T 1/2 . One parameter set for all substituted bpp ligands is insufficient and further LFMM development will be required. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Calcium-decorated carbyne networks as hydrogen storage media.

PubMed

Sorokin, Pavel B; Lee, Hoonkyung; Antipina, Lyubov Yu; Singh, Abhishek K; Yakobson, Boris I

2011-07-13

Among the carbon allotropes, carbyne chains appear outstandingly accessible for sorption and very light. Hydrogen adsorption on calcium-decorated carbyne chain was studied using ab initio density functional calculations. The estimation of surface area of carbyne gives the value four times larger than that of graphene, which makes carbyne attractive as a storage scaffold medium. Furthermore, calculations show that a Ca-decorated carbyne can adsorb up to 6 H(2) molecules per Ca atom with a binding energy of ∼0.2 eV, desirable for reversible storage, and the hydrogen storage capacity can exceed ∼8 wt %. Unlike recently reported transition metal-decorated carbon nanostructures, which suffer from the metal clustering diminishing the storage capacity, the clustering of Ca atoms on carbyne is energetically unfavorable. Thermodynamics of adsorption of H(2) molecules on the Ca atom was also investigated using equilibrium grand partition function.

Body-centered orthorhombic C 16 : A novel topological node-line semimetal

DOE PAGES

Wang, Jian -Tao; Weng, Hongming; Nie, Simin; ...

2016-05-11

We identify by ab initio calculations a novel topological semimetal carbon phase in all-sp 2 bonding networks with a 16-atom body-centered orthorhombic unit cell, termed bco-C 16. Total-energy calculations show that bco-C 16 is comparable to solid fcc-C 60 in energetic stability, and phonon and molecular dynamics simulations confirm its dynamical stability. This all-sp 2 carbon allotrope can be regarded as a three-dimensional modification of graphite, and its simulated x-ray diffraction (XRD) pattern matches well a previously unexplained diffraction peak in measured XRD spectra of detonation and chimney soot, indicating its presence in the specimen. Electronic band structure calculations revealmore » that bco-C 16 is a topological node-line semimetal with a single nodal ring. Lastly, these findings establish a novel carbon phase with intriguing structural and electronic properties of fundamental significance and practical interest.« less

Ab Initio Predictions of Strong Interfaces in Transition-Metal Carbides and Nitrides for Superhard Nanocomposite Coating Applications

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

Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G.

Conceiving strong interfaces represents an effective direction in the development of superhard nanocomposite materials for practical applications in protective coatings. Additionally, in the pursuit of engineering strong nanoscale interfaces between cubic rock-salt (B1) domains, we investigate using density functional theory (DFT) coherent interface models designed based on hexagonal (HX) NiAs and WC structures, as well as experiment. The DFT screening of a collection of transition-metal (M = Zr, Hf, Nb, Ta) carbides and nitrides indicates that the interface models provided by the HX polymorphs store little coherency strain and develop an energetic advantage as the valence-electron concentration increases. Finally, ourmore » result suggests that harnessing the polymorphism encountered in transition-metal (M = Zr, Hf, Nb, Ta) carbides and nitrides for interface design represents a promising strategy for advancing superhard nanomaterials.« less

Viabilty of atomistic potentials for thermodynamic properties of carbon dioxide at low temperatures.

PubMed

Kuznetsova, Tatyana; Kvamme, Bjørn

2001-11-30

Investigation into volumetric and energetic properties of several atomistic models mimicking carbon dioxide geometry and quadrupole momentum covered the liquid-vapor coexistence curve. Thermodynamic integration over a polynomial and an exponential-polynomial path was used to calculate free energy. Computational results showed that model using GROMOS Lennard-Jones parameters was unsuitable for bulk CO(2) simulations. On the other hand, model with potential fitted to reproduce only correct density-pressure relationship in the supercritical region proved to yield correct enthalpy of vaporization and free energy of liquid CO(2) in the low-temperature region. Except for molar volume at the upper part of the vapor-liquid equilibrium line, the bulk properties of exp-6-1 parametrization of ab initio CO(2) potential were in a close agreement with the experimental results. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1772-1781, 2001

Excited-state dynamics of bis(9-fluorenyl)methane and its derivative 9-(9-ethylfluorenyl)-9'-fluorenylmethane: steric effect on energetics and dynamics of ground- and excited-state conformations.

PubMed

Boo, Bong Hyun; Lee, Minyung; Jeon, Ki-Seok; Kim, Seung-Joon

2014-03-27

Intramolecular excimer formation of bis(9-fluorenyl)methane (BFM) and 9-(9'-ethylfluorenyl)-9-fluorenylmethane (EFFM), in which an ethyl group is substituted to a 9-H atom in BFM, was studied by means of steady-state and time-resolved fluorescence. Ab initio and DFT calculations enabled the prediction of three conformers as stable species of orthogonal, trans-gauche, and gauche-gauche. The theoretical and experimental results reveal that the substitution effect is also found to appreciably influence the energies, spectroscopy, and kinetics associated with the interconversion of various conformers of the diaryl compounds. We have not observed the rising components in the excimer fluorescence decay of BFM and EFFM in PMMA as observed in the liquid solutions probably because of the existence of the sandwich conformer responsible for the excimer fluorescence prior to the laser irradiation.

Theoretical Study of Decomposition Pathways for HArF and HKrF

NASA Technical Reports Server (NTRS)

Chaban, Galina M.; Lundell, Jan; Gerber, R. Benny; Kwak, Donchan (Technical Monitor)

2002-01-01

To provide theoretical insights into the stability and dynamics of the new rare gas compounds HArF and HKrF, reaction paths for decomposition processes HRgF to Rg + HF and HRgF to H + Rg + F (Rg = Ar, Kr) are calculated using ab initio electronic structure methods. The bending channels, HRgF to Rg + HF, are described by single-configurational MP2 and CCSD(T) electronic structure methods, while the linear decomposition paths, HRgF to H + Rg + F, require the use of multi-configurational wave functions that include dynamic correlation and are size extensive. HArF and HKrF molecules are found to be energetically stable with respect to atomic dissociation products (H + Rg + F) and separated by substantial energy barriers from Rg + HF products, which ensure their kinetic stability. The results are compatible with experimental data on these systems.

Ab Initio Predictions of Strong Interfaces in Transition-Metal Carbides and Nitrides for Superhard Nanocomposite Coating Applications

DOE PAGES

Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G.; ...

2018-04-19

Conceiving strong interfaces represents an effective direction in the development of superhard nanocomposite materials for practical applications in protective coatings. Additionally, in the pursuit of engineering strong nanoscale interfaces between cubic rock-salt (B1) domains, we investigate using density functional theory (DFT) coherent interface models designed based on hexagonal (HX) NiAs and WC structures, as well as experiment. The DFT screening of a collection of transition-metal (M = Zr, Hf, Nb, Ta) carbides and nitrides indicates that the interface models provided by the HX polymorphs store little coherency strain and develop an energetic advantage as the valence-electron concentration increases. Finally, ourmore » result suggests that harnessing the polymorphism encountered in transition-metal (M = Zr, Hf, Nb, Ta) carbides and nitrides for interface design represents a promising strategy for advancing superhard nanomaterials.« less

Two-dimensional tricycle arsenene with a direct band gap.

PubMed

Ma, ShuangYing; Zhou, Pan; Sun, L Z; Zhang, K W

2016-03-28

Based on a comprehensive investigation including ab initio phonon and finite-temperature molecular dynamics calculations, we find that two-dimensional tricycle-shaped arsenene (T-As) is robust and even stable under high temperature. T-As is energetically comparable to previously reported chair-shaped arsenene (C-As) and more stable than stirrup-shaped arsenene (S-As). In contrast to C-As and S-As, the monolayer T-As is a direct band gap semiconductor with an energy gap of 1.377 eV. Our results indicate that the electronic structure of T-As can be effectively modulated by stacking, strain, and patterning, which shows great potential of T-As in future nano-electronics. Moreover, by absorbing H or F atoms on the surface of T-As along a specific direction, nanoribbons with desired edge type and even width can be obtained, which is suitable for the fabrication of nano-devices.

Ab initio studies of isolated hydrogen vacancies in graphane

NASA Astrophysics Data System (ADS)

Mapasha, R. E.; Molepo, M. P.; Chetty, N.

2016-05-01

We present a density functional study of various hydrogen vacancies located on a single hexagonal ring of graphane (fully hydrogenated graphene) considering the effects of charge states and the position of the Fermi level. We find that uncharged vacancies that lead to a carbon sublattice balance are energetically favorable and are wide band gap systems just like pristine graphane. Vacancies that do create a sublattice imbalance introduce spin polarized states into the band gap, and exhibit a half-metallic behavior with a magnetic moment of 1.00 μB per vacancy. The results show the possibility of using vacancies in graphane for novel spin-based applications. When charging such vacancy configurations, the deep donor (+1/0) and deep acceptor (0/-1) transition levels within the band gap are noted. We also note a half-metallic to metallic transition and a significant reduction of the induced magnetic moment due to both negative and positive charge doping.

3D hybrid carbon composed of multigraphene bridged by carbon chains

NASA Astrophysics Data System (ADS)

Liu, Lingyu; Hu, Meng; Liu, Chao; Shao, Cancan; Pan, Yilong; Ma, Mengdong; Wu, Yingju; Zhao, Zhisheng; Gao, Guoying; He, Julong

2018-01-01

The element carbon possesses various stable and metastable allotropes; some of them have been applied in diverse fields. The experimental evidences of both carbon chain and graphdiyne have been reported. Here, we reveal the mystery of an enchanting carbon allotrope with sp-, sp2-, and sp3-hybridized carbon atoms using a newly developed ab initio particle-swarm optimization algorithm for crystal structure prediction. This crystalline allotrope, namely m-C12, can be viewed as braided mesh architecture interwoven with multigraphene and carbon chains. The m-C12 meets the criteria for dynamic and mechanical stabilities and is energetically more stable than carbyne and graphdiyne. Analysis of the B/G and Poisson's ratio indicates that this allotrope is ductile. Notably, m-C12 is a superconducting carbon with Tc of 1.13 K, which is rare in the family of carbon allotropes.

Ab initio study of the barrier to internal rotation in simple amides. 1. N, N-dimethylformamide and N, N-dimethylcarbamic halogenides

NASA Astrophysics Data System (ADS)

Vassilev, Nikolay G.; Dimitrov, Valentin S.

1999-06-01

Free energies of activation for rotation about the amide C-N bond in X-C(O)N(CH 3) 2 (X=H, F, Cl and Br) were calculated at the MP2(fc)/6-31+G*//6-31G* and MP2(fc)/6-311++G**//6-311++G** levels and compared with NMR gas-phase data. The results of calculations indicate that the repulsion between X and methyl group in ground state and the repulsion between X or oxygen and nitrogen lone pair in transition states (TS) are largely responsible for the difference in the free energies of the studied amides. For X=H (DMF), the anti TS is more stable; for the cases X=Cl, Br, the syn TS is more stable, while for the case X=F the two transition states are energetically almost equivalent.

Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

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.

Pseudopotential for ab initio calculations of uranium compounds

NASA Astrophysics Data System (ADS)

Smirnov, G. S.; Pisarev, V. V.; Stegailov, V. V.

2018-01-01

The density functional theory (DFT) is a research tool of the highest importance for electronic structure calculations. It is often the only affordable method for ab initio calculations of complex materials. The pseudopotential approach allows reducing the total number of electrons in the model that speeds up calculations. However, there is a lack of pseudopotentials for heavy elements suitable for condensed matter DFT models. In this work, we present a pseudopotential for uranium developed in the Goedecker-Teter-Hutter form. Its accuracy is illustrated using several molecular and solid-state calculations.

Ab-initio study of several static and dynamic properties of liquid palladium and platinum

NASA Astrophysics Data System (ADS)

González, L. E.; González, D. J.; Molla, Mohammad Riazuddin; Ahmed, A. Z. Ziauddin; Bhuiyan, G. M.

2017-08-01

We report a study on several static and dynamic properties of liquid Pd and Pt metals at thermodynamic conditions near their respective triple points. The calculations have been carried out by an ab initio molecular dynamics simulation technique. Results are reported for several static structural magnitudes which are compared with the available X-ray diffraction. As for the dynamic properties, results have been obtained for both single and collective dynamical magnitudes as well as for some transport coeffcients which are compared with the corresponding experimental data.

Comment on 'Parametrization of Stillinger-Weber potential based on a valence force field model: application to single-layer MoS2 and black phosphorus'.

PubMed

Midtvedt, Daniel; Croy, Alexander

2016-06-10

We compare the simplified valence-force model for single-layer black phosphorus with the original model and recent ab initio results. Using an analytic approach and numerical calculations we find that the simplified model yields Young's moduli that are smaller compared to the original model and are almost a factor of two smaller than ab initio results. Moreover, the Poisson ratios are an order of magnitude smaller than values found in the literature.

Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen

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

Holst, Bastian; French, Martin; Redmer, Ronald

2011-06-15

Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law, which is strictly valid only for degenerate systems, and give an estimate for its valid scope of application toward lower densities.

High order discretization techniques for real-space ab initio simulations

NASA Astrophysics Data System (ADS)

Anderson, Christopher R.

2018-03-01

In this paper, we present discretization techniques to address numerical problems that arise when constructing ab initio approximations that use real-space computational grids. We present techniques to accommodate the singular nature of idealized nuclear and idealized electronic potentials, and we demonstrate the utility of using high order accurate grid based approximations to Poisson's equation in unbounded domains. To demonstrate the accuracy of these techniques, we present results for a Full Configuration Interaction computation of the dissociation of H2 using a computed, configuration dependent, orbital basis set.

Ab initio study of the alkaline hydrolysis of a thio-β-lactam structure

NASA Astrophysics Data System (ADS)

Coll, Miguel; Frau, Juan; Vilanova, Bartolomé; Donoso, Josefa; Muñoz, Francisco

2000-08-01

The alkaline hydrolysis of a thio-β-lactam in the gas phase was examined in the light of RHF and DFT ab initio calculations. The solvent effect was considered via IPCM computations. The tetrahedral intermediate for the thio-β-lactam studied is unstable, so the compound evolves directly to the corresponding thio-azethidin-2-one open ring with cleavage of the C-S bond. The end-products obtained bear a carbamate group, which suggests that the thio-β-lactam might be an effective inhibitor for β-lactamases.

Ab initio R-matrix calculations of e+-molecule scattering

NASA Technical Reports Server (NTRS)

Danby, Grahame; Tennyson, Jonathan

1990-01-01

The adaptation of the molecular R-matrix method, originally developed for electron-molecule collision studies, to positron scattering is discussed. Ab initio R-matrix calculations are presented for collisions of low energy positrons with a number of diatomic systems including H2, HF and N2. Differential elastic cross sections for positron-H2 show a minimum at about 45 deg for collision energies between 0.3 and 0.5 Ryd. The calculations predict a bound state of positronHF. Calculations on inelastic processes in N2 and O2 are also discussed.

Electronic states of Zn2 - Ab initio calculations of a prototype for Hg2

NASA Technical Reports Server (NTRS)

Hay, P. J.; Dunning, T. H., Jr.; Raffenetti, R. C.

1976-01-01

The electronic states of Zn2 are investigated by ab initio polarization configuration-interaction calculations. Molecular states dissociating to Zn(1S) + Zn(1S, 3P, 1P) and Zn(3P) + Zn(3P) are treated. Important effects from states arising from Zn(+)(25) + Zn(-)(2P) are found in the potential-energy curves and electronic-transition moments. A model calculation for Hg2 based on the Zn2 curves and including spin-orbit coupling leads to a new interpretation of the emission bands in Hg vapor.

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.

Ab initio molecular dynamics simulations of the initial stages of solid-electrolyte interphase formation on lithium ion battery graphitic anodes.

PubMed

Leung, Kevin; Budzien, Joanne L

2010-07-07

The decomposition of ethylene carbonate (EC) during the initial growth of solid-electrolyte interphase (SEI) films at the solvent-graphitic anode interface is critical to lithium ion battery operations. Ab initio molecular dynamics simulations of explicit liquid EC/graphite interfaces are conducted to study these electrochemical reactions. We show that carbon edge terminations are crucial at this stage, and that achievable experimental conditions can lead to surprisingly fast EC breakdown mechanisms, yielding decomposition products seen in experiments but not previously predicted.

Hybrid classical/quantum simulation for infrared spectroscopy of water

NASA Astrophysics Data System (ADS)

Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

2018-05-01

We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

75 FR 41277 - Central of Georgia Railroad Company-Discontinuance of Service Exemption-Newton County, GA; Great...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-15

... misleading information, the exemptions are void ab initio. Board decisions and notices are available on our... DEPARTMENT OF TRANSPORTATION Surface Transportation Board [Docket No. AB 290 (Sub-No. 319X); Docket No. AB 1060X] Central of Georgia Railroad Company--Discontinuance of Service Exemption--Newton...

Relating Ab Initio Mechanical Behavior of Intergranular Glassy Films in Γ-Si3N4 to Continuum Scales

NASA Astrophysics Data System (ADS)

Ouyang, L.; Chen, J.; Ching, W.; Misra, A.

2006-05-01

Nanometer thin intergranular glassy films (IGFs) form in polycrystalline ceramics during sintering at high temperatures. The structure and properties of these IGFs are significantly changed by doping with rare earth elements. We have performed highly accurate large-scale ab initio calculations of the mechanical properties of both undoped and Yittria doped (Y-IGF) model by theoretical uniaxial tensile experiments. Uniaxial strain was applied by incrementally stretching the super cell in one direction, while the other two dimensions were kept constant. At each strain, all atoms in the model were fully relaxed using Vienna Ab initio Simulation Package VASP. The relaxed model at a given strain serves as the starting position for the next increment of strain. This process is carried on until the total energy (TE) and stress data show that the "sample" is fully fractured. Interesting differences are seen between the stress-strain response of undoped and Y-doped models. For the undoped model, the stress-strain behavior indicates that the initial atomic structure of the IGF is such that there is negligible coupling between the x- and the y-z directions. However, once the behavior becomes non- linear the lateral stresses increase, indicating that the atomic structure evolves with loading [1]. To relate the ab initio calculations to the continuum scales we analyze the atomic-scale deformation field under this uniaxial loading [1]. The applied strain in the x-direction is mostly accommodated by the IGF part of the model and the crystalline part experiences almost negligible strain. As the overall strain on the sample is incrementally increased, the local strain field evolves such that locations proximal to the softer spots attract higher strains. As the load progresses, the strain concentration spots coalesce and eventually form persistent strain localization zone across the IGF. The deformation pattern obtained through ab initio calculations indicates that it is possible to construct discrete grain-scale models that may be used to bridge these calculations to the continuum scale for finite element analysis. Reference: 1. J. Chen, L. Ouyang, P. Rulis, A. Misra, W. Y. Ching, Phys. Rev. Lett. 95, 256103 (2005)

Zinc complexation in chloride-rich hydrothermal fluids (25-600 °C): A thermodynamic model derived from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Mei, Yuan; Sherman, David M.; Liu, Weihua; Etschmann, Barbara; Testemale, Denis; Brugger, Joël

2015-02-01

The solubility of zinc minerals in hydrothermal fluids is enhanced by chloride complexation of Zn2+. Thermodynamic models of these complexation reactions are central to models of Zn transport and ore formation. However, existing thermodynamic models, derived from solubility measurements, are inconsistent with spectroscopic measurements of Zn speciation. Here, we used ab initio molecular dynamics simulations (with the PBE exchange-correlation functional) to predict the speciation of Zn-Cl complexes from 25 to 600 °C. We also obtained in situ XAS measurements of Zn-Cl solutions at 30-600 °C. Qualitatively, the simulations reproduced the main features derived from in situ XANES and EXAFS measurements: octahedral to tetrahedral transition with increasing temperature and salinity, stability of ZnCl42- at high chloride concentration up to ⩾500 °C, and increasing stability of the trigonal planar [ZnCl3]- complex at high temperature. Having confirmed the dominant species, we directly determined the stability constants for the Zn-Cl complexes using thermodynamic integration along constrained Zn-Cl distances in a series of MD simulations. We corrected our stability constants to infinite dilution using the b-dot model for the activity coefficients of the solute species. In order to compare the ab initio results with experiments, we need to re-model the existing solubility data using the species we identified in our MD simulations. The stability constants derived from refitting published experimental data are in reasonable agreement with those we obtained using ab initio MD simulations. Our new thermodynamic model accurately predicts the experimentally observed changes in ZnO(s) and ZnCO3(s) solubility as a function of chloride concentration from 200 (Psat) to 600 °C (2000 bar). This study demonstrates that metal speciation and geologically useful stability constants can be derived for species in hydrothermal fluids from ab initio MD simulations even at the generalized gradient approximation for exchange-correlation. We caution, however, that simulations are mostly reliable at high T where ligand exchange is fast enough to yield thermodynamic averages over the timescales of the simulations.

ExoMol line list - XXI. Nitric Oxide (NO)

NASA Astrophysics Data System (ADS)

Wong, Andy; Yurchenko, Sergei N.; Bernath, Peter; Müller, Holger S. P.; McConkey, Stephanie; Tennyson, Jonathan

2017-09-01

Line lists for the X 2Π electronic ground state for the parent isotopologue of nitric oxide (14N16O) and five other major isotopologues (14N17O, 14N18O, 15N16O, 15N17O and 15N18O) are presented. The line lists are constructed using empirical energy levels (and line positions) and high-level ab initio intensities. The energy levels were obtained using a combination of two approaches, from an effective Hamiltonian and from solving the rovibronic Schrödinger equation variationally. The effective Hamiltonian model was obtained through a fit to the experimental line positions of NO available in the literature for all six isotopologues using the programs spfit and spcat. The variational model was built through a least squares fit of the ab initio potential and spin-orbit curves to the experimentally derived energies and experimental line positions of the main isotopologue only using the duo program. The ab initio potential energy, spin-orbit and dipole moment curves (PEC, SOC and DMC) are computed using high-level ab initio methods and the marvel method is used to obtain energies of NO from experimental transition frequencies. The line lists are constructed for each isotopologue based on the use of the most accurate energy levels and the ab initio DMC. Each line list covers a wavenumber range from 0 to 40 000 cm-1 with approximately 22 000 rovibronic states and 2.3-2.6 million transitions extending to Jmax = 184.5 and vmax = 51. Partition functions are also calculated up to a temperature of 5000 K. The calculated absorption line intensities at 296 K using these line lists show excellent agreement with those included in the HITRAN and HITEMP data bases. The computed NO line lists are the most comprehensive to date, covering a wider wavenumber and temperature range compared to both the HITRAN and HITEMP data bases. These line lists are also more accurate than those used in HITEMP. The full line lists are available from the CDS http://cdsarc.u-strasbg.fr and ExoMol www.exomol.com data bases; data will also be available from CDMS http://www.cdms.de.

Ab initio based potential energy surface and kinetics study of the OH + NH3 hydrogen abstraction reaction.

PubMed

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.

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations

NASA Astrophysics Data System (ADS)

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A.; Ferreira, Rafaela Salgado

2018-05-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50 = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

The hydrogen abstraction reaction O({sup 3}P) + CH{sub 4}: A new analytical potential energy surface based on fit to ab initio calculations

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

González-Lavado, Eloisa; Corchado, Jose C.; Espinosa-Garcia, Joaquin, E-mail: joaquin@unex.es

2014-02-14

Based exclusively on high-level ab initio calculations, a new full-dimensional analytical potential energy surface (PES-2014) for the gas-phase reaction of hydrogen abstraction from methane by an oxygen atom is developed. The ab initio information employed in the fit includes properties (equilibrium geometries, relative energies, and vibrational frequencies) of the reactants, products, saddle point, points on the reaction path, and points on the reaction swath, taking especial caution respecting the location and characterization of the intermediate complexes in the entrance and exit channels. By comparing with the reference results we show that the resulting PES-2014 reproduces reasonably well the whole setmore » of ab initio data used in the fitting, obtained at the CCSD(T) = FULL/aug-cc-pVQZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical surface we perform an extensive dynamics study using quasi-classical trajectory calculations, comparing the results with recent experimental and theoretical data. The excitation function increases with energy (concave-up) reproducing experimental and theoretical information, although our values are somewhat larger. The OH rotovibrational distribution is cold in agreement with experiment. Finally, our results reproduce experimental backward scattering distribution, associated to a rebound mechanism. These results lend confidence to the accuracy of the new surface, which substantially improves the results obtained with our previous surface (PES-2000) for the same system.« less

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations

NASA Astrophysics Data System (ADS)

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A.; Ferreira, Rafaela Salgado

2018-03-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50 = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

Accurate double many-body expansion potential energy surface of HS2A2A‧) by scaling the external correlation

NASA Astrophysics Data System (ADS)

Lu-Lu, Zhang; Yu-Zhi, Song; Shou-Bao, Gao; Yuan, Zhang; Qing-Tian, Meng

2016-05-01

A globally accurate single-sheeted double many-body expansion potential energy surface is reported for the first excited state of HS2 by fitting the accurate ab initio energies, which are calculated at the multireference configuration interaction level with the aug-cc-pVQZ basis set. By using the double many-body expansion-scaled external correlation method, such calculated ab initio energies are then slightly corrected by scaling their dynamical correlation. A grid of 2767 ab initio energies is used in the least-square fitting procedure with the total root-mean square deviation being 1.406 kcal·mol-1. The topographical features of the HS2(A2A‧) global potential energy surface are examined in detail. The attributes of the stationary points are presented and compared with the corresponding ab initio results as well as experimental and other theoretical data, showing good agreement. The resulting potential energy surface of HS2(A2A‧) can be used as a building block for constructing the global potential energy surfaces of larger S/H molecular systems and recommended for dynamic studies on the title molecular system. Project supported by the National Natural Science Foundation of China (Grant No. 11304185), the Taishan Scholar Project of Shandong Province, China, the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014AM022), the Shandong Province Higher Educational Science and Technology Program, China (Grant No. J15LJ03), the China Postdoctoral Science Foundation (Grant No. 2014M561957), and the Post-doctoral Innovation Project of Shandong Province, China (Grant No. 201402013).

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.

Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations.

PubMed

Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A; Ferreira, Rafaela Salgado

2018-05-01

Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC 50  = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

Electronic Structures of Anti-Ferromagnetic Tetraradicals: Ab Initio and Semi-Empirical Studies.

PubMed

Zhang, Dawei; Liu, Chungen

2016-04-12

The energy relationships and electronic structures of the lowest-lying spin states in several anti-ferromagnetic tetraradical model systems are studied with high-level ab initio and semi-empirical methods. The Full-CI method (FCI), the complete active space second-order perturbation theory (CASPT2), and the n-electron valence state perturbation theory (NEVPT2) are employed to obtain reference results. By comparing the energy relationships predicted from the Heisenberg and Hubbard models with ab initio benchmarks, the accuracy of the widely used Heisenberg model for anti-ferromagnetic spin-coupling in low-spin polyradicals is cautiously tested in this work. It is found that the strength of electron correlation (|U/t|) concerning anti-ferromagnetically coupled radical centers could range widely from strong to moderate correlation regimes and could become another degree of freedom besides the spin multiplicity. Accordingly, the Heisenberg-type model works well in the regime of strong correlation, which reproduces well the energy relationships along with the wave functions of all the spin states. In moderately spin-correlated tetraradicals, the results of the prototype Heisenberg model deviate severely from those of multi-reference electron correlation ab initio methods, while the extended Heisenberg model, containing four-body terms, can introduce reasonable corrections and maintains its accuracy in this condition. In the weak correlation regime, both the prototype Heisenberg model and its extended forms containing higher-order correction terms will encounter difficulties. Meanwhile, the Hubbard model shows balanced accuracy from strong to weak correlation cases and can reproduce qualitatively correct electronic structures, which makes it more suitable for the study of anti-ferromagnetic coupling in polyradical systems.

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials.

PubMed

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. Copyright 2008 Wiley Periodicals, Inc.

Molecular transitions as probes of the physical conditions of extragalactic environments

NASA Astrophysics Data System (ADS)

Viti, Serena

2017-11-01

Aims: We present a method to interpret molecular observations and molecular line ratios in nearby extragalactic regions. Methods: Ab initio grids of time dependent chemical models, varying in gas density, temperature, cosmic ray ionization rate, and radiation field, are used as inputs into RADEX calculations. Tables of abundances, column densities, theoretical line intensities, and line ratios for some of the most used dense gas tracers are provided. The degree of correlation as well as degeneracy inherent in molecular ratios is discussed. Comparisons of the theoretical intensities with example observations are also provided. Results: We find that, within the parameters space explored, chemical abundances can be constrained by a well-defined set of gas density, gas temperature, and cosmic ray ionization rates for the species we investigate here. However, line intensities, and more importantly line ratios, from different chemical models can be very similar, thereby leading to a clear degeneracy. We also find that the gas subjected to a galactic cosmic ray ionization rate will not necessarily have reached steady state in 1 million years. The species most affected by time dependency effects are HCN and CS, which are both high density tracers. We use our ab initio method to fit an example set of data from two galaxies, I.e. M 82 and NGC 253. We find that (I) molecular line ratios can be easily matched even with erroneous individual line intensities; (II) no set of species can be matched by a one-component interstellar medium (ISM); and (III) a species may be a good tracer of an energetic process but only under specific density and temperature conditions. Conclusions: We provide tables of chemical abundances and line intensities ratios for some of the most commonly observed extragalactic tracers of dense gas for a grid of models. We show that by taking the chemistry behind each species and the individual line intensities into consideration, many degeneracies that arise by just using molecular line ratios can be avoided. Finally we show that using a species or a ratio as a tracer of an individual energetic process, such as cosmic rays and UV, ought to be done with caution. Tables 2-11 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/607/A118

Theoretical determination of molecular structure and conformation. Part X. Geometry and puckering potential of azetidine, (CH 2) 3NH, combination of electron diffraction and ab initio studies

NASA Astrophysics Data System (ADS)

Cremer, Dieter; Dorofeeva, Olga V.; Mastryukov, Vladimir S.

1981-09-01

Restricted Hartree—Fock calculations on 21 planar and puckered conformers of azetidine have been done employing a split valence basis augmented by d functions. Complete geometry optimizations have been performed for eight conformers. In this way the puckering potential of azetidine is explored over the range -40° < ø (puckering angle) < 40°, for both sp3 and sp2 hybridization of the nitrogen atom. In its equatorial form, azetidine is slightly more puckered than cyclobutane. This is because of a decrease of van der Waals' repulsion between H atoms. Charge effects lead to destabilization of the axial forms. There is only moderate coupling between puckering and methylene group rocking. Previously published electron diffraction (ED) data are reinvestigated using vibrational corrections and information from the ab initio calculations. On the basis of this MO constrained ED (MOCED) analysis a puckering angle φ = 35.1(1.8)° is found. Observed rg and re bond distances are compared with ab initio values.

Ab initio quantum direct dynamics simulations of ultrafast photochemistry with Multiconfigurational Ehrenfest approach

NASA Astrophysics Data System (ADS)

Makhov, Dmitry V.; Symonds, Christopher; Fernandez-Alberti, Sebastian; Shalashilin, Dmitrii V.

2017-08-01

The Multiconfigurational Ehrenfest (MCE) method is a quantum dynamics technique which allows treatment of a large number of quantum nuclear degrees of freedom. This paper presents a review of MCE and its recent applications, providing a summary of the formalisms, including its ab initio direct dynamics versions and also giving a summary of recent results. Firstly, we describe the Multiconfigurational Ehrenfest version 2 (MCEv2) method and its applicability to direct dynamics and report new calculations which show that the approach converges to the exact result in model systems with tens of degrees of freedom. Secondly, we review previous ;on the fly; ab initio Multiple Cloning (AIMC-MCE) MCE dynamics results obtained for systems of a similar size, in which the calculations treat every electron and every nucleus of a polyatomic molecule on a fully quantum basis. We also review the Time Dependent Diabatic Basis (TDDB) version of the technique and give an example of its application. We summarise the details of the sampling techniques and interpolations used for calculation of the matrix elements, which make our approach efficient. Future directions of work are outlined.

Ab initio study of the structure and dynamics of bulk liquid Fe

NASA Astrophysics Data System (ADS)

Marqués, M.; González, L. E.; González, D. J.

2015-10-01

Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.

A new ab initio potential energy surface of LiClH (1A') system and quantum dynamics calculation for Li + HCl (v = 0, j = 0-2) → LiCl + H reaction

NASA Astrophysics Data System (ADS)

Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying

2017-04-01

A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.

Thermal Conductivities in Solids from First Principles: Accurate Computations and Rapid Estimates

NASA Astrophysics Data System (ADS)

Carbogno, Christian; Scheffler, Matthias

In spite of significant research efforts, a first-principles determination of the thermal conductivity κ at high temperatures has remained elusive. Boltzmann transport techniques that account for anharmonicity perturbatively become inaccurate under such conditions. Ab initio molecular dynamics (MD) techniques using the Green-Kubo (GK) formalism capture the full anharmonicity, but can become prohibitively costly to converge in time and size. We developed a formalism that accelerates such GK simulations by several orders of magnitude and that thus enables its application within the limited time and length scales accessible in ab initio MD. For this purpose, we determine the effective harmonic potential occurring during the MD, the associated temperature-dependent phonon properties and lifetimes. Interpolation in reciprocal and frequency space then allows to extrapolate to the macroscopic scale. For both force-field and ab initio MD, we validate this approach by computing κ for Si and ZrO2, two materials known for their particularly harmonic and anharmonic character. Eventually, we demonstrate how these techniques facilitate reasonable estimates of κ from existing MD calculations at virtually no additional computational cost.

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.

Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory.

PubMed

Frandsen, Benjamin A; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J; Staunton, Julie B; Billinge, Simon J L

2016-05-13

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.

In search of a viable reaction pathway in the chelation of a metallo-protein

NASA Astrophysics Data System (ADS)

Rose, Frisco; Hodak, Miroslav; Bernholc, Jerry

2010-03-01

Misfolded metallo-proteins are potential causal agents in the onset of neuro-degenerative diseases, such as Alzheimer's and Parkinson's Diseases (PD). Experimental results involving metal chelation have shown significant promise in symptom reduction and misfolding reversal. We explore, through atomistic simulations, potential reaction pathways for the chelation of Cu^2+ from the metal binding site in our representation of a partially misfolded α-synuclein, the protein implicated in PD. Our ab initio simulations use Density Functional Theory (DFT) and nudged elastic band to obtain the minimized energy coordinates of this reaction. Our simulations include ab initio water at the interaction site and in its first solvation shells, while the remainder is fully solvated with orbital-free DFT water representation [1]. Our ongoing studies of viable chelation agents include nicotine, caffeine and other potential reagents, we will review the best case agents in this presentation. [4pt] [1] Hodak M, Lu W, Bernholc J. Hybrid ab initio Kohn-Sham density functional theory/frozen-density orbital-free density functional theory simulation method suitable for biological systems. J. Chem. Phys. 2008 Jan;128(1):014101-9.

Thermodynamic properties by equation of state and from Ab initio molecular dynamics of liquid potassium under pressure

NASA Astrophysics Data System (ADS)

Li, Huaming; Tian, Yanting; Sun, Yongli; Li, Mo; Nonequilibrium materials; physics Team; Computational materials science Team

In this work, we apply a general equation of state of liquid and Ab initio molecular-dynamics method to study thermodynamic properties in liquid potassium under high pressure. Isothermal bulk modulus and molar volume of molten sodium are calculated within good precision as compared with the experimental data. The calculated internal energy data and the calculated values of isobaric heat capacity of molten potassium show the minimum along the isothermal lines as the previous result obtained in liquid sodium. The expressions for acoustical parameter and nonlinearity parameter are obtained based on thermodynamic relations from the equation of state. Both parameters for liquid potassium are calculated under high pressure along the isothermal lines by using the available thermodynamic data and numeric derivations. Furthermore, Ab initio molecular-dynamics simulations are used to calculate some thermodynamic properties of liquid potassium along the isothermal lines. Scientific Research Starting Foundation from Taiyuan university of Technology, Shanxi Provincial government (``100-talents program''), China Scholarship Council and National Natural Science Foundation of China (NSFC) under Grant No. 51602213.

Electron transport in extended carbon-nanotube/metal contacts: Ab initio based Green function method

NASA Astrophysics Data System (ADS)

Fediai, Artem; Ryndyk, Dmitry A.; Cuniberti, Gianaurelio

2015-04-01

We have developed a new method that is able to predict the electrical properties of the source and drain contacts in realistic carbon nanotube field effect transistors (CNTFETs). It is based on large-scale ab initio calculations combined with a Green function approach. For the first time, both internal and external parts of a realistic CNT-metal contact are taken into account at the ab initio level. We have developed the procedure allowing direct calculation of the self-energy for an extended contact. Within the method, it is possible to calculate the transmission coefficient through a contact of both finite and infinite length; the local density of states can be determined in both free and embedded CNT segments. We found perfect agreement with the experimental data for Pd and Al contacts. We have explained why CNTFETs with Pd electrodes are p -type FETs with ohmic contacts, which can carry current close to the ballistic limit (provided contact length is large enough), whereas in CNT-Al contacts transmission is suppressed to a significant extent, especially for holes.