Resolution of ab initio shapes determined from small-angle scattering
Tuukkanen, Anne T.; Kleywegt, Gerard J.; Svergun, Dmitri I.
2016-01-01
Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models. PMID:27840683
Resolution of ab initio shapes determined from small-angle scattering.
Tuukkanen, Anne T; Kleywegt, Gerard J; Svergun, Dmitri I
2016-11-01
Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.
van der Spoel, D; Berendsen, H J
1996-01-01
In this work we give an overview of the methodologies required to compute the rate of proton transfer in hydrogen bonded systems in solution. Using ab initio or density functional methods we determine proton potentials of a truncated system as a function of proton-donor proton-acceptor distance as well as nonbonding parameters. By classical molecular dynamics we evaluate a swarm of proton potentials with the proton fixed in the reactant well. The rate of proton transfer is calculated perturbatively using the Density Matrix Evolution (DME) method, going beyond the Born Oppenheimer approximation. The method is illustrated by two examples: hydrogen malonate and the active center of HIV-1 protease.
Kassab, E.; Seiti, K.; Allavena, M.
1988-11-17
SCF ab initio calculations at the 6-31G level have been used to investigate the structure of several aggregates simulating some of the proton donor sites within faujasite-type zeolites. The Si(OH)/sub 4/, H/sub 3/SiOHAlH/sub 3/, and (OH)/sub 3/SiOHAl(OH)/sub 3/ clusters have been successively examined. Deprotonation energies and charge distribution are determined at a higher level by using a 6-31G basis set augmented with polarization and diffuse functions. The results are compared with values obtained by using pseudopotential methods. The small differences between the two sets of results demonstrate that comparable accuracy should be expected from both procedures. Finally, deprotonation energies of (OH)/sub 3/T/sub 1/OHT/sub 2/(OH)/sub 3/ aggregates (T/sub 1/, T/sub 2/ = AlSi, BSi, GaSi; AlGe, BGe, GaGe) are calculated by using pseudopotential methods and compared with the results given by the semiempirical MNDO method. In some cases ab initio SCF calculations were also performed. The results confirm that the inclusion of boron atom lowers the acidity as already demonstrated by experimental investigation. The effects due to the inclusion of Ga are discussed and compared to available experimental data.
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions.
Changlani, Hitesh J; Zheng, Huihuo; Wagner, Lucas K
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U(∗)/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
Ab initio determination of the instability growth rate of warm dense beryllium-deuterium interface
Wang, Cong; Zhang, Ping; Li, Zi; Li, DaFang
2015-10-15
Accurate knowledge about the interfacial unstable growth is of great importance in inertial confinement fusion. During implosions, the deuterium-tritium capsule is driven by laser beams or X-rays to access the strongly coupled and partially degenerated warm dense matter regime. At this stage, the effects of dissipative processes, such as diffusion and viscosity, have significant impact on the instability growth rates. Here, we present ab initio molecular dynamics simulations to determine the equations of state and the transport coefficients. Several models are used to estimate the reduction in the growth rate dispersion curves of Rayleigh-Taylor and Richtmyer-Meshkov instabilities with considering the presence of these dissipative effects. We show that these instability growth rates are effectively reduced when considering diffusion. The findings provide significant insights into the microscopic mechanism of the instability growth at the ablator-fuel interface and will refine the models used in the laser-driven hydrodynamic instability experiments.
Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface
NASA Technical Reports Server (NTRS)
Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)
1997-01-01
A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.
Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface
NASA Technical Reports Server (NTRS)
Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)
1997-01-01
A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions
Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
Ab initio Structure Determination of Mg10Ir19B16
Xu, Qiang; Klimczuk, T.; Gortenmulder, T.; Jansen, J.; McGuire, Michael A; Cava, R. J.; Zandbergen, H
2009-01-01
The ab initio structure determination of a novel unconventional noncentro-symmetric superconductor Mg{sub 10}Ir{sub 19}B{sub 16} (T{sub c} = 5 K) has been performed using a method that involves a combination of experimental data and calculations. Electron diffraction, X-ray powder diffraction, phase estimation routines, quantum mechanical calculations, high-resolution electron microscopy, and structural chemistry arguments are used. With the strengths of different methods used to eliminate the ambiguities encountered in others, the complete structure, including a very light B atom, has been determined with a high accuracy from impure polycrystalline powder samples, which suggests that the type of analysis described may be used to successfully address other similar intractable problems. The solved structure of Mg{sub 10}Ir{sub 19}B{sub 16} shows a complex nature that irregular coordination environments preclude a conversional description of compact packing of coordination polyhedra; however, it can be easier understood as ordered in an onion-skin-like series of nested polyhedra.
Al-Terkawi, Abdal-Azim; Scholz, Gudrun; Buzanich, Ana Guilherme; Reinsch, Stefan; Emmerling, Franziska; Kemnitz, Erhard
2017-05-09
New fluorinated coordination polymers were prepared mechanochemically by milling the alkaline earth metal hydroxides M(II)(OH)2·xH2O (M(II): Ca, Sr) with tetrafluoroisophthalic acid (H2mBDC-F4). The structures of [{Ca(mBDC-F4)(H2O)2}·H2O] (1) and [{Sr(mBDC-F4)(H2O)2}·H2O] (2) were determined based on ab initio calculations and their powder X-ray diffraction (PXRD) data. The compounds are isomorphous and crystallize in the orthorhombic space group P212121. The determined structures were validated by using extended X-ray absorption (EXAFS) data. The new materials were thoroughly characterized using elemental analysis, thermal analysis, magic angle spinning NMR, and attenuated total reflection-infrared spectroscopy. Further characterization methods such as BET, dynamic vapor sorption, and scanning electron microscopy imaging were also used. Our investigations indicate that mechanochemistry is an efficient method for preparing such materials.
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.
A high-precision ab initio determination of the equilibrium geometry and force field of HOC(+)
NASA Technical Reports Server (NTRS)
Defrees, D. J.; Bunker, P. R.; Binkley, J. S.; Mclean, A. D.
1987-01-01
The results of an ab initio molecular orbital investigation of the isoformyl cation, HOC(+), shape are reported. The effects of expanding the basis set to near the Hartree-Fock limit and of electron correlation were examined, and the results indicate that near the Hartree-Fock limit the HOC(+) is linear. An analytic potential function is presented, from which the calculated rotational energies are only 0.03 percent different from the experimental values. This represents a nearly two orders of magnitude reduction in error from earlier work.
A high-precision ab initio determination of the equilibrium geometry and force field of HOC(+)
NASA Technical Reports Server (NTRS)
Defrees, D. J.; Bunker, P. R.; Binkley, J. S.; Mclean, A. D.
1987-01-01
The results of an ab initio molecular orbital investigation of the isoformyl cation, HOC(+), shape are reported. The effects of expanding the basis set to near the Hartree-Fock limit and of electron correlation were examined, and the results indicate that near the Hartree-Fock limit the HOC(+) is linear. An analytic potential function is presented, from which the calculated rotational energies are only 0.03 percent different from the experimental values. This represents a nearly two orders of magnitude reduction in error from earlier work.
New developments in the ab initio'' determination of transition metal alloy phase diagrams
Wolverton, C.; Asta, M. . Dept. of Physics); Quannasser, S.; Dreysse, H. . Lab. de Physique des Solides); de Fontaine, D. . Dept. of Materials Science and Mineral Engineering)
1992-04-01
Certain classes of temperature-composition binary alloy phase diagrams can now be computed in an ab-initio'' approach. No adjustable or experimentally fitted parameter is used. The expectation value of the energy is expressed in terms of an expansion of cluster probabilities, where the prefactors, the Effective Cluster Interaction, are related to the alloy electronic structure. This framework is used to study the MoRe alloy for two situations: bulk and semi-infinite crystal bounded by a (001) surface. In both cases, good agreement with experimental data is found.
New developments in the ``ab initio`` determination of transition metal alloy phase diagrams
Wolverton, C.; Asta, M.; Quannasser, S.; Dreysse, H.; de Fontaine, D.
1992-04-01
Certain classes of temperature-composition binary alloy phase diagrams can now be computed in an ``ab-initio`` approach. No adjustable or experimentally fitted parameter is used. The expectation value of the energy is expressed in terms of an expansion of cluster probabilities, where the prefactors, the Effective Cluster Interaction, are related to the alloy electronic structure. This framework is used to study the MoRe alloy for two situations: bulk and semi-infinite crystal bounded by a (001) surface. In both cases, good agreement with experimental data is found.
Ab initio determination of the proton affinities of small neutral and anionic molecules
NASA Technical Reports Server (NTRS)
DeFrees, D. J.; McLean, A. D.
1986-01-01
The proton affinity of a molecule in the gas phase is a fundamental measure of its basicity and is the factor controlling the course of many ion-molecule reactions. In this article, ab initio molecular orbital theory at the MP4/6-311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol-1. Furthermore, the errors are random, indicating that there are likely no systematic errors in either the experimental or theoretical PA's. Also, this level of theory is used to calibrate less sophisticated theoretical models which are suitable for larger molecules; the MP4/6-311 ++ G(2d, 2p) and MP2/6-311 ++ G(d, p) theoretical models should be particularly useful. A procedure for predicting the vibrational frequencies for anion is proposed and applied to CH3-, NH2-, OH-, and CN-.
Ab initio determination of effective electron-phonon coupling factor in copper
NASA Astrophysics Data System (ADS)
Ji, Pengfei; Zhang, Yuwen
2016-04-01
The electron temperature Te dependent electron density of states g (ε), Fermi-Dirac distribution f (ε), and electron-phonon spectral function α2 F (Ω) are computed as prerequisites before achieving effective electron-phonon coupling factor Ge-ph. The obtained Ge-ph is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing Ge-ph from ab initio calculation shows a faster decrease of Te and increase of Tl than those using Ge-ph from phenomenological treatment. The approach of calculating Ge-ph and its implementation into MD-TTM simulation is applicable to other metals.
Initial stages of salt crystal dissolution determined with ab initio molecular dynamics.
Liu, Li-Min; Laio, Alessandro; Michaelides, Angelos
2011-08-07
The initial stages of NaCl dissolution in liquid water have been examined with state-of-the-art ab initio molecular dynamics and free energy sampling techniques. Our simulations reveal a complex multi-step process triggered by the departure of Cl ions from the lattice, with a well-defined intermediate state wherein departing ions are partially solvated but remain in contact with the crystal. The polarizability of Cl(-) is identified as the source of the anion's preferential initial dissolution, an effect which leads a forcefield based description of NaCl dissolution to fail to identify a preference for Cl over Na dissolution. This journal is © the Owner Societies 2011
Ab initio determination of coarse-grained interactions in double stranded DNA
NASA Astrophysics Data System (ADS)
Hsu, Chia Wei; Fyta, Maria; Lakatos, Greg; Melchionna, Simone; Kaxiras, Efthimios
2012-02-01
We derive the coarse-grained interactions between DNA nucleotides from ab initio calculations using density functional theory (DFT). The interactions take into account the base and sequence specificity, and are decomposed into physically distinct contributions. The interactions energies calculated from DFT for a wide range of configurations are fitted to simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This non-empirical model accurately yields structural properties of B-DNA even in extreme conditions, and predicts persistence length in excellent agreement with experiments. The model enables quantitative an efficient investigations of the dynamics of long DNA strands in various environments, making it possible to reach microsecond time scales and beyond.
Ab initio determination of coarse-grained interactions in double-stranded DNA
NASA Astrophysics Data System (ADS)
Hsu, Chia Wei; Fyta, Maria; Lakatos, Greg; Melchionna, Simone; Kaxiras, Efthimios
2012-09-01
We derive the coarse-grained interactions between DNA nucleotides from ab initio total-energy calculations based on density functional theory (DFT). The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that include hydrogen bonding, stacking interactions, backbone, and backbone-base interactions. The interaction energies of each contribution are calculated from DFT for a wide range of configurations and are fitted by simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This model is not derived from experimental data, yet it successfully reproduces the stable B-DNA structure and gives good predictions for the persistence length. It may be used to realistically probe dynamics of DNA strands in various environments at the μs time scale and the μm length scale.
Bylaska, Eric J.; Dixon, David A.; Felmy, Andrew R.; Tratnyek, Paul G.
2002-12-17
Substituted chloromethyl radicals and anions are potential intermediates in the reduction of substituted chlorinated methanes (CHxCl3-xL, with L- ) F-, OH-, SH-, NO3 -, HCO3 - and (x 0-3). Thermochemical properties, Hf (298.15 K), S(298.15 K,1 bar), and GS(298.15 K, 1 bar), were calculated by using ab initio electronic structure methods for the substituted chloromethyl radicals and anions: CHyCl2-yL and CHyCl2-yL-, for y 0-2. In addition, thermochemical properties were calculated for the aldehyde, ClHCO, and the gemchlorohydrin anions, CCl3O-, CHCl2O-, and CH2ClO-. The thermochemical properties of these additional compounds were calculated because the nitrate-substituted compounds, CHyCl2-y(NO3) and CHyCl2-y(NO3)-,
Peterson, Charles; Penchoff, Deborah A.; Wilson, Angela K.
2015-11-21
An effective approach for the determination of lanthanide energetics, as demonstrated by application to the third ionization energy (in the gas phase) for the first half of the lanthanide series, has been developed. This approach uses a combination of highly correlated and fully relativistic ab initio methods to accurately describe the electronic structure of heavy elements. Both scalar and fully relativistic methods are used to achieve an approach that is both computationally feasible and accurate. The impact of basis set choice and the number of electrons included in the correlation space has also been examined.
AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS
Turchi, P A
2004-04-14
Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.
Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung
2016-01-01
Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380
Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela
2015-06-17
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.
NASA Astrophysics Data System (ADS)
Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela
2015-06-01
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.
Ab initio Determination of Formation Energies and Charge Transfer Levels of Charged Ions in Water
NASA Astrophysics Data System (ADS)
Vatti, Anoop Kishore; Todorova, Mira; Neugebauer, Joerg
The ability to describe the complex atomic and electronic structure of liquid water and hydrated ions on a microscopic level is a key requirement to understand and simulate electro-chemical and biological processes. Identifying theoretical concepts which enable us to achieve an accurate description in a computationally efficient way is thereby of central importance. Aiming to unravel the importance and influence of different contributions on the hydration energy of ions we perform extensive ab-initio molecular dynamics simulations for charged and neutral cations (Zn, Mg) and anions (Cl, Br, I) in water. The structural correlations and electronic properties of the studied ions are analysed and compared to experimental observations. Following an approach inspired by the defect chemistry in semiconductors and aligning the water band edges on an absolute scale allows us to benchmark the calculated formation energies, identify transition states and compare the results to experiment. Based on these results we discuss the performance of various DFT xc-functionals to predict charge transfer levels and photo-emission experiments.
Ab initio study of phosphaalkenes
Liu, M.
1992-01-01
This dissertation presents the application of computational chemistry to investigate a new class of organic compound-phosphaalkenes. The history of room temperature stable phosphaalkenes is a matter of the last 20 years. The existence of the C[double bond]P [pi] bond has challenged the concept that the 2p-3p [pi] bond is supposed to be very unstable and weak. Theoretical study of this type of compound can clear up the unknown properties, reactivities and reaction mechanisms of phosphaalkenes. The aim of this research is to theoretically determine the electronic and molecular properties, the chemical properties, and predict synthetic candidates for this family. Employing ab initio quantum chemistry, the authors have completed 7 related projects. First, the authors examined the reaction mechanism in the general synthesis of 1,3-diphosphallene and located the step that controls the stereo-outcome of the final product. Second, the authors predicted 4-phosphamethylenecylopropene to be a stable compound, which has been successfully synthesized after this research appeared. Third, the rotational energy surface of the rotation from s-trans to s-cis for mon- and di-phospha-1,3-butadienes were examined and concluded that the rotation does not have a high barrier. Fourth, fifth, and sixth, the authors continued their interest in phospha-1,3-butadienes and investigated [2+2] and Diels-Alder reactions. The energetics and stereo consequences of these reactions have been explored in this research. Finally, they also systematically studied the bonding properties of phosphacumulenes and provided some structural insight for this unsettled area.
NASA Astrophysics Data System (ADS)
Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.
2008-05-01
Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s26p4 (Z = 84). The low temperature α-phase transforms into the rhombohedral (trigonal) β structure at ˜348 K. The sc α-Po unit cell constant is a = 3.345 Å. The beta form of polonium (β-Po) has the lattice parameters, aR = 3.359 Å and a rhombohedral angle 98°13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), Γ (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and Γ (0, 0, 0). Other directions of k-points are Γ (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and Γ (0, 0, 0). The SO splittings of p states at the Γ point in the GGA+SO scheme for α-Po are 0.04 eV and 0.02 eV while for the β-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the β phase.
Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.
2008-05-20
Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.
Ab initio infrared and Raman spectra
NASA Astrophysics Data System (ADS)
Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.
1983-06-01
mechanically, using gradient techniques step by step along a classical trajectory whose path is determined by these quantum forces. We believe the QFCT method to be a more practical ab initio route to spectral band contours for large molecules, clusters, and solutions, and it can be equally applied to equilibrium and nonequilibrium systems. It is pointed out that a similar ab initio QFCT molecular dynamic approach could be used to compute other types of spectra, e.g., electronic absorption, as well as other parameters such as transport properties and thermodynamic functions and their quantum corrections. For parameters not depending on momenta, a parallel ab initio Monte Carlo approach would use electronic energies and other parameters of interest generated quantum mechanically, and ``classical'' trial moves of the nuclei.
Ab initio dynamical vertex approximation
NASA Astrophysics Data System (ADS)
Galler, Anna; Thunström, Patrik; Gunacker, Patrik; Tomczak, Jan M.; Held, Karsten
2017-03-01
Diagrammatic extensions of dynamical mean-field theory (DMFT) such as the dynamical vertex approximation (DΓ A) allow us to include nonlocal correlations beyond DMFT on all length scales and proved their worth for model calculations. Here, we develop and implement an Ab initio DΓ A approach (AbinitioDΓ A ) for electronic structure calculations of materials. The starting point is the two-particle irreducible vertex in the two particle-hole channels which is approximated by the bare nonlocal Coulomb interaction and all local vertex corrections. From this, we calculate the full nonlocal vertex and the nonlocal self-energy through the Bethe-Salpeter equation. The AbinitioDΓ A approach naturally generates all local DMFT correlations and all nonlocal G W contributions, but also further nonlocal correlations beyond: mixed terms of the former two and nonlocal spin fluctuations. We apply this new methodology to the prototypical correlated metal SrVO3.
NASA 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.
Smeyers; Villa; Senent
1998-10-01
The infrared band structure for the methyl torsion and amine hydrogen symmetric wagging in methylamine is calculated by ab initio procedures. The influence of the amine hydrogen symmetric bending on the wagging spectrum is considered explicitly. For this purpose, the potential energy surfaces and kinetic parameters were determined at the RHF/MP2 level with the 6-311G++(3df, 3dp) basis set. The numerical results were fitted to symmetry adapted functional forms. The Schrödinger equations for the nuclear motions were solved by expanding the solutions into products of trigonometric functions. The band frequencies and intensities were calculated from the energy levels, the vibrational functions, and the electric dipole moment variations. The calculated spectra were compared with the available experimental data. It was found that the torsional splittings and frequencies are relatively well reproduced, whereas the wagging and bending frequencies are slightly too high. Copyright 1998 Academic Press.
Ghosh, Debashree; Golan, Amir; Takahashi, Lynelle K; Krylov, Anna I; Ahmed, Musahid
2012-01-05
The ionization energy of gas-phase deoxyribose was determined using tunable vacuum ultraviolet synchrotron radiation coupled to an effusive thermal source. Adiabatic and vertical ionization energies of the ground and first four excited states of α-pyranose, the structure that dominates in the gas phase, were calculated using high-level electronic structure methods. An appearance energy of 9.1(±0.05) eV was recorded, which agrees reasonably well with a theoretical value of 8.8 eV for the adiabatic ionization energy. A clear picture of the dissociative photoionization dynamics of deoxyribose emerges from the fragmentation pattern recorded using mass spectrometry and from ab initio molecular dynamics calculations. The experimental threshold 9.4 (±0.05) eV for neutral water elimination upon ionization is captured well in the calculations, and qualitative insights are provided by molecular orbital analysis and molecular dynamics snapshots along the reaction coordinate.
Ab initio derivation of model energy density functionals
NASA Astrophysics Data System (ADS)
Dobaczewski, Jacek
2016-08-01
I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.
Łodyga, Wiesław; Makarewicz, Jan
2012-05-07
Geometries, anharmonic vibrations, and torsion-wagging (TW) multiplets of hydrazine and its deuterated species are studied using high-level ab initio methods employing the second-order Mo̸ller-Plesset perturbation theory (MP2) as well as the coupled cluster singles and doubles model including connected triple corrections, CCSD(T), in conjunction with extended basis sets containing diffuse and core functions. To describe the splitting patterns caused by tunneling in TW states, the 3D potential energy surface (PES) for the large-amplitude TW modes is constructed. Stationary points in the 3D PES, including equivalent local minima and saddle points are characterized. Using this 3D PES, a flexible Hamiltonian is built numerically and then employed to solve the vibrational problem for TW coupled motion. The calculated ground state r(av) structure is expected to be more reliable than the experimental one that has been determined using a simplified structural model. The calculated fundamental frequencies allowed resolution of the assignment problems discussed earlier in the literature. The determined energy barriers, including the contributions from the small-amplitude vibrations, to the tunneling of the symmetric and antisymmetric wagging mode of 1997 cm(-1) and 3454 cm(-1), respectively, are in reasonable agreement with the empirical estimates of 2072 cm(-1) and 3312 cm(-1), respectively [W. Łodyga et al. J. Mol. Spectrosc. 183, 374 (1997)]. However, the empirical torsion barrier of 934 cm(-1) appears to be overestimated. The ab initio calculations yield two torsion barriers: cis and trans of 744 cm(-1) and 2706 cm(-1), respectively. The multiplets of the excited torsion states are predicted from the refined 3D PES.
NASA Astrophysics Data System (ADS)
Łodyga, Wiesław; Makarewicz, Jan
2012-05-01
Geometries, anharmonic vibrations, and torsion-wagging (TW) multiplets of hydrazine and its deuterated species are studied using high-level ab initio methods employing the second-order Møller-Plesset perturbation theory (MP2) as well as the coupled cluster singles and doubles model including connected triple corrections, CCSD(T), in conjunction with extended basis sets containing diffuse and core functions. To describe the splitting patterns caused by tunneling in TW states, the 3D potential energy surface (PES) for the large-amplitude TW modes is constructed. Stationary points in the 3D PES, including equivalent local minima and saddle points are characterized. Using this 3D PES, a flexible Hamiltonian is built numerically and then employed to solve the vibrational problem for TW coupled motion. The calculated ground state rav structure is expected to be more reliable than the experimental one that has been determined using a simplified structural model. The calculated fundamental frequencies allowed resolution of the assignment problems discussed earlier in the literature. The determined energy barriers, including the contributions from the small-amplitude vibrations, to the tunneling of the symmetric and antisymmetric wagging mode of 1997 cm-1 and 3454 cm-1, respectively, are in reasonable agreement with the empirical estimates of 2072 cm-1 and 3312 cm-1, respectively [W. Łodyga et al. J. Mol. Spectrosc. 183, 374 (1997), 10.1006/jmsp.1997.7271]. However, the empirical torsion barrier of 934 cm-1 appears to be overestimated. The ab initio calculations yield two torsion barriers: cis and trans of 744 cm-1 and 2706 cm-1, respectively. The multiplets of the excited torsion states are predicted from the refined 3D PES.
Ab-initio phasing in protein crystallography
NASA Astrophysics Data System (ADS)
van der Plas, J. L.; Millane, Rick P.
2000-11-01
The central problem in the determination of protein structures form x-ray diffraction dada (x-ray crystallography) corresponds to a phase retrieval problem with undersampled amplitude data. Algorithms for this problem that have an increased radius of convergence have the potential for reducing the amount of experimental work, and cost, involved in determining protein structures. We describe such an algorithm. Application of the algorithm to a simulated crystallographic problem shows that it converges to the correct solution, with no initial phase information, where currently used algorithms fail. The results lend support to the possibility of ab initio phasing in protein crystallography.
Ab initio phonon limited transport
NASA Astrophysics Data System (ADS)
Verstraete, Matthieu
We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)
Saldin, D K; Poon, H C; Bogan, M J; Marchesini, S; Shapiro, D A; Kirian, R A; Weierstall, U; Spence, J C H
2011-03-18
We report on the first experimental ab initio reconstruction of an image of a single particle from fluctuations in the scattering from an ensemble of copies, randomly oriented about an axis. The method is applicable to identical particles frozen in space or time (as by snapshot diffraction from an x-ray free electron laser). These fluctuations enhance information obtainable from an experiment such as conventional small angle x-ray scattering.
NASA Astrophysics Data System (ADS)
Gambino, D.; Sangiovanni, D. G.; Alling, B.; Abrikosov, I. A.
2017-09-01
We use the color diffusion (CD) algorithm in nonequilibrium (accelerated) ab initio molecular dynamics simulations to determine Ti monovacancy jump frequencies in NaCl-structure titanium nitride (TiN), at temperatures ranging from 2200 to 3000 K. Our results show that the CD method extended beyond the linear-fitting rate-versus-force regime [Sangiovanni et al., Phys. Rev. B 93, 094305 (2016), 10.1103/PhysRevB.93.094305] can efficiently determine metal vacancy migration rates in TiN, despite the low mobilities of lattice defects in this type of ceramic compound. We propose a computational method based on gamma-distribution statistics, which provides unambiguous definition of nonequilibrium and equilibrium (extrapolated) vacancy jump rates with corresponding statistical uncertainties. The acceleration-factor achieved in our implementation of nonequilibrium molecular dynamics increases dramatically for decreasing temperatures from 500 for T close to the melting point Tm, up to 33 000 for T ≈0.7 Tm .
AIDA: ab initio domain assembly server.
Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam
2014-07-01
AIDA: ab initio domain assembly server, available at http://ffas.burnham.org/AIDA/ is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements. The server is free and open to all users, and there is an option for a user to provide an e-mail to get the link to result page. Domains are evolutionary conserved and often functionally independent units in proteins. Most proteins, especially eukaryotic ones, consist of multiple domains while at the same time, most experimentally determined protein structures contain only one or two domains. As a result, often structures of individual domains in multi-domain proteins can be accurately predicted, but the mutual arrangement of different domains remains unknown. To address this issue we have developed AIDA program, which combines steps of identifying individual domains, predicting (separately) their structures and assembling them into multiple domain complexes using an ab initio folding potential to describe domain-domain interactions. AIDA server not only supports the assembly of a large number of continuous domains, but also allows the assembly of domains inserted into other domains. Users can also provide distance restraints to guide the AIDA energy minimization. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
NASA Astrophysics Data System (ADS)
Ehlers, F. J. H.; Seydou, M.; Tingaud, D.; Maurel, F.; Charles, Y.; Queyreau, S.
2016-12-01
We have performed a uniaxial tensile test on the Σ5 [1 0 0] 36.87° twist grain boundary (GB) in face-centred cubic Al within the framework of density functional theory in order to derive an atomistic cohesive traction-separation law. Addressing the importance of kinetics to GB breakage, we accompanied our energy-separation curve calculations by two additional studies. Firstly, using the nudged elastic band method, we determined for a series of GB separations the heights of the zero temperature barriers separating intact and broken GB configurations. Secondly, a representative subset of these transition paths was examined at finite temperature with ab initio molecular dynamics. Contrasting prevalent conclusions on GB breakage behaviour, our results suggest that the GB likely stays intact at room temperature well into the range of separations where a broken GB represents the thermodynamically favourable configuration. Given the non-negligible resulting influence on critical tensile stress and work of separation, our findings may be viewed as stressing the need for a kinetic analysis in a general first principles based uniaxial tensile test.
Castro, G T; Ferretti, F H; Blanco, S E
2005-11-01
The overlapping pK(a) values of 5,7-dihydroxyflavone (chrysin) in EtOH-water solutions were determined by means of a UV-vis spectroscopic method that uses absorbance diagrams, at constant ionic strength (0.050 M) and temperature (25.0+/-0.1 degrees C). It was observed that the pK(a) values increase when the polarity-polarizability and solvation abilities of the reaction medium decrease. In order to calculate the pK(a1) and pK(a2) of chrysin in pure water, various relationships between the determined pK(a) and properties of solvents (relative permittivity, alpha-parameter of Taft and parameter Acity), are proposed. Moreover, with the aim of explaining the first pK(a1) value obtained, the molecular conformations and solute-solvent interactions of the 7(O(-))chrysinate monoanion were also investigated, using ab initio methods. Several ionization reactions and equilibria in water, which possesses a high hydrogen-bond-donor ability, are proposed. These reactions and equilibria constituted the necessary theoretical basis to calculate the first acidity constant of chrysin. The HF/6-31G(d) and HF/6-31+G(d) methods were used for calculations. Tomasi's method was used to analyze the formation of intermolecular hydrogen bonds between the 7(O(-))chrysinate monoanion and water molecules. It was proposed that in alkaline aqueous solutions the monoanion of chrysin is solvated with one water molecule. The agreement between the experimental and theoretical pK(a1) values provides good support for the acid-base reactions proposed in this paper.
NASA Astrophysics Data System (ADS)
Lamouroux, J.; Gamache, R. R.; Schwenke, D. W.
2014-11-01
The calculations of the reduced matrix elements for 441 rotational collisional transitions for rotational quantum numbers of the lower state up to J″=20 in the vibrational ground state of H216O are presented using effective and ab initio wavefunctions. Effective wavefunctions are derived from a Watson A-reduced Hamiltonian with the effective parameters determined by Matsushima et al. [Matsushima et al., J Mol Struct 1995;352-353:371]. The ab initio wavefunctions used in this study are from the work of Partridge and Schwenke [Partridge, H, Schwenke, DW. J Chem Phys 1997;106:4618]. The comparison of the reduced matrix elements obtained by both methods is described. It is demonstrated that, even for the rotational band, the effective wavefunctions show problems for some states.
An ab-initio Computational Method to Determine Dielectric Properties of Biological Materials
Abeyrathne, Chathurika D.; Halgamuge, Malka N.; Farrell, Peter M.; Skafidas, Efstratios
2013-01-01
Frequency dependent dielectric properties are important for understanding the structure and dynamics of biological materials. These properties can be used to study underlying biological processes such as changes in the concentration of biological materials, and the formation of chemical species. Computer simulations can be used to determine dielectric properties and atomic details inaccessible via experimental methods. In this paper, a unified theory utilizing molecular dynamics and density functional theory is presented that is able to determine the frequency dependent dielectric properties of biological materials in an aqueous solution from their molecular structure alone. The proposed method, which uses reaction field approximations, does not require a prior knowledge of the static dielectric constant of the material. The dielectric properties obtained from our method agree well with experimental values presented in the literature. PMID:23652459
Ab-initio structure determination of β-La 2WO 6
NASA Astrophysics Data System (ADS)
Chambrier, M.-H.; Kodjikian, S.; Ibberson, R. M.; Goutenoire, F.
2009-02-01
The structure of the low-temperature form of β-La 2WO 6 has been determined from laboratory X-ray, neutron time-of-flight and electron diffraction data. This tungstate crystallizes in the non-centrosymmetric orthorhombic space group (no. 19) P2 12 12 1, with Z=8, a=7.5196(1) Å, b=10.3476(1) Å, c=12.7944(2) Å, and a measured density 7.37(1) g cm -3. The structure consists of tungsten [WO 6] octahedra and tetrahedral [OLa 4]. Tungsten polyhedra are connected such that [W 2O 11] 10- units are formed.
Ab initio structure determination of novel borate NaSrBO 3
NASA Astrophysics Data System (ADS)
Wu, L.; Chen, X. L.; Zhang, Y.; Kong, Y. F.; Xu, J. J.; Xu, Y. P.
2006-04-01
A novel orthoborate, NaSrBO 3, has been successfully synthesized by standard solid-state reaction, and the crystal structure has been determined from powder X-ray diffraction data. It crystallizes in the monoclinic space group P2/c with lattice parameters: a=5.32446(7) Å, b=9.2684(1) Å, c=6.06683(8) Å, β=100.589(1)°. The fundamental building units are isolated BO 3 groups, which are parallelly distributed along two different directions. Because of the anisotropic polarizations of planar BO 3 groups, a considerable birefringence can be expected in it. The Na atoms are six-coordinated with O atoms to form octahedra, and the Sr atoms are nine-coordinated, forming tri-capped trigonal prisms. Those polyhedra connect with each other by bridging-oxygen atoms, forming infinite three-dimensional network, which indicates that the cleaving problem is expected to be overcome during the course of single-crystal growth. The infrared spectrum has been measured, and the result is consistent with the crystallographic study. Moreover, a comparison of the new structure type with the other known orthoborates is presented here.
Ab-initio structure determination of {beta}-La{sub 2}WO{sub 6}
Chambrier, M-H.; Kodjikian, S.; Ibberson, R.M.; Goutenoire, F.
2009-02-15
The structure of the low-temperature form of {beta}-La{sub 2}WO{sub 6} has been determined from laboratory X-ray, neutron time-of-flight and electron diffraction data. This tungstate crystallizes in the non-centrosymmetric orthorhombic space group (no. 19) P2{sub 1}2{sub 1}2{sub 1}, with Z=8, a=7.5196(1) A, b=10.3476(1) A, c=12.7944(2) A, and a measured density 7.37(1) g cm{sup -3}. The structure consists of tungsten [WO{sub 6}] octahedra and tetrahedral [OLa{sub 4}]. Tungsten polyhedra are connected such that [W{sub 2}O{sub 11}]{sup 10-} units are formed. - Graphical abstract: Projection of La{sub 2}WO{sub 6} structure along [100]. The structure could be described by [W{sub 2}O{sub 11}]{sup -10} structural unit formed by two corner-sharing octahedra.
A Nonparametrized Ab Initio Determination of the Heat of Formation of Hydroxylamine, NH2OH
Feller, David F.; Dixon, David A.
2003-12-04
Large basis set coupled cluster calculations through noniterative triple excitations were used to compute optimized structures, harmonic vibrational frequencies, atomization energies at 0 K and heats of formation at 298 K for hydroxylamine (NH2OH) and three related compounds (NH3, HNO and H2O2). The use of basis sets as large as augmented sextuple zeta resulted in small extrapolations to the complete basis set limit in order to achieve chemical accuracy ( 1 kcal/mol) in the thermodynamic properties. Complete basis set estimates were determined from several simple extrapolation formulas. In addition, four other corrections were applied to the frozen core atomization energies, (1) a zero point vibrational correction: (2) a core/valence correlation correction; (3) a Douglas-Kroll-Hess scalar relativistic correction; and (4) a first order atomic spin-orbit correction. For NH3 and HNO we incorporated a fifth correction term intended to approximate the difference between coupled cluster theory and the full configuration interact result. This correction was based on coupled cluster theory through iterative quadruple excitations (CCSDTQ). Excellent agreement with experiment was found for the heats of formation of NH3, HNO and H2O2. For NH2OH the best current estimate of the heat of formation at 298 K is 10.1 0.3 kcal/mol, which falls roughly midway between two experimental values at 12.0 2.4 and 7.9 1.5 kcal/mol.
Pradhan, Ekadashi; Carreón-Macedo, José-Luis; Cuervo, Javier E; Schröder, Markus; Brown, Alex
2013-08-15
The ground state potential energy and dipole moment surfaces for CS2 have been determined at the CASPT2/C:cc-pVTZ,S:aug-cc-pV(T+d)Z level of theory. The potential energy surface has been fit to a sum-of-products form using the neural network method with exponential neurons. A generic interface between neural network potential energy surface fitting and the Heidelberg MCTDH software package is demonstrated. The potential energy surface has also been fit using the potfit procedure in MCTDH. For fits to the low-energy regions of the potential, the neural network method requires fewer parameters than potfit to achieve high accuracy; global fits are comparable between the two methods. Using these potential energy surfaces, the vibrational energies have been computed for the four most abundant CS2 isotopomers. These results are compared to experimental and previous theoretical data. The current potential energy surfaces are shown to accurately reproduce the low-lying vibrational energies within a few wavenumbers. Hence, the potential energy and dipole moments surfaces will be useful for future study on the control of quantum dynamics in CS2.
Ab initio alpha-alpha scattering
NASA Astrophysics Data System (ADS)
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.
2015-12-01
Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Ab initio alpha-alpha scattering.
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-12-03
Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Parkes, Marie V; Greathouse, Jeffery A; Hart, David B; Gallis, Dorina F Sava; Nenoff, Tina M
2016-04-28
The separation of oxygen from nitrogen using metal-organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O2 on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O2 and N2 in the M2(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. This unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize the process of multiple guests competitively binding to coordinatively unsaturated metal sites of a MOF.
Ab initio Theory of Semiconductor Nanocrystals
NASA Astrophysics Data System (ADS)
Wang, Lin-Wang
2007-03-01
With blooming experimental synthesis of various nanostructures out of many semiconductor materials, there is an urgent need to calculate the electronic structures and optical properties of these nanosystems based on reliable ab initio methods. Unfortunately, due to the O(N^3) scaling of the conventional ab initio calculation methods based on the density functional theory (DFT), and the >1000 atom sizes of the most experimental nanosystems, the direct applications of these conventional ab intio methods are often difficult. Here we will present the calculated results using our O(N) scaling charge patching method (CPM) [1,2] to nanosystems up to 10,000 atoms. The CPM yields the charge density of a nanosystem by patching the charge motifs generated from small prototype systems. The CPM electron/hole eigen energies differ from the directly calculated results by only ˜10-20 meV. We will present the optical band gaps of quantum dots and wires, quantum rods, quantum dot/quantum well, and quantum dots doped with impurities. Besides good agreements with experimental measurements, we will demonstrate why it is important to perform ab initio calculations, in contrast with the continuum model k.p calculations. We will show the effects of surface polarization potentials and the internal electric fields. Finally, a linear scaling 3 dimensional fragment (LS3DF) method will be discussed. The LS3DF method can be used to calculate the total energy and atomic forces of a large nanosystem, with the results practically the same as the direct DFT method. Our work demonstrates that, with the help of supercomputers, it is now feasible to calculate the electronic structures and optical properties of >10,000 atom nanocrystals with ab initio accuracy. [1] L.W. Wang, Phys. Rev. Lett. 88, 256402 (2002). [2] J. Li, L.W. Wang, Phys. Rev. B 72, 125325 (2005).
Rowley, Christopher N; Roux, Benoıt
2012-10-09
Knowledge of the hydration structure of Na(+) and K(+) in the liquid phase has wide ranging implications in the field of biological chemistry. Despite numerous experimental and computational studies, even basic features such as the coordination number of these alkali ions in liquid water, thought to play a critical role in selectivity, continue to be the subject of intensive debates. Simulations based on accurate potential energy surfaces offer one approach to resolve these issues by providing reliable results on ion hydration. In this article, we report the results from molecular dynamics simulations of Na(+) and K(+) hydration based on a novel and rigorous strategy designed to overcome the challenges of QM/MM simulations of solvent molecules in the liquid phase. In this method, which we call Flexible Inner Region Ensemble Separator (FIRES), the ion and a fixed number of nearest water molecules form a dynamical and flexible inner region that is represented with high level ab initio quantum mechanical (QM) methods, while the water molecules from the surrounding bulk form an outer region that is represented by a polarizable molecular mechanical (MM) force field. Simulations yield rigorously correct thermodynamic averages as long as the solvent molecules in the flexible inner and outer regions are not allowed to exchange. Extensive FIRES simulations were carried out based on a QM/MM model in which the Na(+) or K(+) ion and the 12 nearest water molecules were represented by high level ab initio methods (RI-MP2/def2-TZVP and density functional theory with PBE/def2-TZVP), while the surrounding MM water molecules were represented by the polarizable SWM4-NDP potential. On the basis of these results, the ion coordination numbers are estimated to be within the range of 5.7-5.8 for Na(+) and 6.9-7.0 for K(+).
Ab initio infrared and Raman spectra
NASA Technical Reports Server (NTRS)
Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.
1983-01-01
It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.
Ab initio torsional potentials in silole dimers
Yamaguchi, Yoichi; Yamabe, Tokio
1996-01-05
The potential barriers for the internal rotation of silole dimers are studied theoretically using the ab initio molecular orbital method at the RHF/6-31G** level of calculations. In 2,2{prime}-bisilole, it is found that the anti-conformation is the most stable structure in the ground state and that the potential barrier height for rotation over the perpendicular conformation is 3.3 kcal/mol. 21 refs., 4 figs., 2 tabs.
Ab Initio Crystal Field for Lanthanides.
Ungur, Liviu; Chibotaru, Liviu F
2017-03-13
An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc)2 ](-) (Pc=phthalocyanine) and Dy4 K2 ([Dy(4) K(2) O(OtBu)(12) ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides.
AB initio infrared and Raman spectra
NASA Astrophysics Data System (ADS)
Fredkin, D. R.; Komornicki, A.; White, S. R.; Wilson, K. R.
1982-08-01
We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schroedinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques, are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules.
NASA Astrophysics Data System (ADS)
Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.
From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.
Ab Initio and Ab Exitu No-Core Shell Model
Vary, J P; Navratil, P; Gueorguiev, V G; Ormand, W E; Nogga, A; Maris, P; Shirokov, A
2007-10-02
We outline two complementary approaches based on the no core shell model (NCSM) and present recent results. In the ab initio approach, nuclear properties are evaluated with two-nucleon (NN) and three-nucleon interactions (TNI) derived within effective field theory (EFT) based on chiral perturbation theory (ChPT). Fitting two available parameters of the TNI generates good descriptions of light nuclei. In a second effort, an ab exitu approach, results are obtained with a realistic NN interaction derived by inverse scattering theory with off-shell properties tuned to fit light nuclei. Both approaches produce good results for observables sensitive to spin-orbit properties.
Ab initio phase diagram of iridium
NASA Astrophysics Data System (ADS)
Burakovsky, L.; Burakovsky, N.; Cawkwell, M. J.; Preston, D. L.; Errandonea, D.; Simak, S. I.
2016-09-01
The phase diagram of iridium is investigated using the Z methodology. The Z methodology is a technique for phase diagram studies that combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. In the direct Z method, the solid phases along the melting curve are determined by comparing the solid-liquid equilibrium boundaries of candidate crystal structures. The inverse Z method involves quenching the liquid into the most stable solid phase at various temperatures and pressures to locate a solid-solid boundary. Although excellent agreement with the available experimental data (to ≲65 GPa) is found for the equation of state (EOS) of Ir, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes our ab initio data to higher pressure (P ) . Our results suggest the existence of a random-stacking hexagonal close-packed structure of iridium at high P . We offer an explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.
Accurate ab Initio Spin Densities.
Boguslawski, Katharina; Marti, Konrad H; Legeza, Ors; Reiher, Markus
2012-06-12
We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].
Accurate ab Initio Spin Densities
2012-01-01
We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740]. PMID:22707921
Ab-initio Studies Of Lithium Oxide
NASA Astrophysics Data System (ADS)
Gupta, M. K.; Goel, Prabhatasree; Mittal, R.; Chaplot, S. L.
2010-12-01
Lithium oxide is an important material because of its high thermal conductivity and superionic behavior at high temperature. It behaves like a superionic conductor above 1200 K. Phonon frequencies have been calculated using ab-initio method. The calculations of phonon dispersion relation near unit cell volume corresponding to the superionic transition indicate softening of zone boundary transverse acoustic phonon mode along (110). The instability of phonon mode could lead to the dynamical disorder of lithium sub lattice. Thermal expansion and equation of states are also computed. The results compare well with our previous semi-empirical potential calculations.
Ab initio quantum chemistry: Methodology and applications
Friesner, Richard A.
2005-01-01
This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212
Germacrene D Cyclization: An Ab Initio Investigation
Setzer, William N.
2008-01-01
Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G*) and post Hartree-Fock (MP2/6-31G* *) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils. PMID:19325722
Molecular associations from ab initio pair potentials
NASA Astrophysics Data System (ADS)
Iglesias, E.; Sordo, T. L.; Sordo, J. A.
1991-12-01
A method of building up stable molecular associations by using pair potentials from ab initio calculations is presented. The Matsuoka-Clementi-Yoshimine potential has been chosen to emulate the water-water interactions while 1-6-12 potentials are used to compute both solute-solvent and solute-solute interactions. Parameters for neutral-amino-acid-water and neutral- amino-acid-neutral-amino-acid interactions are provided by the program. Supermolecules are constructed by minimization of the interaction energy of the molecules involved. Both steepest-decent and Fletcher-Powell algorithms are available to carry out such a minimization.
Ab initio studies of hydrocarbon peroxyl radicals
Besler, B.H.; Sevilla, M.D.; MacNeille, P.
1986-11-20
Extensive ab initio molecular orbital calculations have been performed for the importance series of peroxyl radicals (O/sub 2//sup .-/), HO/sub 2//sup ./, CH/sub 3/O/sub 2//sup ./, (CH/sub 3/)/sub 2/CHO/sub 2//sup ./, and (CH/sub 3/CH/sub 2/)/sub 2/CHO/sub 2//sup ./. Parameters calculated include equilibrium geometries, harmonic vibrational frequencies, dipole moments, and isotropic and anisotropic hyperfine couplings. Equilibrium geometries were of primary interest. In the two large hydrocarbon peroxyl radicals the carbon atoms and appropriate hydrogen atoms were constrained to be coplanar and the O-O group was forced to be perpendicular to the carbon chain in order to stimulate the presence of a peroxyl radical site in a polyethylene chain. Calculations were performed with large Gaussian basis sets (up to 6-311 ++G(d,p)). Calculations for HO/sub 2//sup ./ including electron correlation utilizing Moeller-Plesset perturbation theory were performed at the following levels: MP2(6-31G(d)) and 6-311G(d,p), MP3(6-311G(d,p)) and MP4SDTQ(6-311(d,p)). Calculated values are compared against the highly accurate experimental data for HO/sub 2//sup ./ known from microwave, laser magnetic resonance, and diode laser studies in order to determine the level of calculation necessary for accurate predictions. Comparison of the various calculations shows that MP2(6-31G(d)) compares favorably with MP4SDTQ(6-311G(d,p)) at a considerable savings in computation time.
Ab initio non-relativistic spin dynamics
Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong; Frisch, Michael J.
2014-12-07
Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.
Ab initio based polarizable force field parametrization
NASA Astrophysics Data System (ADS)
Masia, Marco
2008-05-01
Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by ˜30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.
Ab-initio calculations on melting of thorium
Mukherjee, D. Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.
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 as 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.
Towards Accurate Ab Initio Predictions of the Spectrum of Methane
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Kwak, Dochan (Technical Monitor)
2001-01-01
We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.
NASA Astrophysics Data System (ADS)
Dąbrowska, Aleksandra; Makowski, Mariusz; Jacewicz, Dagmara; Chylewska, Agnieszka; Chmurzyński, Lech
2008-12-01
UV absorption spectra of methyl 3-azido-6-iodo-2,3,6-trideoxy-α- D- arabino-hexopyranoside were recorded over a wide pH range. On this basis, a relationship between absorbance and pH was plotted, from which deprotonation equilibrium constants of this compound were determined. Further, quantum-mechanical calculations were performed at the ab initio level both in the gas phase by using the Restricted Hartree Fock (RHF), Møller-Plesset (MP2) methods and under consideration of solvation effects within the Polarizable Continuum Model (PCM), which enabled location of preferred protonation and deprotonation centers of this compound. The results provided the basis for discussion of the influence of substituents in the sugar ring on protolytic equilibria occurring in aqueous solutions of 3-azido-2,3-dideoxy sugars.
van Genderen, E.; Clabbers, M. T. B.; Das, P. P.; Stewart, A.; Nederlof, I.; Barentsen, K. C.; Portillo, Q.; Pannu, N. S.; Nicolopoulos, S.; Gruene, T.; Abrahams, J. P.
2016-01-01
Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014). PMID:26919375
Barrett, Bruce R.; Navrátil, Petr; Vary, James P.
2012-11-17
A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.
Ab Initio Calculation of the Hoyle State
Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.
2011-05-13
The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.
Ab Initio Reactive Computer Aided Molecular Design.
Martínez, Todd J
2017-03-21
Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. We argue that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.
An ab initio study of hydroxylated graphane.
Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola
2017-09-14
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.
An ab initio study of hydroxylated graphane
NASA Astrophysics Data System (ADS)
Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola
2017-09-01
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less
Guiding ab initio calculations by alchemical derivatives
NASA Astrophysics Data System (ADS)
to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.
2016-03-01
We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.
Ab Initio Modeling of Molecular Radiation
NASA Technical Reports Server (NTRS)
Jaffe, Richard; Schwenke, David
2014-01-01
Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.
Discovering chemistry with an ab initio nanoreactor
NASA Astrophysics Data System (ADS)
Martinez, Todd
Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.
Discovering chemistry with an ab initio nanoreactor
NASA Astrophysics Data System (ADS)
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Discovering chemistry with an ab initio nanoreactor.
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S; Martínez, Todd J
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-01-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881
NASA Astrophysics Data System (ADS)
Krosley, Kevin; Hagen, Kolbjørn; Hedberg, Kenneth
1995-06-01
Gas-phase electron diffraction data at 23°C together with molecular mechanics (MM3) and ab initio (HF/6-31G∗, gaussian 86) calculations have been used to determine the structure and conformations of 1,4-difluorobutane. The object was to ascertain whether effects similar to the gauche effect in 1,2-difluoroethane, which serves to stabilize the gauche form with the fluorine atoms in close proximity, could also operate in 1,4-difluorobutane. It was found both theoretically and experimentally that the proportion of those conformers having close fluorine atoms was small, implying the absence of effects similar to the gauche effect. The conformational composition estimated from the theoretical calculations is in good agreement with the experimental data. The experimental electron diffraction results constrained by assumptions drawn from the theoretical calculations, ED/MM3 [ED/ab initio], for the principal distances ( {r g}/{Å}) and angles ( {∠ α}/{deg}) with estimated 2σ uncertainties are as follows: r(CH) = 1.105(3) [1.106(3)], r(CF) = 1.398(2) [1.398(2)], r(C 1C 2) = 1.513(2) [1.516(2)], r(C 2C 3) = 1.537(2) [1.532(2)], ∠FCC = 110.9(3) [111.1(3)], ∠CCC = 112.9(4) [112.9(4)], and ∠HCH = 100(3) [100(3)].
On the hierarchical parallelization of ab initio simulations
NASA Astrophysics Data System (ADS)
Ruiz-Barragan, Sergi; Ishimura, Kazuya; Shiga, Motoyuki
2016-02-01
A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.
Comparison of SAMO and ab initio model calculations for pyrazine
NASA Astrophysics Data System (ADS)
Duke, B. J.; Collins, M. P. S.
1981-04-01
The simulated ab initio molecular orbital (SAMO) technique and the ab initio model calculation of Butkus and Fink are compared for the pyrazine molecule. Both methods construct the wave function of pyrazine from wave functions of smaller pattern molecules. The methods are complimentary in that the strengths of one are often the weakness of the other. The SAMO method gives good orbital energies which are not given by the ab initio model method, while the latter is more readily extended to the ionic protonated molecules.
Experimental and ab initio study of the mechanical properties of hydroxyapatite
NASA Astrophysics Data System (ADS)
Snyders, R.; Music, D.; Sigumonrong, D.; Schelnberger, B.; Jensen, J.; Schneider, J. M.
2007-05-01
The authors have studied the elastic properties of radio frequency sputtered phase pure, stoichiometric, and dense hydroxyapatite films by nanoindentation. The measured elastic modulus values have been compared to ab initio calculated data. The calculation technique was based on the determination of all elastic constants. The calculated and measured elastic modulus values differ by ˜10%. The good agreement indicates that the elasticity of hydroxyapatite can be described using ab initio calculations, establishing the elastic modulus thereof.
Ab Initio: And a New Era of Airline Pilot Training.
ERIC Educational Resources Information Center
Gesell, Laurence E.
1995-01-01
Expansion of air transportation and decreasing numbers seeking pilot training point to a shortage of qualified pilots. Ab initio training, in which candidates with no flight time are trained to air transport proficiency, could resolve the problem. (SK)
Ab initio phonon scattering by dislocations
NASA Astrophysics Data System (ADS)
Wang, Tao; Carrete, Jesús; van Roekeghem, Ambroise; Mingo, Natalio; Madsen, Georg K. H.
2017-06-01
Heat management in thermoelectric and power devices as well as in random access memories poses a grand challenge and can make the difference between a working and an abandoned device design. Despite the prevalence of dislocations in all these technologies, the modeling of their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce an efficient ab initio approach based on Green's functions computed by two-dimensional reciprocal space integration. By combining elasticity theory and density functional theory, we calculate the scattering strength of a 90∘ misfit edge dislocation in Si. Because of the breakdown of the Born approximation, earlier literature models fail, even qualitatively. We find that a dislocation density larger than 109cm-2 is necessary to substantially influence thermal conductivity at room temperature and above. We quantify how much of the reduction of thermal conductivity measured in nanograined samples can be explained by realistic dislocation concentrations.
Ab initio calculations of nitramine dimers
NASA Astrophysics Data System (ADS)
Koh-Fallet, Sharon; Schweigert, Igor
2015-06-01
Elevated temperatures and pressures are typically thought to have opposing effects on the reaction channels of nitramine decomposition. These high temperatures promote reactions with loose transition structures (positive activation entropies and volumes), such as N-N bond homolysis. Elevated pressures promote reactions with tight transition structures (negative activation entropies and volumes), such as intramolecular and intermolecular H transfer. However, no quantitative data exists regarding the range of temperatures and pressures at which these effects become pronounced. We are pursuing ab initio calculations of the corresponding unimolecular and bimolecular transition structures with the objective of estimating the relevant thermochemical parameters and quantifying the effects of elevated temperature and pressures on the corresponding rate constants. Here, we present density functional theory and complete active space calculations of gas-phase molecular dimers of nitramines as an intermediate step toward modeling transition structures directly in the condensed phase. This work was supported by the Naval Research Laboratory via the American Society for Engineering and Education and by the Office of Naval Research, both directly and through the Naval Research Laboratory.
Ab Initio Quantum Simulations of Liquid Water
NASA Astrophysics Data System (ADS)
Gergely, John; Ceperley, David; Gygi, Francois
2007-03-01
Some recent efforts at simulating liquid water have employed ``ab initio'' molecular dynamics (AIMD) methods with forces from a version of density functional theory (DFT) and, in some cases, imaginary-time path integrals (PI) to study quantum effects of the protons. Although AIMD methods have met with many successes, errors introduced by the approximations and choices of simulation parameters are not fully understood. We report on path integral Monte Carlo (PIMC) studies of liquid water using DFT energies that provide quantitative benchmarks for PI-AIMD work. Specifically, we present convergence studies of the path integrals and address whether the Trotter number can be reduced by improving the form of the (approximate) action. Also, we assess 1) whether typical AIMD simulations are sufficiently converged in simulation time, i.e., if there is reason to suspect that nonergodic behavior in PI-AIMD methods leads to poor convergence, and 2) the relative efficiency of the methods. E. Schwegler, J.C. Grossman, F. Gygi, G. Galli, J. Chem. Phys 121, 5400 (2004).
Phonocatalysis. An ab initio simulation experiment
Kim, Kwangnam; Kaviany, Massoud
2016-06-15
Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF{sub 6} on h-BN surface leads to formation of XeF{sub 4} and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon) energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent) requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.
Ab initio two-component Ehrenfest dynamics
Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong
2015-09-21
We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H{sub 2} and O{sub 2}. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.
Ab Initio Calculation of NH_3 Spectrum
NASA Astrophysics Data System (ADS)
Polyansky, Oleg; Ovsyannikov, Roman I.; Kyuberis, Aleksandra; Lodi, Lorenzo; Tennyson, Jonathan; Yurchenko, Sergei N.; Yachmenev, Andrey; Zobov, Nikolay Fedorovich
2016-06-01
An ab initio potential energy surface (PES) for NH_3 is computed using the methodology pioneered for water (Polyansky et al. J. Phys. Chem. A, 117, 9633 (2013)). A multireference configuration calclulations are performed at 50000 points using quadruple and 5z basis sets to give a complete basis set (CBS) extrapolation. Relativistic and adiabatic surfaces are also computed. The points are fitted to an analytical PES. The rovibrational energy levels are computed using the program TROVE in both linearized and curvilinear coordinates. Better convergence is obtained for the higher energy levels using curvilinear coordinates: an accuracy of about 1 wn is achieved for the levels up to 12 000 wn. The levels up to 18 000 wn are reproduced with the accuracy of a few wn. These results are used to assign the visible spectrum of 14NH_3 recorded by Coy and Lehmann (J. Chem. Phys., 84, 5239 (1988)). Predicted rovibrational levels for NH_2D, NHD_2, ND_3 and 15NH_3 are given.
Ab-initio study of hexagonal apatites
NASA Astrophysics Data System (ADS)
Calderin, Lazaro; Stott, Malcom J.
2001-03-01
A silicon stabilized mixture of calcium phosphate phases has been recognized as playing an important role in actively resorbable coatings and in ceramics as bone materials. The nature of this material is being investigated using a variety of techniques including a combination of crystallographic analysis of measured x-ray diffraction spectra, and ab initio quantum mechanics simulations. We have used all-electron, density functional based calculations to investigate a group of hexagonal apatites. The fully relaxed crystallographic structures of hydroxyapatite, and related apatites have been obtained. We will present the results and discuss the nature of the bonding in these materials. The x-ray diffraction pattern and the infra-red spectra have also been obtained and will be compared with experiment. Acknowledgments:This work is part of a collaboration with the Applied Ceramics group of M.Sayer, and with Millenium Biologix Inc. Support of the NSERC of Canada through the award of a Co-operative R & D grant to the collaboration is acknowledged.
NASA Astrophysics Data System (ADS)
Dakkouri, Marwan; Grosser, Martin
2002-06-01
As a continuation of our systematic investigation of the effect of substituents on the ring geometry and dynamics in silacyclobutanes and in order to explore the role of the silicon atom as a mediator for electronic interactions between the attached fragments, we studied the molecular structure of 1,1-diethynylsilacyclobutane (DESCB) by means of gas-phase electron diffraction and ab initio calculations. The structural refinement of the electron diffraction data yielded the following bond lengths (ra) and bond angles (uncertainties are 3σ): r(Si-C)=1.874(2) Å,r(Si-Ctbnd)=1.817(1) Å,r(-Ctbnd C-)=1.209(1)Å,r(C-C)=1.563(2)Å, ∠(C-Si-C)=79.2(6)°, ∠(tbnd C-Si-Ctbnd)=106.5(6)°. The geminal Si-Ctbnd C moieties were found to be bent outwards by 3.1(15)° and the puckering angle was determined to be 30.0(15)°. The evidently short Si-Ctbnd bond length, which was also reproduced by the ab initio calculations, could be rationalized as being the consequence of the electronic interaction between the outer π charges of the triple bond and the 3pπ orbitals at the silicon atom. It is also likely that the conjugation of the geminal ethynyl groups leads to an enhancement of this bond contraction. Electrostatic interactions and the subsequent reduction of the covalent radius of the silicon atom may also contribute to this bond shortening. It has been found that the endocyclic Si-C bond length fits nicely within a scheme describing a monotonous decrease of the Si-C bond length with the increase of the electronegativity of the substituent in various geminally substituted silacyclobutanes. A series of related silacyclobutanes and acyclic diethynylsilanes have been studied by applying various ab initio methods and their optimized structures were compared to the structure of DESCB. Among these compounds are 1,1-dicyanosilacyclobutane (DCYSCB), which is isoelectronic to DESCB, 1,1-diethynylcyclobutane (DECB) which is isovalent to DESCB, monoethynylsilacyclobutane (MESCB) and
NASA Astrophysics Data System (ADS)
Novikov, Vladimir P.; Tarasenko, Svetlana A.; Samdal, Svein; Vilkov, Lev V.
1998-04-01
Gas electron diffraction data are applied to determine the geometrical parameters of the 1,1-dichlorosilacyclobutane molecule using a dynamic model where the ring puckering was treated as a large amplitude motion. The structural parameters and parameters of the potential function were refined taking into account the relaxation of the molecular geometry estimated from ab initio calculations at the Hartree-Fock level of theory using a 6-311 + G∗∗ basis set. The potential function has been described as V(ϕ) = V 0[( {ϕ}/{ϕ e}) 2 - 1] 2 with the following parameters V 0 = 0.57 ± 0.32 {kcal}/{mol} and ϕe = 25.9 ± 2.6°, where ϕ is the puckering angle of the ring. The classic distribution function used for averaging the local molecular configurations was found to underestimate the value V0 by 8% as compared with the exact quantum mechanical distribution function. The geometric parameters at the minimum V( ϕ) ( r a in Å, ∠ α in degrees and errors given as three times the standard deviations including a scale error) are: r(Si-Cl ax) = 2.043(2), r(Si-Cl eq) = 2.038(2), r(Si-C) = 1.860(3), r(C-C) = 1.557(4), r(C-H) = 1.091(8), ∠ClSiCl = 105.2(8), ∠CSiC = 81.1(10), ∠SiCH eq = 118.9(54), ∠SiCH ax = 109.7(54), ∠CC 5H eq = 105.3(63), ∠CC 5H ax = 100.9(63), HC 3H = 108.0, ∠ δ(ClSiCl) = 4.1, ∠ δ(HC 3H) = 3.0, where the tilt angle δ, and ∠HC 3H are estimated from ab initio constraints. The structural parameters are compared with those obtained for related compounds. Distortions of the valence angles at the Si atom in silacyclobutanes are shown to be well explained using the VSEPR model complemented by the concept of bent bonds.
NASA Astrophysics Data System (ADS)
Senent, M. L.; Moule, D. C.; Smeyers, Y. G.
1995-04-01
We have calculated the potential energy hypersurface of dimethyl ether with respect to the COC bending coordinate α and the torsional angles of the two methyl groups, θ1 and θ2. Two sets of ab initio calculations were carried out. The first was made at the level MP2/6-31G(d,p) in which the structural coordinates were fully relaxed except for the grid points on the hypersurface. More extensive calculation were carried out with MP4 corrections for electron correlation with the same molecular structure. The torsional bending Hamiltonian matrix was symmetrized by the operations of the G36 nonrigid group and was solved variationally. The effect of explicitly considering the bending mode in the three-dimensional treatment was determined by a comparison to the two-dimensional model in which the flexibility of the frame was absorbed into the calculation by the fully relaxed method. It was found that the three-dimensional calculation gave a much better account of the sin(3θ1)sin(θ2) intermode coupling than the two-dimensional treatment.
NASA Astrophysics Data System (ADS)
Brown, R. E.; Chateauneuf, G. M.; Klassen, P. R.; Luck, R. L.; Mendenhall, G. D.
2001-04-01
A previously unobserved crystalline precipitate in an extract of crude 1-(aminomethyl) pyrene was shown to be 1-(isopropylideneaminomethyl)pyrene. The identity of this compound was established by a single crystal X-ray determination that revealed an overall planar arrangement for the non-hydrogen atoms. The molecule crystallized in the monoclinic space group P2 1/ c, with the following unit cell dimensions: a=11.6650(10) Å, b=8.2850(9) Å, c=16.0220(9) Å, β=108.297(6)°, V=1470(2) Å3, and Z=4. The structure was refined to R=0.059 ( Rw=0.150) for 2576 data points with Fo2>2 σ( Fo2). The results of ab-initio-calculations at the STO-3G level suggest that the difference in rotational conformer energy for rotation about the C-N single bond varied by less than 1 kcal/mol between the maximum (-30°) and minimum (90°) values. Packing forces in the solid state arrangement are believed to be responsible for the difference between this result and experiment, since an AM1 calculation with 1 constrained between two molecules of 1 at the experimental distances led to the planar structure as the one with lowest energy.
Genderen, E. van; Clabbers, M. T. B.; Das, P. P.; Stewart, A.; Nederlof, I.; Barentsen, K. C.; Portillo, Q.; Pannu, N. S.; Nicolopoulos, S.; Gruene, T.; Abrahams, J. P.
2016-02-05
A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)
Skutterudites under pressure: An ab initio study
Ram, Swetarekha; Kanchana, V.; Valsakumar, M. C.
2014-03-07
Ab initio results on the band structure, density of states, and Fermi surface (FS) properties of LaRu{sub 4}X{sub 12} (X = P, As, Sb) are presented at ambient pressure as well as under compression. The analysis of density of states reveals the major contribution at the Fermi level to be mainly from the Ru-d and X-p states. We have a complicated Fermi surface with both electron and hole characters for all the three compounds which is derived mainly from the Ru-d and X-p states. There is also a simpler FS with hole character derived from the P-p{sub z} orbital for LaRu{sub 4}P{sub 12} and Ru-d{sub z{sup 2}} orbital in the case of As and Sb containing compounds. More interestingly, Fermi surface nesting feature is observed only in the case of the LaRu{sub 4}P{sub 12}. Under compression, we observe the topology of the complicated FS sheet of LaRu{sub 4}As{sub 12} to change around V/V{sub 0} = 0.85, leading to a behaviour similar to that of a multiband superconductor, and in addition, we have two more hole pockets centered around Γ at V/V{sub 0} = 0.8 for the same compound. Apart from this, we find the hole pocket to vanish at V/V{sub 0} = 0.8 in the case of LaRu{sub 4}Sb{sub 12} and the opening of the complicated FS sheet gets reduced. The de Haas van Alphen calculation shows the number of extremal orbits in the complicated sheet to change in As and Sb containing compounds under compression, where we also observe the FS topology to change.
AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT
French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes
2012-09-15
We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.
Ab initio thermodynamic model for magnesium carbonates and hydrates.
Chaka, Anne M; Felmy, Andrew R
2014-09-04
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.
Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates
Chaka, Anne M.; Felmy, Andrew R.
2014-03-28
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.
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.
THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY
Turchi, P A
2004-09-24
Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics '{acute a} la CALPHAD'. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys. Finally, comments will be made on challenges and future prospects.
Ab Initio Studies of Stratospheric Ozone Depletion Chemistry
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.
Ab initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
Ab initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
Kellö, Vladimir
2015-01-22
Highly correlated scalar relativistic calculations of electric field gradients at nuclei in diatomic molecules in combination with accurate nuclear quadrupole coupling constants obtained from microwave spectroscopy are used for determination of nuclear quadrupole moments.
ERIC Educational Resources Information Center
Lord, Richard L.; Davis, Lisa; Millam, Evan L.; Brown, Eric; Offerman, Chad; Wray, Paul; Green, Susan M. E.
2008-01-01
We present a first-principles determination of the photoelectron spectra of water and hypochlorous acid as a laboratory exercise accessible to students in an undergraduate physical chemistry course. This paper demonstrates the robustness and user-friendliness of software developed for the Franck-Condon factor calculation. While the calculator is…
ERIC Educational Resources Information Center
Lord, Richard L.; Davis, Lisa; Millam, Evan L.; Brown, Eric; Offerman, Chad; Wray, Paul; Green, Susan M. E.
2008-01-01
We present a first-principles determination of the photoelectron spectra of water and hypochlorous acid as a laboratory exercise accessible to students in an undergraduate physical chemistry course. This paper demonstrates the robustness and user-friendliness of software developed for the Franck-Condon factor calculation. While the calculator is…
Real-world predictions from ab initio molecular dynamics simulations.
Kirchner, Barbara; di Dio, Philipp J; Hutter, Jürg
2012-01-01
In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.
Stephens, Susanna L; Mizukami, Wataru; Tew, David P; Walker, Nicholas R; Legon, Anthony C
2012-02-14
Pure rotational spectra of the ground vibrational states of six isotopologues of OC···AgI have been measured by chirped-pulse Fourier transform microwave spectroscopy. The spectra are assigned to determine the rotational constant, B(0), centrifugal distortion constant, D(J), and nuclear quadrupole coupling constant of the iodine atom, χ(aa)(I). The complex is linear. Isotopic substitutions at the silver, carbon, and oxygen atoms allow bond lengths to be established by the r(0), r(s), and r(m)((1)) methods of structure determination. The length of the C-O bond, r(CO), in the r(0) geometry for OC···AgI is 0.008 Å shorter than that found in the free CO molecule. The length of the Ag-I bond, r(AgI), is 0.013 Å shorter than in free AgI. χ(aa)(I) is determined to be -769.84(22) MHz for OC···(107)AgI implying an ionic character of 0.66 for the metal halide bond. Attachment of carbon monoxide to the isolated AgI molecule results in an increase of the ionic character of AgI of 0.12. The molecular structure and spectroscopic parameters determined from the experimental data are presented alongside the results of calculations at the explicitly correlated coupled-cluster singles, doubles and perturbative triples level. Vibrational frequencies, the electric dipole moment, the nuclear quadrupole coupling constant, and the dissociation energy of the molecule have been calculated.
The ab-initio crystal structure determination of UPd 2Sn by synchrotron X-ray powder diffraction
NASA Astrophysics Data System (ADS)
Marezio, M.; Cox, D. E.; Rossel, C.; Maple, M. B.
1988-09-01
The structure of the heavy-fermion compound UPd 2Sn has been determined by synchrotron x-ray radiation powder diffraction techniques. It is orthorhombic, space group Pnma [lattice parameters a = 9.9787(1), b = 4.58843(5), c = 6.89166(8) Å at room temperature] and Z = 4. All atoms, one U, one Sn, and two Pd are in 4d special positions at (x {1}/{4} z). The refinements were carried out by the Rietveld method with a pseudo-Voigt peak shape function. The final conventional R factors were: R wp = 21.3% and R E = 14.3%. The U positions in the unit cell were unequivocally located, but because of the similarity in x-ray scattering factors it was not possible to determine whether the Pd atoms and the Sn atoms are ordered or disordered on the other three sites. The structural arrangement of UPd 2Sn is of either MnCu 2Al, or ordered NaTl, or disordered Fe 3Al type, all these structures being cubic and b.c.c. related. The orthorhombic distortion is large and is probably due to a size effect of the U atoms which would be in a mixed ( {3+}/{4+}) valence state.
NASA Astrophysics Data System (ADS)
Powers, Nathan Lee
2008-10-01
The [Fe2S2]2+/[Fe2S 2]+ electronic structure of seven Rieske protein active sites (bovine mitochondrial cytochrome bc1 complex, spinach chloroplast cytochrome b6f complex, Rieske-type ferredoxin associated with biphenyl dioxygenase from Burkholderia cepacia, yeast cytochrome bcl complex from Saccharomyces cerevisiae, Rieske subunit of arsenite oxidase from Alcaligenes faecalis, respiratory-type Rieske protein from Thermus thermophilus, and Rieske protein II (soxF) from Sulfolobus acidocaldarius), which lie in a reduction potential range from -150 mV to 375 mV, have been studied by both single and multi-determinant quantum mechanical methods. Calculated reduction potentials and magnetic properties are found comparable to experimental values.
Ab initio determination of potential energy surfaces for the first two UV absorption bands of SO2
NASA Astrophysics Data System (ADS)
Xie, Changjian; Hu, Xixi; Zhou, Linsen; Xie, Daiqian; Guo, Hua
2013-07-01
Three-dimensional potential energy surfaces for the two lowest singlet (tilde A{}^1B_1 and tilde B{}^1A_2 ) and two lowest triplet (tilde a^3 B_1 and tilde b^3 A_2 ) states of SO2 have been determined at the Davidson corrected internally contracted multi-reference configuration interaction level with the augmented correlation-consistent polarized triple-zeta basis set (icMRCI+Q/AVTZ). The non-adiabatically coupled singlet states, which are responsible for the complex Clements bands of the B band, are expressed in a 2 × 2 quasi-diabatic representation. The triplet state potential energy surfaces, which are responsible for the weak A band, were constructed in the adiabatic representation. The absorption spectrum spanning both the A and B bands, which is calculated with a three-state non-adiabatic coupled Hamiltonian, is in good agreement with experiment, thus validating the potential energy surfaces and their couplings.
NASA Astrophysics Data System (ADS)
Holka, Filip; Szalay, Péter G.; Fremont, Julien; Rey, Michael; Peterson, Kirk A.; Tyuterev, Vladimir G.
2011-03-01
High level ab initio potential energy functions have been constructed for LiH in order to predict vibrational levels up to dissociation. After careful tests of the parameters of the calculation, the final adiabatic potential energy function has been composed from: (a) an ab initio nonrelativistic potential obtained at the multireference configuration interaction with singles and doubles level including a size-extensivity correction and quintuple-sextuple ζ extrapolations of the basis, (b) a mass-velocity-Darwin relativistic correction, and (c) a diagonal Born-Oppenheimer (BO) correction. Finally, nonadiabatic effects have also been considered by including a nonadiabatic correction to the kinetic energy operator of the nuclei. This correction is calculated from nonadiabatic matrix elements between the ground and excited electronic states. The calculated vibrational levels have been compared with those obtained from the experimental data [J. A. Coxon and C. S. Dickinson, J. Chem. Phys. 134, 9378 (2004)]. It was found that the calculated BO potential results in vibrational levels which have root mean square (rms) deviations of about 6-7 cm-1 for LiH and ˜3 cm-1 for LiD. With all the above mentioned corrections accounted for, the rms deviation falls down to ˜1 cm-1. These results represent a drastic improvement over previous theoretical predictions of vibrational levels for all isotopologues of LiH.
Holka, Filip; Szalay, Péter G; Fremont, Julien; Rey, Michael; Peterson, Kirk A; Tyuterev, Vladimir G
2011-03-07
High level ab initio potential energy functions have been constructed for LiH in order to predict vibrational levels up to dissociation. After careful tests of the parameters of the calculation, the final adiabatic potential energy function has been composed from: (a) an ab initio nonrelativistic potential obtained at the multireference configuration interaction with singles and doubles level including a size-extensivity correction and quintuple-sextuple ζ extrapolations of the basis, (b) a mass-velocity-Darwin relativistic correction, and (c) a diagonal Born-Oppenheimer (BO) correction. Finally, nonadiabatic effects have also been considered by including a nonadiabatic correction to the kinetic energy operator of the nuclei. This correction is calculated from nonadiabatic matrix elements between the ground and excited electronic states. The calculated vibrational levels have been compared with those obtained from the experimental data [J. A. Coxon and C. S. Dickinson, J. Chem. Phys. 134, 9378 (2004)]. It was found that the calculated BO potential results in vibrational levels which have root mean square (rms) deviations of about 6-7 cm(-1) for LiH and ∼3 cm(-1) for LiD. With all the above mentioned corrections accounted for, the rms deviation falls down to ∼1 cm(-1). These results represent a drastic improvement over previous theoretical predictions of vibrational levels for all isotopologues of LiH.
Ab initio computations of photodissociation products of CFC alternatives
Tai, S.; Illinger, K.H.; Kenny, J.E.
1995-12-31
Ab initio computations, have already been used to examine the energetics of the photodissociation of stratospheric chlorofluorocarbons. Our awn research has investigated the ab initio computation of vibrational frequencies and infrared intensities of CF{sub 3}CH{sub 2}F, CF{sub 3}CF{sub 2}H, and CF{sub 3}CH{sub 3}; continuing research will attempt to expand these computations to the energetics of the photodissociation of these molecules, since sane of the most common types of chlorofluorocarbon substitutes are hydrofluoroethanes.
Strak, Pawel; Sakowski, Konrad; Kempisty, Pawel
2015-09-07
Properties of bare and nitrogen-covered Al-terminated AlN(0001) surface were determined using density functional theory (DFT) calculations. At a low nitrogen coverage, the Fermi level is pinned by Al broken bond states located below conduction band minimum. Adsorption of nitrogen is dissociative with an energy gain of 6.05 eV/molecule at a H3 site creating an overlap with states of three neighboring Al surface atoms. During this adsorption, electrons are transferred from Al broken bond to topmost N adatom states. Accompanying charge transfer depends on the Fermi level. In accordance with electron counting rule (ECR), the DFT results confirm the Fermi level is not pinned at the critical value of nitrogen coverage θ{sub N}(1) = 1/4 monolayer (ML), but it is shifted from an Al-broken bond state to Np{sub z} state. The equilibrium thermodynamic potential of nitrogen in vapor depends drastically on the Fermi level pinning being shifted by about 4 eV for an ECR state at 1/4 ML coverage. For coverage above 1/4 ML, adsorption is molecular with an energy gain of 1.5 eV at a skewed on-top position above an Al surface atom. Electronic states of the admolecule are occupied as in the free molecule, no electron transfer occurs and adsorption of a N{sub 2} molecule does not depend on the Fermi level. The equilibrium pressure of molecular nitrogen above an AlN(0001) surface depends critically on the Fermi level position, being very low and very high for low and high coverage, respectively. From this fact, one can conclude that at typical growth conditions, the Fermi level is not pinned, and the adsorption and incorporation of impurities depend on the position of Fermi level in the bulk.
Dissociation of NaCl in water from ab initio molecular dynamics simulations.
Timko, Jeff; Bucher, Denis; Kuyucak, Serdar
2010-03-21
We perform ab initio molecular dynamics simulations to study the dissociation of NaCl in water. The potential of mean force (PMF) between the two ions is determined using the constrained-force method. The simulation windows corresponding to the contact and solvent-separated minima, and the transition state in between, are further analyzed to determine the changes in the properties of hydration waters such as coordination number, dipole moment, and orientation. The ab initio results are compared with those obtained from classical molecular dynamics simulations of aqueous NaCl using several common force fields. The ab initio PMF is found to have a shallower contact minimum and a smaller transition barrier compared with the classical ones. Also the binding free energy calculated from the ab initio PMF almost vanishes whereas it is negative for all the classical PMFs. Water dipole moments are observed to exhibit little change during dissociation, indicating that description of NaCl with a nonpolarizable force field may be feasible. However, overcoordination of the ion pair at all distances remains as a serious shortcoming of the current classical models. The ab initio results presented here provide useful guidance for alternative parametrizations of the nonpolarizable force fields as well as the polarizable ones currently under construction.
High-throughput ab-initio dilute solute diffusion database
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-01-01
We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308
Ab initio study of II-(VI)2 dichalcogenides
NASA Astrophysics Data System (ADS)
Olsson, P.; Vidal, J.; Lincot, D.
2011-10-01
The structural stabilities of the (Zn,Cd)(S,Se,Te)2 dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe2 pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications.
Ab initio study of electron-phonon coupling in rubrene
NASA Astrophysics Data System (ADS)
Ordejón, P.; Boskovic, D.; Panhans, M.; Ortmann, F.
2017-07-01
The use of ab initio methods for accurate simulations of electronic, phononic, and electron-phonon properties of molecular materials such as organic crystals is a challenge that is often tackled stepwise based on molecular properties calculated in gas phase and perturbatively treated parameters relevant for solid phases. In contrast, in this work we report a full first-principles description of such properties for the prototypical rubrene crystals. More specifically, we determine a Holstein-Peierls-type Hamiltonian for rubrene, including local and nonlocal electron-phonon couplings. Thereby, a recipe for circumventing the issue of numerical inaccuracies with low-frequency phonons is presented. In addition, we study the phenyl group motion with a molecular dynamics approach.
High-throughput ab-initio dilute solute diffusion database
NASA Astrophysics Data System (ADS)
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-07-01
We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.
Ab initio calculation of (hyper)polarizabilities using a sum-over-states formalism.
NASA Astrophysics Data System (ADS)
Taylor, Caroline M.; Chaudhuri, Rajat K.; Potts, Davin M.; Freed, Karl F.
2001-03-01
Hyperpolarizabilities are relevant to a wide range of non-linear optical properties. Ab initio computations often require a high level of correlation for accurate determination of β and γ , and especially of thier frequency dependence. While sum-over-states methods are widely used within semi-empirical frameworks, they have not been employed with high level ab initio methods because of the computational costs associated with calculating a sufficient number of states. The effective valence shell Hamiltonian method (H^v) is a highly correlated, size-extensive, ab initio, multireference, perturbative (``perturb-then-diagonalize'') method. A single H^v calculation yields a large number of states, making it ideal for use with the sum-over-states fomalism for determination of molecular properties. The method has been used to calculate the (hyper)polarizabilities of small polyene systems.
Bicanonical ab Initio Molecular Dynamics for Open Systems.
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.
Multiple time step integrators in ab initio molecular dynamics
Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.
2014-02-28
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.
Ab-Initio Theory of Charge Transport in Organic Crystals
NASA Astrophysics Data System (ADS)
Hannewald, K.; Bobbert, P. A.
2005-06-01
A theory of charge transport in organic crystals is presented. Using a Holstein-Peierls model, an explicit expression for the charge-carrier mobilities as a function of temperature is obtained. Calculating all material parameters from ab initio calculations, the theory is applied to oligo-acene crystals and a brief comparison to experiment is given.
Ab initio interatomic potentials and the thermodynamic properties of fluids.
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.
Towards SiC Surface Functionalization: An Ab Initio Study
Cicero, G; Catellani, A
2005-01-28
We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.
Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures
Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan
2006-04-05
A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.
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.
The application of ab initio calculations to molecular spectroscopy
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.
1989-01-01
The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.
The application of ab initio calculations to molecular spectroscopy
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.
1989-01-01
The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.
Ab initio MCDHF calculations of electron-nucleus interactions
NASA Astrophysics Data System (ADS)
Bieroń, Jacek; Froese Fischer, Charlotte; Fritzsche, Stephan; Gaigalas, Gediminas; Grant, Ian P.; Indelicato, Paul; Jönsson, Per; Pyykkö, Pekka
2015-05-01
We present recent advances in the development of atomic ab initio multiconfiguration Dirac-Hartree-Fock theory, implemented in the GRASP relativistic atomic structure code. For neutral atoms, the deviations of properties calculated within the Dirac-Hartree-Fock (DHF) method (based on independent particle model of an atomic cloud) are usually dominated by electron correlation effects, i.e. the non-central interactions of individual electrons. We present the recent advances in accurate calculations of electron correlation effects in small, medium, and heavy neutral atoms. We describe methods of systematic development of multiconfiguration expansions leading to systematic, controlled improvement of the accuracy of the ab initio calculations. These methods originate from the concept of the complete active space (CAS) model within the DHF theory, which, at least in principle, permits fully relativistic calculations with full account of electron correlation effects. The calculations within the CAS model on currently available computer systems are feasible only for very light systems. For heavier atoms or ions with more than a few electrons, restrictions have to be imposed on the multiconfiguration expansions. We present methods and tools, which are designed to extend the numerical calculations in a controlled manner, where multiconfiguration expansions account for all leading electron correlation effects. We show examples of applications of the GRASP code to calculations of hyperfine structure constants, but the code may be used for calculations of arbitrary bound-state atomic properties. In recent years it has been applied to calculations of atomic and ionic spectra (transition energies and rates), to determinations of nuclear electromagnetic moments, as well as to calculations related to interactions of bound electrons with nuclear electromagnetic moments leading to violations of discrete symmetries.
Ab Initio Infrared and Raman Spectra.
1982-08-01
tions. For parameters not depending on momenta, a parallel ab fhti Monte Carlo approach would use electronic energies and other parameters of... Monte Carlo approach. Specifically, as one of us has suggested,t I classical molecular dynamics may be integrated with ab iniHo quan- tum force...alternative approach, for phenomena which are not explicitly time dependent, is a Monte Carlo procedure in which at each trial nuclear configuration
Parkes, Marie V.; Greathouse, Jeffery A.; Hart, David B.; ...
2016-04-04
The separation of oxygen from nitrogen using metal–organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O2 on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O2 and N2 in the M2(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. Lastly, this unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize the process of multiple guestsmore » competitively binding to coordinatively unsaturated metal sites of a MOF.« less
Magnetic ordering of Fe and Tb in the ab initio determined FeRGe2O7 structure (R=Y, Tb)
NASA Astrophysics Data System (ADS)
Cascales, C.; Bucio, L.; Gutiérrez Puebla, E.; Rasines, I.; Fernández-Díaz, M. T.
1998-03-01
The crystal structure of FeRGe2O7 (R=Y, Tb) has been solved ab initio from x-ray powder diffraction data. It is monoclinic, space group P21/m (No. 11), Z=4, a (Å)=9.6552(4) and 9.6388(8); b (Å)=8.5197(3) and 8.4789(7), c (Å)=6.6746(3) and 6.7383(5), β (°)=100.761(2) and 100.377(4), and V(Å3)=539.39 and 541.69, for R=Y and Tb, respectively. Precise oxygen positions were determined for the Tb compound from a room temperature neutron diffraction profile, refined by the Rietveld method to an Rf=3.99% using 58 parameters. The FeYGe2O7 crystal structure contains three kinds of coordination polyhedra: R3+ coordinated to seven oxygens at slightly different lengths forming a capped octahedron, FeO6 distorted octahedra, and four types of GeO4 tetrahedra. Its most interesting feature is the existence of flattened chains of RO7 polyhedra linked in the c direction through pairs of FeO6 octahedra with which they share edges, forming layers running parallel to the bc crystal plane. Magnetization measurements between 350 and 1.7 K show one peak at 38 K for R=Y and two maxima at 42 and 20 K for the Tb compound, which could indicate transitions to antiferromagnetically ordered states. From low-temperature neutron diffraction data on FeTbGe2O7, three-dimensional antiferromagnetic ordering is established, both Fe and Tb sublattices getting simultaneously ordered at TN=42 K. The propagation vector of the magnetic structure is k=[0,0,0]. At 1.7 K the magnetic moments 3.91(7)μB (Fe3+) and 7.98(6)μB (Tb3+) lie ferromagnetically coupled in the ac planes, which contain TbO7-FeO6-TbO7- chains in the c direction, forming relatively small angles with the c axis. The coupling between parallel ac planes is antiferromagnetic along the b direction. This model leads to a best fit of Rmag=3.02%. The thermal evolution of the magnetic moments suggests that below ~20 K the faster increase of the Tb3+ moments is due to the stronger Fe-Tb interactions and crystal field effects. The maximum in
NASA Astrophysics Data System (ADS)
Okubo, Tsuyoshi; Shinjo, Kazuya; Yamaji, Youhei; Kawashima, Naoki; Sota, Shigetoshi; Tohyama, Takami; Imada, Masatoshi
2017-08-01
We investigate the ground state properties of Na2IrO3 based on numerical calculations of the recently proposed ab initio Hamiltonian represented by Kitaev and extended Heisenberg interactions. To overcome the limitation posed by small tractable system sizes in the exact diagonalization study employed in a previous study [Y. Yamaji et al., Phys. Rev. Lett. 113, 107201 (2014), 10.1103/PhysRevLett.113.107201], we apply a two-dimensional density matrix renormalization group and an infinite-size tensor-network method. By calculating at much larger system sizes, we critically test the validity of the exact diagonalization results. The results consistently indicate that the ground state of Na2IrO3 is a magnetically ordered state with zigzag configuration in agreement with experimental observations and the previous diagonalization study. Applications of the two independent methods in addition to the exact diagonalization study further uncover a consistent and rich phase diagram near the zigzag phase beyond the accessibility of the exact diagonalization. For example, in the parameter space away from the ab initio value of Na2IrO3 controlled by the trigonal distortion, we find three phases: (i) an ordered phase with the magnetic moment aligned mutually in 120 degrees orientation on every third hexagon, (ii) a magnetically ordered phase with a 16-site unit cell, and (iii) an ordered phase with presumably incommensurate periodicity of the moment. It suggests that potentially rich magnetic structures may appear in A2IrO3 compounds for A other than Na. The present results also serve to establish the accuracy of the first-principles approach in reproducing the available experimental results thereby further contributing to finding a route to realize the Kitaev spin liquid.
Ab Initio Calculations of Water Line Strengths
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Partridge, Harry
1998-01-01
We report on the determination of a high quality ab initiu potential energy surface (PES) and dipole moment function for water. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base with J less than 6 for H2O. The changes in the PES are small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Using this adjusted PES, we can match 30,092 of the 30,117 transitions in the HITRAN 96 data base for H2O with theoretical lines. The 10,25,50,75, and 90 percentiles of the difference between the calculated and tabulated line positions are -0.11, -0.04, -0.01, 0.02, and 0.07 l/cm. Non-adiabatic effects are not explicitly included. About 3% of the tabulated line positions appear to be incorrect. Similar agreement using this adjusted PES is obtained for the oxygen 17 and oxygen 18 isotopes. For HDO, the agreement is not as good, with root-mean-square error of 0.25 l/cm for lines with J less than 6. This error is reduced to 0.02 l/cm by including a small asymmetric correction to the PES, which is parameterized by simultaneously fitting to HDO md D2O data. Scaling this correction by mass factors yields good results for T2O and HTO. The intensities summed over vibrational bands are usually in good agreement between the calculations and the tabulated results, but individual lines strengths can differ greatly. A high temperature list consisting of 307,721,352 lines is generated for H2O using our PES and dipole moment function.
The Use of Ab Initio Wavefunctions in Line-Shape Calculations for Water Vapor
NASA Astrophysics Data System (ADS)
Gamache, Robert R.; Lamouroux, Julien; Schwenke, David W.
2014-06-01
In semi-classical line-shape calculations, the internal motions of the colliding pair are treated via quantum mechanics and the collision trajectory is determined by classical dynamics. The quantum mechanical component, i.e. the determination of reduced matrix elements (RME) for the colliding pair, requires the wavefunctions of the radiating and the perturbing molecules be known. Here the reduced matrix elements for collisions in the ground vibrational state of water vapor are calculated by two methods and compared. First, wavefunctions determined by diagonalizing an effective (Watson) Hamiltonian are used to calculate the RMEs and, second, the ab initio wavefunctions of Partridge and Schwenke are used. While the ground vibrational state will yield the best approximation of the wavefunctions from the effective Hamiltonian approach, this study clearly identifies problems for states not included in the fit of the Hamiltonian and for extrapolated states. RMEs determined using ab initio wavefunctions use ˜100000 times more computational time; however, all ro-vibrational interactions are included. Hence, the ab initio approach will yield better RMEs as the number of vibrational quanta exchanged in the optical transition increases, resulting in improvements in calculated half-widths and line shifts. It is important to note that even for pure rotational transitions the use of ab initio wavefunctions will yield improved results.
Le, Hung M; Dinh, Thach S; Le, Hieu V
2011-10-13
The singlet-triplet transformation and molecular dissociation of ozone (O(3)) gas is investigated by performing quasi-classical molecular dynamics (MD) simulations on an ab initio potential energy surface (PES) with visible and near-infrared excitations. MP4(SDQ) level of theory with the 6-311g(2d,2p) basis set is executed for three different electronic spin states (singlet, triplet, and quintet). In order to simplify the potential energy function, an approximation is adopted by ignoring the spin-orbit coupling and allowing the molecule to switch favorably and instantaneously to the spin state that is more energetically stable (lowest in energy among the three spin states). This assumption has previously been utilized to study the SiO(2) system as reported by Agrawal et al. (J. Chem. Phys. 2006, 124 (13), 134306). The use of such assumption in this study probably makes the upper limits of computed rate coefficients the true rate coefficients. The global PES for ozone is constructed by fitting 5906 ab initio data points using a 60-neuron two-layer feed-forward neural network. The mean-absolute error and root-mean-squared error of this fit are 0.0446 eV (1.03 kcal/mol) and 0.0756 eV (1.74 kcal/mol), respectively, which reveal very good fitting accuracy. The parameter coefficients of the global PES are reported in this paper. In order to identify the spin state with high confidence, we propose the use of a pattern-recognition neural network, which is trained to predict the spin state of a given configuration (with a prediction accuracy being 95.6% on a set of testing data points). To enhance the prediction effectiveness, a buffer series of five points are validated to confirm the spin state during the MD process to gain better confidence. Quasi-classical MD simulations from 1.2 to 2.4 eV of total internal energy (including zero-point energy) result in rate coefficients of singlet-triplet transformation in the range of 0.027 ps(-1) to 1.21 ps(-1). Also, we find very
Ab Initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
Ab Initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
High Level Ab Initio Kinetics as a Tool for Astrochemistry
NASA Astrophysics Data System (ADS)
Klippenstein, Stephen
2015-05-01
We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.
Separable metamaterials: analytical ab-initio homogenization and chirality
NASA Astrophysics Data System (ADS)
Ciattoni, Alessandro; Rago, Domenico; Rizza, Carlo
2016-11-01
We investigate the ab-initio homogenization of separable metamaterials with factorized dielectric permittivity profiles, which can be achieved through suitable grey-scale permittivity design techniques. Separability allows such metamaterials to be physically regarded as the superposition of three fictitious 1D generating media. We prove that, in the long-wavelength limit, separable metamaterials admit a simple and analytical description of their electromagnetic bi-anisotropic response, which can be reconstructed from the properties of the 1D generating media. Our approach provides a strategy that allows the full ab-initio and flexible design of a complex bianisotropic response by using the simple and well-known properties of 1D metamaterials.
Ab initio calculations of light-ion fusion reactions
Hupin, G.; Quaglioni, S.; Navratil, P.
2012-10-20
The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. Above all nuclear scattering and reactions, which require the solution of the many-body quantum-mechanical problem in the continuum, represent an extraordinary theoretical as well as computational challenge for ab initio approaches. The ab initio No-Core Shell Model/Resonating-Group Method (NCSM/RGM) complements a microscopic cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach is capable of describing simultaneously both bound and scattering states in light nuclei. Recent applications to light nuclei scattering and fusion reactions relevant to energy production in stars and Earth based fusion facilities, such as the deuterium-{sup 3}He fusion, are presented. Progress toward the inclusion of the three nucleon force into the formalism is outlined.
Ab Initio Calculations Of Light-Ion Reactions
Navratil, P; Quaglioni, S; Roth, R; Horiuchi, W
2012-03-12
The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.
Ab initio Monte Carlo investigation of small lithium clusters.
Srinivas, S.
1999-06-16
Structural and thermal properties of small lithium clusters are studied using ab initio-based Monte Carlo simulations. The ab initio scheme uses a Hartree-Fock/density functional treatment of the electronic structure combined with a jump-walking Monte Carlo sampling of nuclear configurations. Structural forms of Li{sub 8} and Li{sub 9}{sup +} clusters are obtained and their thermal properties analyzed in terms of probability distributions of the cluster potential energy, average potential energy and configurational heat capacity all considered as a function of the cluster temperature. Details of the gradual evolution with temperature of the structural forms sampled are examined. Temperatures characterizing the onset of structural changes and isomer coexistence are identified for both clusters.
Spin-orbit decomposition of ab initio nuclear wave functions
NASA Astrophysics Data System (ADS)
Johnson, Calvin W.
2015-03-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.
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).
Study of Nuclear Clustering from an Ab Initio Perspective
NASA Astrophysics Data System (ADS)
Kravvaris, Konstantinos; Volya, Alexander
2017-08-01
We put forward a new ab initio approach that seamlessly bridges the structure, clustering, and reactions aspects of the nuclear quantum many-body problem. The configuration interaction technique combined with the resonating group method based on a harmonic oscillator basis allows us to treat the reaction and multiclustering dynamics in a translationally invariant way and preserve the Pauli principle. Our presentation includes studies of Be,108 and an exploration of 3 α clustering in 12C.
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-Based Predictions of Hydrocarbon Combustion Chemistry
2015-07-15
computed with high-levels electronic structure theory to predict rates of elementary reaction occurring in 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND... reactions , reaction rates, energy transfer REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT NUMBER(S) 10. SPONSOR/MONITOR’S ACRONYM(S) ARO...methods for using ab initio potential energy surfaces (PESs) computed with high-levels electronic structure theory to predict rates of elementary reaction
Thermochemical data for CVD modeling from ab initio calculations
Ho, P.; Melius, C.F.
1993-12-31
Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.
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.
Ab initio calculations for industrial materials engineering: successes and challenges.
Wimmer, Erich; Najafabadi, Reza; Young, George A; Ballard, Jake D; Angeliu, Thomas M; Vollmer, James; Chambers, James J; Niimi, Hiroaki; Shaw, Judy B; Freeman, Clive; Christensen, Mikael; Wolf, Walter; Saxe, Paul
2010-09-29
Computational materials science based on ab initio calculations has become an important partner to experiment. This is demonstrated here for the effect of impurities and alloying elements on the strength of a Zr twist grain boundary, the dissociative adsorption and diffusion of iodine on a zirconium surface, the diffusion of oxygen atoms in a Ni twist grain boundary and in bulk Ni, and the dependence of the work function of a TiN-HfO(2) junction on the replacement of N by O atoms. In all of these cases, computations provide atomic-scale understanding as well as quantitative materials property data of value to industrial research and development. There are two key challenges in applying ab initio calculations, namely a higher accuracy in the electronic energy and the efficient exploration of large parts of the configurational space. While progress in these areas is fueled by advances in computer hardware, innovative theoretical concepts combined with systematic large-scale computations will be needed to realize the full potential of ab initio calculations for industrial applications.
A highly accurate ab initio potential energy surface for methane
NASA Astrophysics Data System (ADS)
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2016-09-01
A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of 12CH4 reproduced with a root-mean-square error of 0.70 cm-1. The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.
Ab initio rotation-vibration spectra of HCN and HNC
NASA Astrophysics Data System (ADS)
Harris, Gregory J.; Polyansky, Oleg L.; Tennyson, Jonathan
2002-03-01
We have calculated an ab initio HCN/HNC linelist for all transitions up to J=25 and 18 000 cm -1 above the zero point energy. This linelist contains more than 200 million lines each with frequencies and transition dipoles. The linelist has been calculated using our semi-global HCN/HNC VQZANO+PES and dipole moment surface, which were reported in van Mourik et al. (J. Chem. Phys. 115 (2001) 3706). With this linelist we synthesise absorption spectra of HCN and HNC at 298 K and we present the band centre and band transition dipoles for the bands which are major features in these spectra. Several of the HCN bands and many of the HNC bands have not been previously studied. Our line intensities reproduce via fully ab initio methods the unusual intensity structure of the HCN CN stretch fundamental (00 01) for the first time and also the forbidden (02 20) HCN bending overtone. We also compare the J=1→0 pure rotational transition dipole in the HCN/HNC ground and vibrationally excited states with experimental and existing ab initio results.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
NASA Astrophysics Data System (ADS)
Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.
2014-08-01
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab initio molecular dynamics using hybrid density functionals.
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; VandeVondele, Joost
2008-06-07
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Ab initio molecular dynamics using hybrid density functionals
NASA Astrophysics Data System (ADS)
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost
2008-06-01
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Diffusion in liquid Germanium using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.
1996-03-01
We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.
Ab Initio Theory of Light-ion Reactions
NASA Astrophysics Data System (ADS)
Navrátil, Petr; Quaglioni, Sofia; Roth, Robert
2011-09-01
The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. Above all nuclear scattering and reactions, which require the solution of the many-body quantum-mechanical problem in the continuum, represent a theoretical and computational challenge for ab initio approaches. After a brief overview of the field, we present a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster technique with the use of realistic interactions and a microscopic and consistent description of the clusters. We show results for neutron and proton scattering on light nuclei, including p-7Be and n-8He. We also highlight the first results of the d-3He and d-3H fusion calculations obtained within this approach.
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Draayer, Jerry P.
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.
Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab initio study of the far infrared spectrum of glycine
NASA Astrophysics Data System (ADS)
Senent, M. L.; Villa, M.; Domínguez-Gómez, R.; Fernández-Clavero, A.
In glycine, four large amplitude vibrations, the three internal rotations of the CC, COH, and CN bonds, and the amine group inversion are responsible for the nonrigidity of the molecule. They present 12 potential energy surface minima corresponding to eight different conformers. The energy levels for the four motions mentioned above and the HNH bending were determined using ab initio calculations and three different flexible models in one, two, and three dimensions. For this purpose, eight different MP4/cc-pVTZ potential energy surfaces, five one-dimensional for each internal coordinate, one two-dimensional potential depending on the amine wagging and bending coordinates, and one three-dimensional potential depending on the three internal rotation coordinates, were calculated. For the most stable conformer, the harmonic frequencies corresponding to the HNH bending, NH2 inversion, and the CC, COH, and CN torsions were calculated at 1677, 955, 65, 657, and 218 cm-1, and the anharmonic fundamental frequencies to be 1454, 803, 78, 522, and 175 cm-1 with the one-dimensional model. The NHN bending and amine wagging fundamentals are determined to be 1688, and 799 with the two-dimensional model. The fundamentals of the CC, COH and CN torsions were calculated to be 86, 546, and 189 cm-1 with the three-dimensional model.
Ab initio calculation of the potential bubble nucleus 34Si
NASA Astrophysics Data System (ADS)
Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.
2017-03-01
Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to
NASA Astrophysics Data System (ADS)
Colombo, Valentina; Cimino, Alessandro; Maspero, Angelo; Tollari, Stefano; Palmisano, Giovanni; Sironi, Angelo
2017-09-01
The synthesis of a novel Cu(II) bifunctional (N,O,O‧) coordination polymer, the Cu(PzHP) compound, has been carried out by coupling Cu(II) salts and the newely synthesized H2(PzHP) organic linker (H2(PzHP) = 1-[4-(1H) -pyrazolyl]-2-methyl-3-hydroxy-4(1H)-pyridinone). Despite to the numerous attempts done for the growth of suitable single crystals and to the synthetic trials carried out to ameliorate the crystallinity of the Cu(PzHP) coordination polymer, its diffraction pattern was always characterized by a discouraging, less-than-ideal, crystallinity. Notwithstanding the extended disorder, leading to a higher than required space group symmetry, we succeeded in the description of its relevant structural features by following an unconventional route to ab-initio structure solution. In this process consideration on the coordination ability of the ligand and on the space group symmetry have been taken into account to 'manually' achieve the initial structural model, highlighting that, in some cases, it is still possible to ascertain by PXRD the crystal structure of a material that shows challenging, broad, PXRD pattern.
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
Ab initio molecular crystal structures, spectra, and phase diagrams.
Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni
2014-09-16
Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling
Ab initio modelling of methane hydrate thermophysical properties.
Jendi, Z M; Servio, P; Rey, A D
2016-04-21
The key thermophysical properties of methane hydrate were determined using ab initio modelling. Using density functional theory, the second-order elastic constants, heat capacity, compressibility, and thermal expansion coefficient were calculated. A wide and relevant range of pressure-temperature conditions were considered, and the structures were assessed for stability using the mean square displacement and radial distribution functions. Methane hydrate was found to be elastically isotropic with a linear dependence of the bulk modulus on pressure. Equally significant, multi-body interactions were found to be important in hydrates, and water-water interactions appear to strongly influence compressibility like in ice Ih. While the heat capacity of hydrate was found to be higher than that of ice, the thermal expansion coefficient was significantly lower, most likely due to the lower rigidity of hydrates. The mean square displacement gave important insight into stability, heat capacity, and elastic moduli, and the radial distribution functions further confirmed stability. The presented results provide a much needed atomistic thermoelastic characterization of methane hydrates and are essential input for the large-scale applications of hydrate detection and production.
Predicting lattice thermal conductivity with help from ab initio methods
NASA Astrophysics Data System (ADS)
Broido, David
2015-03-01
The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. This research was supported primarily by the NSF under Grant CBET-1402949, and by the S3TEC, an Energy Frontier Research Center funded by the US DOE, office of Basic Energy Sciences under Award No. DE-SC0001299.
An Ab Initio Based Potential Energy Surface for Water
NASA Technical Reports Server (NTRS)
Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)
1996-01-01
We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.
An Ab Initio Based Potential Energy Surface for Water
NASA Technical Reports Server (NTRS)
Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)
1996-01-01
We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.
Ab initio solution of macromolecular crystal structures without direct methods.
McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J
2017-04-04
The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.
Ab initio Hadron structure from lattice QCD
J.D. Bratt; R.G. Edwards; M. Engelhardt; G.T. Fleming; Ph. Hägler; B. Musch; J.W. Negele; K. Orginos; A.V. Pochinsky; D.B. Renner; D.G. Richards; W. Schroers
2007-06-01
Early scattering experiments revealed that the proton was not a point particle but a bound state of many quarks and gluons. Deep inelastic scattering (DIS) experiments have accurately determined the probability of struck quarks carrying a fraction of the proton's momentum. The current generation of experiments and Lattice QCD calculations will provide detailed multi-dimensional pictures of the distributions of quarks and gluons inside the proton.
Ab initio characterization of C5
NASA Astrophysics Data System (ADS)
Massó, H.; Veryazov, V.; Malmqvist, P.-A.˚.; Roos, B. O.; Senent, M. L.
2007-10-01
In this paper, the structure and spectroscopic parameters of the C5 cluster are determined using multiconfigurational quantum chemical methods as implemented in the MOLCAS software. A number of spectroscopic properties (band center positions, l-doubling parameters, and rotational constants) have been characterized. From the new results, the assignments of previous astrophysical observations [J. Goicoechea et al., Astrophys. J. 609, 225 (2004)] are discussed. A detailed exploration of the global potential energy surface confirms that C5 has a X 1Σg+ linear isomer of prominent stability and, at least, three minimum energy structures showing singlet electronic ground states. Two of them are cyclic and one has a nonplanar geometry. Vertical and adiabatic electronic transitions and vibrational spectroscopic parameters are determined for the most stable linear isomer using multiconfigurational second order perturbation theory (CASPT2) using an active space containing 12 valence orbitals with 12 active electrons and extended ANO-type basis sets. The infrared spectrum has been analyzed from an anharmonic force field derived form the local surface, determined from the energies of a grid of 1350 geometries. The force field includes four coupling terms. The CASPT2 band center position of the ν7(πu) anharmonic fundamental has been calculated to be at 102 cm-1, which validates the assignment to C5 of the pattern of bands centered at 102 cm-1 observed with the ISO telescope.
Ab initio optical properties of Si(100)
NASA Astrophysics Data System (ADS)
Palummo, Maurizia; Onida, Giovanni; del Sole, Rodolfo; Mendoza, Bernardo S.
1999-07-01
We compute the linear optical properties of different reconstructions of the clean and hydrogenated Si(100) surface within DFT-LDA, using norm-conserving pseudopotentials. The equilibrium atomic geometries of the surfaces, determined from self-consistent total-energy calculations within the Car-Parrinello scheme, strongly influence reflectance anisotropy spectra, showing differences between the p(2×2) and c(4×2) reconstructions. The differential reflectivity spectrum for the c(4×2) reconstruction shows a positive peak at ħω<1 eV, in agreement with experimental results.
Developmental AB Initio Molecular Orbital Theory
NASA Astrophysics Data System (ADS)
Blurock, Edward (Ned) Samuel
The frozen core approximation (FCA) was applied to the main group elements of the first four rows of the periodic table (i.e., through Iodine). For hydride bond lengths, the results of the FCA calculation were consistently closer to experiment. The FCA calculation assumes that the core space is complete and restricts its further optimization. The standard calculation does not have this restriction and further completion of the core space (during the optimization procedure) by valence orbitals on neighboring atoms produced shorter (compared to FCA and experiment) hydride bond lengths. A new set of two-electron integrals was developed combining the use of Rys quadrature and the axis-switch algorithm. The combined algorithm was found to be advantageous only under higher contraction. Also, it was determined that extension of the algorithm to higher angular momentum functions would yield improvement in only selected cases. The SYMGEN program, a symbolic algebra program written by the author, was used to generate and globally optimize the newly developed code. The SYMGEN program is a general program with potential uses in a variety of other coding and global optimization problems.
Ab initio molecular simulations with numeric atom-centered orbitals
NASA Astrophysics Data System (ADS)
Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias
2009-11-01
We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.
Ab initio calculations on the magnetic properties of transition metal complexes
Bodenstein, Tilmann; Fink, Karin
2015-12-31
We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes.
Ab initio Study of He Stability in hcp-Ti
Dai, Yunya; Yang, Li; Peng, SM; Long, XG; Gao, Fei; Zu, Xiaotao T.
2010-12-20
The stability of He in hcp-Ti was studied using ab initio method based on density functional theory. The results indicate that a single He atom prefers to occupy the tetrahedral site rather than the octahedral site. The interaction of He defects with Ti atoms has been used to explain the relative stabilities of He point defects in hcp-Ti. The relative stability of He defects in hcp-Ti is useful for He clustering and bubble nucleation in metal tritides, which provides the basis for development of improved atomistic models.
Ab initio quantum chemical study of electron transfer in carboranes
NASA Astrophysics Data System (ADS)
Pati, Ranjit; Pineda, Andrew C.; Pandey, Ravindra; Karna, Shashi P.
2005-05-01
The electron transfer (ET) properties of 10- and 12-vertex carboranes are investigated by the ab initio Hartree-Fock method within the Marcus-Hush (MH) two-state model and the Koopman theorem (KT) approach. The calculated value of the ET coupling matrix element, VAB, is consistently higher in the KT approach than in the MH two-state model. For the carborane molecules functionalized by -CH 2 groups at C-vertices, VAB strongly depends on the relative orientation of the planes containing the terminal -CH 2 groups. The predicted conformation dependence of VAB offers a molecular mechanism to control ET between two active centers in molecular systems.
Ab-initio study of transition metal hydrides
Sharma, Ramesh; Shukla, Seema Dwivedi, Shalini Sharma, Yamini
2014-04-24
We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.
Morphing ab initio potential energy curve of beryllium monohydride
NASA Astrophysics Data System (ADS)
Špirko, Vladimír
2016-12-01
Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.
Ab initio investigation of supported Au-Mn nanowires
NASA Astrophysics Data System (ADS)
Tsysar, K. M.; Kolesnikov, S. V.; Sitnikov, I. I.; Saletsky, A. M.
2017-05-01
We present an ab initio study of surface supported Au-Mn nanowires. Three different substrates are discussed: Cu(110), stepped Cu(111) and Si(001) surface. The emergence of stable antiferromagnetic (AFM) solutions in Au-Mn nanowires was found in all three cases. We found the nonzero magnetic moments of Mn atoms, however, the bulk of manganese is paramagnetic. The critical temperature of the Au-Mn wires is calculated by means of kinetic Monte Carlo simulation. The strong size-effect of the critical temperature is demonstrated.
Ab initio evidence for nonthermal characteristics in ultrafast laser melting
NASA Astrophysics Data System (ADS)
Lian, Chao; Zhang, S. B.; Meng, Sheng
2016-11-01
Laser melting of semiconductors has been observed for almost 40 years; surprisingly, it is not well understood where most theoretical simulations show a laser-induced thermal process. Ab initio nonadiabatic simulations based on real-time time-dependent density functional theory reveal intrinsic nonthermal melting of silicon, at a temperature far below the thermal melting temperature of 1680 K. Both excitation threshold and time evolution of diffraction intensity agree well with experiment. Nonthermal melting is attributed to excitation-induced drastic changes in bonding electron density, and the subsequent decrease in the melting barrier, rather than lattice heating as previously assumed in the two-temperature models.
Ab initio study of C + H3+ reactions
NASA Technical Reports Server (NTRS)
Talbi, D.; DeFrees, D. J.
1991-01-01
The reaction C + H3+ --> CH(+) + H2 is frequently used in models of dense interstellar cloud chemistry with the assumption that it is fast, i.e. there are no potential energy barriers inhibiting it. Ab initio molecular orbital study of the triplet CH3+ potential energy surface (triplet because the reactant carbon atom is a ground state triplet) supports this hypothesis. The reaction product is 3 pi CH+; the reaction is to exothermic even though the product is not in its electronic ground state. No path has been found on the potential energy surface for C + H3+ --> CH2(+) + H reaction.
Communication: Ab initio Joule-Thomson inversion data for argon
NASA Astrophysics Data System (ADS)
Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter
2013-02-01
The Joule-Thomson coefficient μH(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.
Ab Initio Study of Phase Equilibria in TiCx
NASA Astrophysics Data System (ADS)
Korzhavyi, P. A.; Pourovskii, L. V.; Hugosson, H. W.; Ruban, A. V.; Johansson, B.
2002-01-01
The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx ( x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies ( Ti2C, Ti3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures.
Accelerating ab initio molecular dynamics simulations by linear prediction methods
NASA Astrophysics Data System (ADS)
Herr, Jonathan D.; Steele, Ryan P.
2016-09-01
Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.
Cooperative effects in spherical spasers: Ab initio analytical model
NASA Astrophysics Data System (ADS)
Bordo, V. G.
2017-06-01
A fully analytical semiclassical theory of cooperative optical processes which occur in an ensemble of molecules embedded in a spherical core-shell nanoparticle is developed from first principles. Both the plasmonic Dicke effect and spaser generation are investigated for the designs in which a shell/core contains an arbitrarily large number of active molecules in the vicinity of a metallic core/shell. An essential aspect of the theory is an ab initio account of the feedback from the core/shell boundaries which significantly modifies the molecular dynamics. The theory provides rigorous, albeit simple and physically transparent, criteria for both plasmonic superradiance and surface plasmon generation.
Ab-Initio Shell Model with a Core
Lisetskiy, A F; Barrett, B R; Kruse, M; Navratil, P; Stetcu, I; Vary, J P
2008-06-04
We construct effective 2- and 3-body Hamiltonians for the p-shell by performing 12{h_bar}{Omega} ab initio no-core shell model (NCSM) calculations for A=6 and 7 nuclei and explicitly projecting the many-body Hamiltonians onto the 0{h_bar}{Omega} space. We then separate these effective Hamiltonians into 0-, 1- and 2-body contributions (also 3-body for A=7) and analyze the systematic behavior of these different parts as a function of the mass number A and size of the NCSM basis space. The role of effective 3- and higher-body interactions for A > 6 is investigated and discussed.
Ab-initio study of napthelene based conducting polymer
Ruhela, Ankur; Kanchan, Reena; Srivastava, Anurag; Sinha, O. P.
2014-04-24
In this paper, we have identified structural and electronic properties of conducting polymers by using DFT based ATK-VNL ab-initio tool. Naphthalene derivative structures were stabilized by varying the bond length between two atoms of the molecule C-N and C-C. We have also studied the molecular energy spectrum of naphthalene derivatives and found the HOMOLUMO for the same. A comparison of structural and electronic properties of naphthalene derivatives by attaching the functional group of amine, have been performed and found that they show good semi conducting properties.
Pseudorotation motion in tetrahydrofuran: an ab initio study.
Rayón, Víctor M; Sordo, Jose A
2005-05-22
The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.
Communication: Ab initio Joule-Thomson inversion data for argon.
Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter
2013-02-21
The Joule-Thomson coefficient μ(H)(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.
Ab Initio Calculations Applied to Problems in Metal Ion Chemistry
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)
1994-01-01
Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.
Electric field response in bilayer graphene: Ab initio investigation
NASA Astrophysics Data System (ADS)
Mori, Yutaro; Minamitani, Emi; Ando, Yasunobu; Kasamatsu, Shusuke; Watanabe, Satoshi
2016-11-01
Stimulated by quantum capacitance measurements, we have investigated the electric properties of bilayer graphene (BLG) with carrier doping under an external electric field using ab initio calculations. We found that the relative permittivity of BLG depends weakly on the applied electric field, and that the BLG can be regarded as a dielectric material rather than a pair of metallic films. We also found that carrier doping affects the band gap of BLG under electric fields, although carrier doping has a much smaller effect on the band gap and density of states than the application of electric fields.
Ab Initio Calculations Applied to Problems in Metal Ion Chemistry
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)
1994-01-01
Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.
Recarte, V; Zbiri, M; Jiménez-Ruiz, M; Sánchez-Alarcos, V; Pérez-Landazábal, J I
2016-05-25
The different contributions to the entropy change linked to the austenite-martensitic transition in a Ni-Mn-Sn metamagnetic shape memory alloy have been determined by combining different experimental techniques. The vibrational contribution has been inferred from the vibrational density of states of both the martensitic and austenite phases. This has been accomplished by combining time-of-flight neutron scattering measurements and ab initio calculations. Further, the electronic part of the entropy change has also been calculated. Since the martensitic transformation takes place between two paramagnetic phases, the magnetic contribution can be neglected and the entropy change can be reduced to the sum of two terms: vibrational and electronic. The obtained value of the vibrational contribution ([Formula: see text]) nearly provides the total entropy change measured by calorimetry ([Formula: see text]), the difference being the electronic contribution within the experimental error.
Ab initio molecular dynamics study of liquid sodium and cesium up to critical point
Yuryev, Anatoly A.; Gelchinski, Boris R.
2015-08-17
Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.
Ab initio molecular dynamics study of liquid sodium and cesium up to critical point
NASA Astrophysics Data System (ADS)
Yuryev, Anatoly A.; Gelchinski, Boris R.
2015-08-01
Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.
Ab initio calculations of reactions of light nuclei
NASA Astrophysics Data System (ADS)
Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr
2017-09-01
An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable as a support tool for accurate evaluations of crucial reaction data for nuclear astrophysics, fusion-energy research, and other applications. We present an efficient many-body approach to nuclear bound and scattering states alike, known as the ab initio no-core shell model with continuum. In this approach, square-integrable energy eigenstates of the A-nucleon system are coupled to (A-A)+A target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges. We show that predictive results for nucleon and deuterium scattering on 4He nuclei can be obtained from the direct solution of the Schröedinger equation with modern nuclear potentials.
Unified ab initio approaches to nuclear structure and reactions
Navratil, Petr; Quaglioni, Sofia; Hupin, Guillaume; ...
2016-04-13
The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Bemore » $${({\\rm{p}},\\gamma )}^{8}{\\rm{B}}$$ radiative capture. Lastly, we highlight our efforts to describe transfer reactions including the 3H$${({\\rm{d}},{\\rm{n}})}^{4}$$He fusion.« less
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-01-01
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906
Three-cluster dynamics within an ab initio framework
Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr
2013-09-26
In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to amore » 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core (4He) polarization effects.« less
Ab initio study of hot electrons in GaAs.
Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B; Louie, Steven G
2015-04-28
Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron-phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron-phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron-phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials.
Emission Spectroscopy and Ab Initio Calculations for TaN
NASA Astrophysics Data System (ADS)
Ram, R. S.; Liévin, J.; Bernath, P. F.
2002-10-01
The emission spectra of TaN have been investigated in the region 3000-35 000 cm -1 using a Fourier transform spectrometer. The spectra were observed in a tantalum hollow-cathode lamp by discharging a mixture of 1.5 Torr of Ne and about 6 mTorr of N 2. In addition to previously known bands, numerous additional bands were observed and assigned to a number of new transitions. The spectroscopic properties of the low-lying electronic states of TaN were also predicted by ab initio calculations. A 1Σ + state, with equilibrium constants of Be=0.457 852 1(48) cm -1, α e=0.002 235 9(67) cm -1, and Re=1.683 099 9(88) Å, has been identified as the ground state of TaN based on our experimental observations supported by the ab initio results. The first excited state has been identified as the a3Δ 1 spin component at 2827 cm -1 above the ground state. To higher energies, the states become difficult to assign because of their Hund's case (c) behavior and extensive interactions between the spin components of the electronic terms.
Implementation of renormalized excitonic method at ab initio level.
Zhang, Hongjiang; Malrieu, Jean-Paul; Ma, Haibo; Ma, Jing
2012-01-05
The renormalized excitonic method [Hajj et al., Phys Rev B 2005, 72, 224412], in which the excited state of the whole system may be described as a linear combination of local excitations, has been implemented at ab initio level. Its performance is tested on the ionization potential and the energy gap between singlet ground state and lowest triplet for linear molecular hydrogen chains and more realistic systems, such as polyenes and polysilenes, using full configuration interaction (FCI) wave functions with a minimal basis set. The influence of different block sizes and the extent of interblock interactions are investigated. It has been demonstrated that satisfactory results can be obtained if the near degeneracies between the model space and the outer space are avoided and if interactions between the next-nearest neighbor blocks are considered. The method can be used with larger basis sets and other accurate enough ab initio evaluations (instead of FCI) of local excited states, from blocks, or from dimers or trimers of blocks. It provides a new possibility to accurately and economically describe the low-lying delocalized excited states of large systems, even inhomogeneous ones.
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
NASA Astrophysics Data System (ADS)
Elenewski, Justin E.; Hackett, John C.
2015-02-01
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-02-14
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
An ab initio calculation of the fundamental and overtone HCl stretching vibrations for the HCl dimer
NASA Astrophysics Data System (ADS)
Jensen, Per; Bunker, P. R.; Epa, V. C.; Karpfen, A.
1992-02-01
We have previously determined an analytical ab initio six-dimensional potential energy surface for the HCl dimer, and have used it to determine the minimum energy path for the trans-tunneling motion. In the present paper we refine this path by fitting to data. We calculate a further 178 ab initio points in order to determine the HCl stretching energies, and HCl stretching dipole moment functions, at eight positions along the minimum energy path. We use these ab initio results to compute the stretching wavenumbers and transition moments from the v1 = v2 = 0 state to all states of (HCl) 2 that have v1 + v2 ≤ 3, where v1 and v2 are the local mode quantum numbers for the HCl stretching vibrations. In doing this calculation we have assumed an adiabatic separation of the HCl stretching motion from the other vibrational motions in the dimer, and have used the semirigid bender Hamiltonian to average over the trans-tunneling motion. We obtain the fundamental "free-H" stretch v1 at 2877 cm -1 and the fundamental "bound-H" stretch v2 at 2861 cm -1; the experimental values are 2880 and 2854 cm -1, respectively.
Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon
2013-01-01
The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%. PMID:23445785
Pospíšil, Miroslav; Kovář, Petr; Vácha, Robert; Svoboda, Michal
2012-01-01
Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreement with ab initio calculations obtained in the Gaussian03 program. Dihedral torsions of active groups of betulin were determined for both procedures, and related calculated structures were compared successfully. The selected force field was used for subsequent optimization of betulin in a water environment, and a conformational search was performed using quench molecular dynamics. The total energies of betulin and its interactions in water bulk were calculated, and the influence of water on betulin structure was investigated.
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.
Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna
2016-01-01
Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.
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.
Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations
NASA Technical Reports Server (NTRS)
Good, Brian S.
2003-01-01
We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.
NASA Astrophysics Data System (ADS)
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Thermal neutron scattering law calculations using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Wormald, Jonathan; Hawari, Ayman I.
2017-09-01
In recent years, methods for the calculation of the thermal scattering law (i.e. S(α,β), where α and β are dimensionless momentum and energy transfer variables, respectively) were developed based on ab initio lattice dynamics (AILD) and/or classical molecular dynamics (CMD). While these methods are now mature and efficient, further advancement in the application of such atomistic techniques is possible using ab initio molecular dynamics (AIMD) methods. In this case, temperature effects are inherently included in the calculation, e.g. phonon density of states (DOS), while using ab initio force fields that eliminate the need for parameterized semi-empirical force fields. In this work, AIMD simulations were performed to predict the phonon spectra as a function of temperature for beryllium and graphite, which are representative nuclear reactor moderator and reflector materials. Subsequently, the calculated phonon spectra were utilized to predict S(α,β) using the LEAPR module of the NJOY code. The AIMD models of beryllium and graphite were 5 × 5 × 5 crystal unit cells (250 atoms and 500 atoms respectively). Electronic structure calculations for the prediction of Hellman-Feynman forces were performed using density functional theory with a GGA exchange correlation functional and corresponding core electron pseudopotentials. AIMD simulations of 1000-10,000 time-steps were performed with the canonical ensemble (NVT thermostat) for several temperatures between 300 K and 900 K. The phonon DOS were calculated as the power spectrum of the AIMD predicted velocity autocorrelation functions. The resulting AIMD phonon DOS and corresponding inelastic thermal neutron scattering cross sections at 300 K, where anharmonic effects are expected to be small, were found to be in reasonable agreement with the results generated using traditional AILD. This illustrated the validity of the AIMD approach. However, since the impact of the temperature on the phonon DOS (e.g. broadening of
First fully ab initio potential energy surface of methane with a spectroscopic accuracy
NASA Astrophysics Data System (ADS)
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2016-09-01
Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.
NASA Astrophysics Data System (ADS)
Yurchenko, Sergei N.; Carvajal, Miguel; Thiel, Walter; Jensen, Per
2006-09-01
We report a six-dimensional CCSD(T)/aug-cc-pVTZ dipole moment surface for the electronic ground state of PH 3 computed ab initio on a large grid of 10 080 molecular geometries. Parameterized, analytical functions are fitted through the ab initio data, and the resulting dipole moment functions are used, together with a potential energy function determined by refining an existing ab initio surface in fittings to experimental wavenumber data, for simulating absorption spectra of the first three polyads of PH 3, i.e., ( ν2, ν4), ( ν1, ν3, 2 ν2, 2 ν4, ν2 + ν4), and ( ν1 + ν2, ν3 + ν2, ν1 + ν4, ν3 + ν4, 2 ν2 + ν4, ν2 + 2 ν4, 3 ν2, 3 ν4). The resulting theoretical transition moments show excellent agreement with experiment. A line-by-line comparison of the simulated intensities of the ν2/ ν4 band system with 955 experimental intensity values reported by Brown et al. [L.R. Brown, R.L. Sams, I. Kleiner, C. Cottaz, L. Sagui, J. Mol. Spectrosc. 215 (2002) 178-203] gives an average absolute percentage deviation of 8.7% (and a root-mean-square deviation of 0.94 cm -1 for the transition wavenumbers). This is very remarkable since the calculations rely entirely on ab initio dipole moment surfaces and do not involve any adjustment of these surfaces to reproduce the experimental intensities. Finally, we predict the line strengths for transitions between so-called cluster levels (near-degenerate levels formed at high rotational excitation) for J up to 60.
Sibambo, Sibongile R; Pillay, Viness; Choonara, Yahya E; Khan, Riaz A; Sweet, Joe L
2007-09-01
This study elucidated the in vitro physicomechanical transitions of a crosslinked polylactic-co-glycolic acid (PLGA) scaffold, utilizing quantum mechanics to compute the ab initio energy requirements of a salted-out and subsequently crosslinked PLGA scaffold interacting with simulated physiological fluid, phosphate buffered saline (PBS) (pH 7.4, 37 degrees C) at a molecular level. Twenty-six salted-out PLGA scaffolds were formulated using a four factor, two centerpoint quadratic Face-Centered Central Composite Design (FCCD). PLGA molecular mass, PLGA concentration, water volume and salting-out reaction time were the dependant formulation variables. Subsequent to PLGA solubilization in dimethyl formamide (DMF), protonated water was added to induce salting-out of PLGA into a scaffolds that were immersed in PBS, oscillated at 100 rpm, and analyzed at pre-determined time intervals for their physicomechanical and ab initio quantum energy transitions. Results indicated that the matrix resilience (MR) decreased with longer incubation periods (MR=35-45%) at day 30. Scaffolds salted-out using higher PLGA concentrations exhibited minimal changes in MR and the matrix ability to absorb energy was found to closely correlate with the scaffold residence time in PBS. Spartan-based ab initio quantum energy predictions elucidated the potential scaffold stability from a molecular viewpoint and its suitability for use in rate-modulated drug delivery.
Ab Initio Prediction of Adsorption Isotherms for Small Molecules in Metal-Organic Frameworks.
Kundu, Arpan; Piccini, GiovanniMaria; Sillar, Kaido; Sauer, Joachim
2016-10-17
For CO and N2 on Mg(2+) sites of the metal-organic framework CPO-27-Mg (Mg-MOF-74), ab initio calculations of Gibbs free energies of adsorption have been performed. Combined with the Bragg-Williams/Langmuir model and taking into account the experimental site availability (76.5%), we obtained adsorption isotherms in close agreement with those in experiment. The remaining deviations in the Gibbs free energy (about 1 kJ/mol) are significantly smaller than the "chemical accuracy" limit of about 4 kJ/mol. The presented approach uses (i) a DFT dispersion method (PBE+D2) to optimize the structure and to calculate anharmonic frequencies for vibrational partition functions and (ii) a "hybrid MP2:(PBE+D2)+ΔCCSD(T)" method to determine electronic energies. With the achieved accuracy (estimated uncertainty ±1.4 kJ/mol), the ab initio energies become useful benchmarks for assessing different DFT + dispersion methods (PBE+D2, B3LYP+D*, and vdW-D2), whereas the ab initio heats, entropies, and Gibbs free energies of adsorption are used to assess the reliability of experimental values derived from fitting isotherms or from variable-temperature IR studies.
Dominant Modes in Light Nuclei - Ab Initio View of Emergent Symmetries
NASA Astrophysics Data System (ADS)
Draayer, J. P.; Dytrych, T.; Launey, K. D.; Dreyfuss, A. C.; Langr, D.
2015-01-01
An innovative symmetry-guided concept is discussed with a focus on emergent symmetry patterns in complex nuclei. In particular, the ab initio symmetry-adapted no-core shell model (SA-NCSM), which capitalizes on exact as well as partial symmetries that underpin the structure of nuclei, provides remarkable insight into how simple symmetry patterns emerge in the many-body nuclear dynamics from first principles. This ab initio view is complemented by a fully microscopic no-core symplectic shell-model framework (NCSpM), which, in turn, informs key features of the primary physics responsible for the emergent phenomena of large deformation and alpha-cluster substructures in studies of the challenging Hoyle state in Carbon-12 and enhanced collectivity in intermediate-mass nuclei. Furthermore, by recognizing that deformed configurations often dominate the low-energy regime, the SA-NCSM provides a strategy for determining the nature of bound states of nuclei in terms of a relatively small subspace of the symmetry-reorganized complete model space, which opens new domains of nuclei for ab initio investigations, namely, the intermediate-mass region, including isotopes of Ne, Mg, and Si.
Ab Initio Finite-Temperature Electronic Absorption Spectrum of Formamide.
Besley, Nicholas A; Doltsinis, Nikos L
2006-11-01
A combination of Car-Parrinello molecular dynamics (CP-MD) and high-level ab initio quantum chemical calculations has been used to calculate the electronic absorption spectrum of formamide at finite temperatures. Thermally broadened spectra have been obtained by averaging over a large number of single-point multireference configuration interaction excitation energies calculated for geometries sampled from a CP-MD simulation. Electronic excitation spectra of possible contaminants ammonia and formamidic acid have also been computed. Ammonia exhibits a strong peak in the shoulder region of the experimental formamide spectrum at 6.5 eV, and formamidic acid has a strong absorption above 7.5 eV. The calculations reproduce the shape of the experimental absorption spectrum, in particular, the low-energy shoulder of the main peak, and demonstrate how finite-temperature electronic absorption spectra can be computed from first principles.
Simple calculation of ab initio melting curves: Application to aluminum
NASA Astrophysics Data System (ADS)
Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean
2015-03-01
We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003), 10.1063/1.1624057] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013), 10.1103/PhysRevE.88.062145]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost.
Ab initio correlated calculations of rare-gas dimer quadrupoles
NASA Astrophysics Data System (ADS)
Donchev, Alexander G.
2007-10-01
This paper reports ab initio calculations of rare gas ( RG=Kr , Ar, Ne, and He) dimer quadrupoles at the second order of Møller-Plesset perturbation theory (MP2). The study reveals the crucial role of the dispersion contribution to the RG2 quadrupole in the neighborhood of the equilibrium dimer separation. The magnitude of the dispersion quadrupole is found to be much larger than that predicted by the approximate model of Hunt. As a result, the total MP2 quadrupole moment is significantly smaller than was assumed in virtually all previous related studies. An analytical model for the distance dependence of the RG2 quadrupole is proposed. The model is based on the effective-electron approach of Jansen, but replaces the original Gaussian approximation to the electron density in an RG atom by an exponential one. The role of the nonadditive contribution in RG3 quadrupoles is discussed.
Ab initio study of helium behavior in titanium tritides
Liang, J. H.; Dai, Yunya; Yang, Li; Peng, SM; Fan, K. M.; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei
2013-03-01
Ab initio calculations based on density functional theory have been performed to investigate the relative stability of titanium tritides and the helium behavior in stable titanium tritides. The results show that the β-phase TiT1.5 without two tritium along the [100] direction (TiT1.5[100]) is more stable than other possible structures. The stability of titanium tritides decrease with the increased generation of helium in TiT1.5[100]. In addition, helium generated by tritium decay prefers locating at a tetrahedral site, and favorably migrates between two neighbor vacant tetrahedral sites through an intermediate octahedral site in titanium tritides, with a migration energy of 0.23 eV. Furthermore, helium is easily accumulated on a (100) plane in β-phase TiT1.5[100].
An ab initio study on anionic aerogen bonds
NASA Astrophysics Data System (ADS)
Esrafili, Mehdi D.; Mohammadian-Sabet, Fariba
2017-01-01
An ab initio study is carried out to investigate the anionic aerogen bonds in complexes of KrO3, XeO3 and XeOF2 with F-, Cl-, Br-, CN-, NC-, N3-, SH-, SCN-, NCS-, OH- and OCH3- anions. All of the anionic aerogen bonds analyzed here have a partial covalent character. Charge transfer from the anion to the Kr-O or Xe-O σ∗ orbital stabilizes these complexes and leads to a sizable redshift in the corresponding stretching frequencies. The J(Kr-O) or J(Xe-O) spin-spin coupling constants can be regarded as a useful tool for the characterization of strength of the anionic aerogen-bonded complexes.
Ab initio dynamical exchange interactions in frustrated antiferromagnets
NASA Astrophysics Data System (ADS)
Simoni, Jacopo; Stamenova, Maria; Sanvito, Stefano
2017-08-01
The ultrafast response to an optical pulse excitation of the spin-spin exchange interaction in transition metal antiferromagnets is studied within the framework of the time-dependent spin-density functional theory. We propose a formulation for the full dynamical exchange interaction, which is nonlocal in space, and it is derived starting from ab initio arguments. Then, we investigate the effect of the laser pulse on the onset of the dynamical process. It is found that we can distinguish two types of excitations, both activated immediately after the action of the laser pulse. While the first one can be associated to a Stoner-like excitation and involves the transfer of spin from one site to another, the second one is related to the ultrafast modification of a Heisenberg-like exchange interaction and can trigger the formation of spin waves in the first few hundred femtoseconds of the time evolution.
Ab initio quantum transport in atomic carbon chains
NASA Astrophysics Data System (ADS)
Botello-Méndez, Andrés R.; Charlier, Jean-Christophe; Banhart, Florian; NAPS Team; Carbyne Collaboration
2015-03-01
Carbyne, the sp-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. Recently, detailed electrical measurements and first-principles electronic transport calculations have been performed on monoatomic carbon chains. When the 1D system is under strain, the current-voltage curves exhibit a semiconducting behavior, which corresponds to the polyyne structure of the atomic chain with alternating single and triple bonds. Conversely, when the chain is unstrained, the ohmic behavior is observed in agreement with the metallic cumulene structure with double bonds, confirming recent theoretical predictions, namely that a metal-insulator transition can be induced by adjusting the strain. The key role of the contacting leads is also scrutinized by ab initio quantum conductance calculations, explaining the rectifying behavior measured in monoatomic carbon chains in a non-symmetric contact configuration.
Ab initio modeling of TiO2 nanotubes
NASA Astrophysics Data System (ADS)
Szieberth, Dénes; Ferrari, Anna Maria; Noel, Yves; Ferrabone, Matteo
2010-01-01
TiO2 nanotubes constructed from a lepidocrocite-like TiO2 layer were investigated with ab initio methods employing the periodic CRYSTAL code. The dependence of strain energies, structural and electronic properties on the tube diameter was investigated in the 18-57 Å range. Nanotubes constructed by a (0,n) rollup proved to be the most stable at all diameters. All three types of rollup undergo significant reconstruction at diameters <25 Å. All investigated structures possess a high (~5.4 eV) band gap compared to bulk TiO2 phases (3.96 and 4.63 eV for rutile and anatase calculated with the same functional and basis set).
Quantum plasmonics: from jellium models to ab initio calculations
NASA Astrophysics Data System (ADS)
Varas, Alejandro; García-González, Pablo; Feist, Johannes; García-Vidal, F. J.; Rubio, Angel
2016-08-01
Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT) calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.
Reactive Monte Carlo sampling with an ab initio potential
Leiding, Jeff; Coe, Joshua D.
2016-05-04
Here, we present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We also discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH3 to those of ab initio molecular dynamics (AIMD). Furthermore, we find that there are regions of state space formore » which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.« less
Efficient Ab initio Modeling of Random Multicomponent Alloys
Jiang, Chao; Uberuaga, Blas P.
2016-03-08
Here, we present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multi-component alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we also demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high entropy alloy chemistries. Furthermore, the SSOS methodmore » developed here can be broadly useful for the rapid computational design of multi-component materials, especially those with a large number of alloying elements, a challenging problem for other approaches.« less
Interatomic Coulombic decay widths of helium trimer: Ab initio calculations
Kolorenč, Přemysl; Sisourat, Nicolas
2015-12-14
We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.
Ab initio electron propagator theory of molecular wires. I. Formalism.
Dahnovsky, Yu; Zakrzewski, V G; Kletsov, A; Ortiz, J V
2005-11-08
Ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical approach is developed for the calculation of the retarded and advanced Green functions in terms of the electron propagator matrix for the bridge molecule. The calculation of the current requires integration in a complex half plane for a trace that involves terminal and Green's-function matrices. Because the Green's-function matrices have complex poles represented by matrices, a special scheme is developed to express these "matrix poles" in terms of ordinary poles. An expression for the current is derived for a terminal matrix of arbitrary rank. For a single terminal orbital, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator. It is shown that Dyson orbitals with high pole strengths and overlaps with terminal orbitals are most responsible for the conduction of electrical current.
Molybdenum-titanium phase diagram evaluated from ab initio calculations
NASA Astrophysics Data System (ADS)
Barzilai, Shmuel; Toher, Cormac; Curtarolo, Stefano; Levy, Ohad
2017-07-01
The design of next generation β -type titanium implants requires detailed knowledge of the relevant stable and metastable phases at temperatures where metallurgical heat treatments can be performed. Recently, a standard specification for surgical implant applications was established for Mo-Ti alloys. However, the thermodynamic properties of this binary system are not well known and two conflicting descriptions of the β -phase stability have been presented in the literature. In this study, we use ab initio calculations to investigate the Mo-Ti phase diagram. These calculations predict that the β phase is stable over a wide concentration range, in qualitative agreement with one of the reported phase diagrams. In addition, they predict stoichiometric compounds, stable at temperatures below 300 ∘C , which have not yet been detected by experiments. The resulting solvus, which defines the transition to the β -phase solid solution, therefore occurs at lower temperatures and is more complex than previously anticipated.
Ab Initio Study of KCl and NaCl Clusters
NASA Astrophysics Data System (ADS)
Brownrigg, Clifton; Hira, Ajit; Pacheco, Jose; Salazar, Justin
2013-03-01
We continue our interest in the theoretical study of molecular clusters to examine the chemical properties of small KnCln and NanCln clusters (n = 2 - 15). The potentially important role of these molecular species in biochemical and medicinal processes is well known. This work applies the hybrid ab initio methods of quantum chemistry to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations have been performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. The potential for design of new medicinal drugs is explored.
Ab initio electronic and lattice dynamical properties of cerium dihydride
NASA Astrophysics Data System (ADS)
Gurel, Tanju; Eryigit, Resul
2007-03-01
The rare-earth metal hydrides are interesting systems because of the dramatic structural and electronic changes due to the hydrogen absorption and desorption. Among them, cerium dihydride (CeH2) is one of the less studied rare-earth metal-hydride. To have a better understanding, we have performed an ab initio study of electronic and lattice dynamical properties of CeH2 by using pseudopotential density functional theory within local density approximation (LDA) and a plane-wave basis. Electronic band structure of CeH2 have been obtained within LDA and as well as GW approximation. Lattice dynamical properties are calculated using density functional perturbation theory. The phonon spectrum is found to contain a set of high-frequency (˜ 850-1000 cm-1) optical bands, mostly hydrogen related, and low frequency cerium related acoustic modes climbing to 160 cm^ -1 at the zone boundary.
Efficient Ab initio Modeling of Random Multicomponent Alloys.
Jiang, Chao; Uberuaga, Blas P
2016-03-11
We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches.
Ab initio engineering of materials with stacked hexagonal tin frameworks
Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.
2016-01-01
The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140
Ab initio simulation of permanent densification in silica glass
NASA Astrophysics Data System (ADS)
Ryuo, Emina; Wakabayashi, Daisuke; Koura, Akihide; Shimojo, Fuyuki
2017-08-01
To clarify the microscopic structure of densified Si O2 glass, we have conducted ab initio molecular-dynamics simulations on the decompression process of Si O2 glass in its relaxed state from high pressures up to 40 GPa. When decompressed from high pressures above at least 15 GPa, the density and structure always converge to those of densified glass, while the coordination number of silicon decreases to four rapidly. This is in good agreement with previous experimental studies and strongly suggests that densified glass behaves as a high-pressure polymorph of Si O2 glass. In comparison to ordinary glass, although the coordination number of densified glass is almost the same, the size of an intermediate-range network consisting of Si O4 tetrahedra is smaller. Detailed analyses clarify that Si O4 tetrahedra in densified glass are deformed and the Si-O bonds are less covalent.
Ab Initio energetics of SiO bond cleavage.
Hühn, Carolin; Erlebach, Andreas; Mey, Dorothea; Wondraczek, Lothar; Sierka, Marek
2017-10-15
A multilevel approach that combines high-level ab initio quantum chemical methods applied to a molecular model of a single, strain-free SiOSi bridge has been used to derive accurate energetics for SiO bond cleavage. The calculated SiO bond dissociation energy and the activation energy for water-assisted SiO bond cleavage of 624 and 163 kJ mol(-1) , respectively, are in excellent agreement with values derived recently from experimental data. In addition, the activation energy for H2 O-assisted SiO bond cleavage is found virtually independent of the amount of water molecules in the vicinity of the reaction site. The estimated reaction energy for this process including zero-point vibrational contribution is in the range of -5 to 19 kJ mol(-1) . © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Ab initio simulations of liquid carbon monoxide at high pressure
NASA Astrophysics Data System (ADS)
Leonhardi, Tanis C.; Militzer, Burkhard
2017-03-01
Carbon monoxide occurs as a volatile species in the interiors of terrestrial planets, and as a disequilibrium atmospheric constituent in the giant planets. It plays an important role during the accretionary stages of planet formation reacting with gases to form compounds such as CH4 and H2O. The structure of carbon monoxide is unknown over the majority of the temperature and pressure regime in giant planet interiors. Here we perform ab initio molecular dynamics simulations to characterize CO to 140 GPa and 5,000 K. We find that CO is stable as a molecular liquid at lower P-T conditions, as a polymeric liquid at higher P-T conditions found in ice giant interiors, and as a plasma at high-T.
Ab initio study of the electronic transport properties of silicates.
NASA Astrophysics Data System (ADS)
Soubiran, F.; Militzer, B.
2016-12-01
The Kepler spacecraft led to the discovery of numerous Super-Earths planets. Little is known about them, as there is no equivalent in the Solar System. It is uncertain whether they have a convective mantle like the Earth. It is also unclear if their mantle is insulating or conducting. In the latter case, for instance, the mantle could generate a magnetic field via dynamo processes. In order to better understand the properties of the silicates under pressure-temperature conditions relevant for the interiors of Super-Earth, we performed ab initio simulations based on density functional theory. We specifically explored the electronic transport properties, conductivity and reflectivity, to characterize their behavior in their different phases. We find that liquid and solid silicates behave differently and discuss consequences for the planetary interiors.
Amplitudes and overlaps in ab initio calculations of light nuclei
NASA Astrophysics Data System (ADS)
Nollett, Kenneth
2016-09-01
Some clustering properties of nuclei are usefully interpreted in terms of overlap functions. These functions are projections of an A-body nucleus onto an (A - 1) -body core and an additional nucleon, or an (A - 4) -body core and an additional alpha particle, at varying separation. Long-range limits of overlaps are given by asymptotic normalization constants (ANCs), which suffice to model some reaction processes; their shorter-range parts are also needed to interpret some types of experiments. Naively, one computes overlaps from wave functions using their definition. However, there is an integral relation that allows more accurate calculations from approximate wave functions, using exact terms from the nucleon-nucleon potential. I will describe calculations by this method of overlap functions and ANCs for both nucleon and alpha emission from ab initio variational Monte Carlo wave functions. I will also describe the use of overlaps to probe small components of wave functions like those arising from hadronic parity violation.
Ab initio electronic stopping power of protons in bulk materials
NASA Astrophysics Data System (ADS)
Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia
2016-01-01
The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.
The ab-initio density matrix renormalization group in practice
Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic; Nakatani, Naoki
2015-01-21
The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.
Advances in ab initio theories for nuclear reactions
NASA Astrophysics Data System (ADS)
Quaglioni, Sofia
2016-09-01
Driven by high-performance computing and new ideas, in recent years ab initio theory has made great strides in achieving a unified description of nuclear structure, clustering and reactions from the constituent nucleons and their strong and electroweak interactions. This is giving access to forefront tools and new fertile grounds to further our understanding of the nuclear force and electroweak currents in nuclei in terms of effective degrees of freedom. A fundamental understanding of nuclear reaction mechanisms and a new capability to accurately compute their properties is also relevant for nuclear astrophysics, terrestrial applications of nuclear fusion, and for using nuclei as probes of fundamental physics through, for example, neutrino-nucleus scattering. In this talk, I will present recent highlights and reflect on future perspectives for this area of nuclear theory. Prepared by LLNL under Contract No. DE-AC52-07NA27344.
Vibrational and ab initio molecular dynamics studies of bradykinin
NASA Astrophysics Data System (ADS)
Święch, Dominika; Kubisiak, Piotr; Andrzejak, Marcin; Borowski, Piotr; Proniewicz, Edyta
2016-07-01
In this study, the comprehensive theoretical and experimental investigations of Raman (RS) and infrared absorption (IR) spectra of bradykinin (BK) are presented. The ab initio Born-Oppenheimer molecular dynamics (BOMD) calculations, in the presence of water molecules that form the first coordination sphere, were used for conformational analysis of the BK structure. Based on the Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d) level the vibrational spectra were interpreted. The calculated frequencies were scaled by means of the effective scaling frequency factor (ESFF) method. The theoretical data, which confirm the compact structure of BK in the presence of the water molecules revealed the remarkable effect of the intermolecular hydrogen bonding on the BK structural properties.
Isofulminic acid, HONC: Ab initio theory and microwave spectroscopy.
Mladenović, Mirjana; Lewerenz, Marius; McCarthy, Michael C; Thaddeus, Patrick
2009-11-07
Isofulminic acid, HONC, the most energetic stable isomer of isocyanic acid HNCO, higher in energy by 84 kcal/mol, has been detected spectroscopically by rotational spectroscopy supported by coupled cluster electronic structure calculations. The fundamental rotational transitions of the normal, carbon-13, oxygen-18, and deuterium isotopic species have been detected in the centimeter band in a molecular beam by Fourier transform microwave spectroscopy, and rotational constants and nitrogen and deuterium quadrupole coupling constants have been derived. The measured constants agree well with those predicted by ab initio calculations. A number of other electronic and spectroscopic parameters of isofulminic acid, including the dipole moment, vibrational frequencies, infrared intensities, and centrifugal distortion constants have been calculated at a high level of theory. Isofulminic acid is a good candidate for astronomical detection with radio telescopes because it is highly polar and its more stable isomers (HNCO, HOCN, and HCNO) have all been identified in space.
Ab initio calculations of nuclear widths via an integral relation
NASA Astrophysics Data System (ADS)
Nollett, Kenneth M.
2012-10-01
I describe the computation of energy widths of nuclear states using an integral over the interaction region of ab initio variational Monte Carlo wave functions, and I present calculated widths for many states. I begin by presenting relations that connect certain short-range integrals to widths. I then present predicted widths for 5⩽A⩽9 nuclei, and I compare them against measured widths. They match the data more closely and with less ambiguity than estimates based on spectroscopic factors. I consider the consequences of my results for identification of observed states in 8B, 9He, and 9Li. I also examine failures of the method and conclude that they generally involve broad states and variational wave functions that are not strongly peaked in the interaction region. After examining bound-state overlap functions computed from a similar integral relation, I conclude that overlap calculations can diagnose cases in which computed widths should not be trusted.
Approximate ab initio calculations of electronic structure of amorphous silicon
NASA Astrophysics Data System (ADS)
Durandurdu, M.; Drabold, D. A.; Mousseau, N.
2000-12-01
We report on ab initio calculations of electronic states of two large and realistic models of amorphous silicon generated using a modified version of the Wooten-Winer-Weaire algorithm and relaxed, in both cases, with a Keating and a modified Stillinger-Weber potentials. The models have no coordination defects and a very narrow bond-angle distribution. We compute the electronic density-of-states and pay particular attention to the nature of the band-tail states around the electronic gap. All models show a large and perfectly clean optical gap and realistic Urbach tails. Based on these results and the extended quasi-one-dimensional stringlike structures observed for certain eigenvalues in the band tails, we postulate that the generation of model a-Si without localized states might be achievable under certain circumstances.
Ab initio water pair potential with flexible monomers.
Jankowski, Piotr; Murdachaew, Garold; Bukowski, Robert; Akin-Ojo, Omololu; Leforestier, Claude; Szalewicz, Krzysztof
2015-03-26
A potential energy surface for the water dimer with explicit dependence on monomer coordinates is presented. The surface was fitted to a set of previously published interaction energies computed on a grid of over a quarter million points in the 12-dimensional configurational space using symmetry-adapted perturbation theory and coupled-cluster methods. The present fit removes small errors in published fits, and its accuracy is critically evaluated. The minimum and saddle-point structures of the potential surface were found to be very close to predictions from direct ab initio optimizations. The computed second virial coefficients agreed well with experimental values. At low temperatures, the effects of monomer flexibility in the virial coefficients were found to be much smaller than the quantum effects.
Ab initio engineering of materials with stacked hexagonal tin frameworks
NASA Astrophysics Data System (ADS)
Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.
2016-07-01
The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator.
Ab Initio Multiple Spawning Photochemical Dynamics of DMABN Using GPUs
Curchod, Basile F. E.; Sisto, Aaron; Martinez, Todd J.
2016-12-15
The ultrafast decay dynamics of 4-(N,N-dimethylamino)benzonitrile (DMABN) following photoexcitation was studied with the ab initio multiple spawning (AIMS) method, combined with GPU-accelerated linear-response time-dependent density functional theory (LR-TDDFT). We validate the LR-TDDFT method for this case and then present a detailed analysis of the first ≈200 fs of DMABN excited-state dynamics. Almost complete nonadiabatic population transfer from S2 (the initially populated bright state) to S1 takes place in less than 50 fs, without significant torsion of the dimethylamino (DMA) group. Significant torsion of the DMA group is only observed after the nuclear wavepacket reaches S1 and acquires locally excited electronicmore » character. Here, our results show that torsion of the DMA group is not prerequisite for nonadiabatic transitions in DMABN, although such motion is indeed relevant on the lowest excited state (S1).« less
Ab-initio theory of spin fluctuations in magnets
NASA Astrophysics Data System (ADS)
Antropov, Vladimir; Ke, Liqin; van Schilfgaarde, Mark; Katsnelson, Mikhael
2011-03-01
We propose a framework for a true ab initio theory of magnetism, based on many-body perturbation theory (MPBT). It fits in naturally with methods based MPBT such as the GW approximation; but the approach can be implemented as an extension to any existing static method for electronic structure such as the local spin density approximation to density functional theory, to include spin fluctuations. Initially we calculated the spin fluctuation contributions using random phase approximation. The self consistency procedure similar to the one used in Moryia-Kawabata theory can be naturally implemented. The fluctuation dissipation theorem is used to calculate the reduction of the mean field magnetic moment in itinerant magnets. The applications of the technique includes traditional 3d ferromagnetic metals, their alloys and compounds and 5f systems.
The ab-initio density matrix renormalization group in practice.
Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic
2015-01-21
The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.
Ab initio Calculations of Solvation Processes in Volcanic Gases
NASA Astrophysics Data System (ADS)
Lemke, K.; Seward, T.
2006-12-01
The structures and thermochemical properties of hydrated ions and neutral molecules play an important role in our understanding of solvent clustering and hydrogen bonding in the gas phase. Considerable effort therefore has been devoted to both the experimental and theoretical determination of stepwise hydration energies of geochemically important ions and neutral molecules with solvents, for instance H2O or H2S, over a broad range of temperatures typical of those encountered in volcanic gases. Because volcanic gases contain mutiple solute and solvent components which are subject to proton transfer, competive solvation and solvent switching, characterizing individual clusters has been a fundamental challenge to a molecular-level understanding of high temperature gas-phase solvation. However, recent advances in computational chemistry methods, especially Pople´s Gaussian (G-n) and complete basis set limit (CBS-x) model chemistries, now allow characterization of the dominant cluster structures and thermochemical properties of solute-solvent and solvent-solvent interactions in high temperature volcanic gases. Building on reported measurements of volcanic gases at Vesuvio, Italy, and Showa-Shinzan, Japan, as well as our recent investigations of ion-hydration we have re-examined the high temperature clustering equilibria of the small hydronium (H3O+) and ammonium (NH4+) ions as well as neutral ammonia and sulphur species with H2O and/or H2S using ab initio quantum chemical methods. From our study, we find that most of the gas phase ions tend to associate with a small number of H2O and H2S molecules to yield a hydrated ion cluster even at low humidities. Furthermore, inspection of van´t Hoff data demonstrate that (1) hydration energies of ions are shifted to less exergonic values as the solvent shell grows and the composition shifts from water-rich to hydrogen sulphide rich, (2) ion-cluster size increases with decreasing temperature at constant humidity, (3) attachment
An Ab Initio Study of Alkali-C60 Complexes
NASA Astrophysics Data System (ADS)
Frick, Nathan; Hira, A. S.; Ray, A. K.
2003-03-01
We extend our previous work on fullerene-alkali complexes1-2 by presenting the results of an ab initio theoretical study of the alkali LiC60+, LiC60, NaC60+, NaC60, KC60+, and KC60 complexes. In the endohedral complexes for Li and Na, there is displacement of the adatom from the center. Of the ions, exohedral Li+ will sit closest to the cage, and among the neutrals, exohedral K remains closest. Bond lengths are consistently longer for the fivefold and threefold approaches. Adsorbates inside the fullerene donate negative charge to the carbons, but ions outside obtain a small amount, resulting in a polarization of the molecule. In the ion complexes, there is lowering of the orbital energy levels by 3 to 4 eV, resulting in an increase in the number of bound, but unoccupied, electronic orbitals. The HOMO-LUMO gap, of interest in superconductivity studies, is reduced by about 50 1. A.S. Hira and A.K. Ray, Phys. Rev. A 52, 141(1995); A 54, 2205(1996). 2. Ajit Hira and A. K. Ray, "An Initio Modeling of the Endohedral and Exohedral Complexes of C60Na2+ Complexes", Bull. Am. Phys. Soc. 47 (March 2002).
Ab initio calculations of ten carbon/nitrogen cubanoids
Engelke, R. )
1993-04-07
The results of a uniform set of ab initio quantum-chemical calculations for 10 carbon/nitrogen cubanoids are presented. There are 22 possible C/N cubanoids with formulas (CH)[sub 8[minus]n]N[sub n], where 0 [le] n [le] 8. We give results for one cubanoid for each value of n; for n = 4 both the T[sub d] and C[sub 4v] structures are discussed. The geometries were optimized on the RHF/6-31G*//RHF/6-31G* energy hypersurfaces, and the stationary points so obtained were characterized by vibrational analyses. The effect of electron correlation on the energies of these structures is examined via MP2/6-31G*//RHF/6-31G* theory. All 10 structures are predicted to be stable molecules, and the vibrational analyses indicate that their geometries are well-defined by the RHF/6-31G*//energy hypersurfaces. Heats of formation are predicted via appropriate isodesmic reactions. All the structures are found to have large positive [delta]H[sub f]'s. Perhaps the most interesting result obtained is that the high-energy content of the nitrogen-rich cubanoids is not primarily due to bond strain, but rather to the high-energy content of the NN single bond. Comparisons of the ab initio [delta]H[sub f] values with semiempirical AM1, PM3, and MNDO predictions are made. If they can be synthesized and have reasonable kinetic stability, the C/N cubanoids containing four or more nitrogen atoms are likely to be important energetic materials. A brief discussion is given of the potential of these materials as propellants and explosives. 22 refs., 5 figs., 4 tabs.
Competition between H-bonded and stacked dimers of pyrimidine: IR and theoretical ab-initio study
NASA Astrophysics Data System (ADS)
Carthy, W. M.; Smets, J.; Plokhotnichenko, C. A. M.; Radchenko, E. D.; Sheina, G. G.; Adamowicz, L.; Stepanian, S. G.
A combined matrix isolation Fourier transform infrared experimental and ab-initio theoretical approach has been used to examine the vibrational spectra of pyrimidine dimers. It was found that the presence of pyrimidine dimers resulted in experimentally observed frequencies shifted relative to those of the pyrimidine monomer. Four stable pyrimidine dimer conformers were found via ab-initio calculations. Two of these conformers namely a stacked geometry and a Hbonded geometry in which pyrimidine monomer dipole moments orient antiparallel, had the lowest but very similar energies. Ab-initio harmonic frequencies of these two dimers and their shifts relative to the monomer's values were determined. The effect of Basis Set Superposition error on these calculated frequency shifts was also investigated. The comparison of the abinitio predicted and experimentally observed frequency shifts and an accompanying potential energy distribution analysis suggest that the lowest-energy H-bonded configuration is responsible for the experimentally observed phenomena.
NASA Astrophysics Data System (ADS)
Persico, Maurizio; Cacelli, Ivo; Ferretti, Alessandro
1991-04-01
We have determined ab initio potential energy surfaces of the S0 and S1 states of dimethylnitrosamine, with particular care for the N-N bond dissociation pathway. The electronic correlation has been taken into account by a multireference perturbation method, CIPSI. Classical trajectories in the S1 surface have been run with statistically determined initial conditions. Computed lifetimes and orientation parameters for the recoil velocity and the NO fragment angular momentum are in agreement with experimental data. Large amplitude internal motions are of primary importance in determining such quantities.
Ab initio calculations of the melting temperatures of refractory bcc metals.
Wang, L G; van de Walle, A
2012-01-28
We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental values. We compare the melting temperatures to those obtained from direct ab initio molecular dynamics simulations and see if they are in excellent agreement with each other. The small remaining discrepancies with experiment are thus likely due to inherent limitations associated with exchange-correlation energy approximations within density-functional theory.
Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations
NASA Technical Reports Server (NTRS)
Good, Brian S.
2004-01-01
We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.
Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules
NASA Astrophysics Data System (ADS)
Shiga, Motoyuki; Nakayama, Akira
2008-01-01
The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.
Vibrational energy levels for CH4 from an ab initio potential.
Schwenke, D W; Partridge, H
2001-03-15
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.
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.
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.
Protons in polar media: An ab initio molecular dynamics study
NASA Astrophysics Data System (ADS)
von Rosenvinge, Tycho
1998-10-01
The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations
Corbel, G.; Retoux, R.; Leblanc, M.
1998-08-01
The crystal structures of Ln{sub 3}(BO{sub 3}){sub 2}F{sub 3} (Ln = Sm, Eu, and Gd) are determined ab initio from X-ray powder data. The unit cell is monoclinic, space group C2/c, Z = 4, with a = 12.534(1) {angstrom}, b = 6.237(1) {angstrom}, c = 8.360(1) {angstrom}, {beta} = 97.404(6){degree}, V = 648.1(2) {angstrom}{sup 3} for Gd{sub 3}(BO{sub 3}){sub 2}F{sub 3}. The Rietveld refinement reliability converged to R{sub p} = 0.121, R{sub wp} = 0.147, R{sub exp} = 0.050, {chi}{sup 2} = 8.75. The structure presents a 3D network of Archimedian monocapped antiprisms Gd(1)O{sub 4}F{sub 5} and Gd(2)O{sub 7}F{sub 2}. These polyhedra form trimeric entities Gd{sub 3}O{sub 12}F{sub 9}, which build infinite layers parallel to the (010) plane.
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 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.
Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones
NASA Astrophysics Data System (ADS)
Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng
2004-04-01
A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (Δ G#) and also free energy differences (Δ G0) for benzodiazepines are reported.
NASA Astrophysics Data System (ADS)
Kozlov, Maxim I.; Poddubnyy, Vladimir V.; Glebov, Ilya O.; Belov, Aleksandr S.; Khokhlov, Daniil V.
2016-02-01
The electronic properties of light-harvesting complexes determine the efficiency of energy transfer in photosynthetic antennae. Ab initio calculations of the electronic properties of bacteriochlorophylls (composing the LH1 complex of the purple bacteria Thermochromatium tepidum) were performed. Based on these calculations, the excitonic Hamiltonian of a native cyclic complex and the Hamiltonians of open complexes with several removed bacteriochlorophylls were constructed. Absorption spectra calculated based on these Hamiltonians agree well with the experimental data. We found that the parameters of interaction between the neighboring bacteriochlorophylls are significantly larger than the empirical parameters suggested previously.
The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Jakse, N.; Pasturel, A.
2014-09-01
We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.
Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study.
Payal, Rajdeep Singh; Balasubramanian, Sundaram
2014-09-07
Interactions determining the dissolution of a monomer of β-cellulose, i.e., cellobiose in a room temperature ionic liquid, [Emim][OAc], have been studied using ab initio molecular dynamics simulations. Although anions are the predominant species in the first coordination shell of cellobiose, cations too are present to a minor extent around it. The presence of low concentration of water in the solution does not significantly alter the nature of the coordination environment of cellobiose. All intra-molecular hydrogen bonds of anti-syn cellobiose are replaced by inter-molecular hydrogen bonds formed with the anions, whereas the anti-anti conformer retains an intramolecular hydrogen bond.
The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics.
Jakse, N; Pasturel, A
2014-09-07
We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.
Structure and dynamics of the Lu2Si2O7 lattice: Ab initio calculation
NASA Astrophysics Data System (ADS)
Nazipov, D. V.; Nikiforov, A. E.
2017-01-01
The ab initio calculations have been carried out for the crystal structure and Raman spectrum of a single crystal of lutetium pyrosilicate Lu2Si2O7. The types of fundamental vibrations and their frequencies and intensities in the Raman spectrum for two polarizations of the crystal have been determined. The calculations have been performed within the framework of the density functional theory (DFT) using the hybrid functionals. The ions involved in the vibrations have been identified using the method of isotopic substitution. The results of the calculations are in good agreement with the experiment.
NASA Astrophysics Data System (ADS)
Jenkins, S.; Morrison, I.; Ross, D. K.
2000-02-01
We have determined the normal modes of ice VIII, a 16-molecule supercell, using ab initio calculations. The dynamical matrices so obtained are diagonalized and the eigenvectors projected on to the stretching, bending and libration modes of each water molecule in turn. We can therefore accurately correlate the symmetry assignments of the zone centre modes and the corresponding frequencies of these dynamical results with Raman, infrared and neutron scattering data. In particular, using neutron scattering data, we obtain excellent agreement with the frequencies of the icons/Journals/Common/upsilon" ALT="upsilon" ALIGN="TOP"/> Ry B1u phonon mode which is inactive in Raman or infrared spectroscopy.
Ab initio calculation of the deuterium quadrupole coupling in liquid water
NASA Astrophysics Data System (ADS)
Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc
1992-10-01
The quadrupole coupling constant and asymmetry parameter for the deuteron in liquid heavy water was determined using purely theoretical methods. Molecular-dynamics simulations with the ab initio potential-energy surface of Lie and Clementi were used to generate snapshots of the liquid. The electric-field gradient at the deuteron was then calculated for these configurations and averaged to obtain the liquid quadrupole coupling constant. At 300 K a quadrupole coupling constant of 256±5 kHz and an asymmetry parameter of 0.164±0.003 were obtained. The temperature dependence of the quadrupole coupling constant was investigated.
Ab initio study of the elastic anomalies in Pd-Ag alloys
NASA Astrophysics Data System (ADS)
Delczeg-Czirjak, E. K.; Delczeg, L.; Ropo, M.; Kokko, K.; Punkkinen, M. P. J.; Johansson, B.; Vitos, L.
2009-02-01
Ab initio total-energy calculations, based on the exact muffin-tin orbital method, are used to determine the elastic properties of Pd1-xAgx random alloys in the face-centered-cubic crystallographic phase. The compositional disorder is treated within the coherent-potential approximation. The single crystal and polycrystalline elastic constants and the Debye temperature are calculated for the whole range of concentration, 0≤x≤1 . It is shown that the variation in the elastic parameters of Pd-Ag alloys with chemical composition strongly deviates from a simple linear or parabolic trend. The complex electronic origin of these anomalies is demonstrated.
Engineering Room-temperature Superconductors Via ab-initio Calculations
NASA Astrophysics Data System (ADS)
Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen
The BCS, or bosonic model of superconductivity, as Little and Ginzburg have first argued, can bring in superconductivity at room temperatures in the case of high-enough frequency of bosonic mode. It was further elucidated by Kirzhnitset al., that the condition for existence of high-temperature superconductivity is closely related to negative values of the real part of the dielectric function at finite values of the reciprocal lattice vectors. In view of these findings, the task is to calculate the dielectric function for real materials. Then the poles of this function will indicate the existence of bosonic excitations which can serve as a "glue" for Cooper pairing, and if the frequency is high enough, and the dielectric matrix is simultaneously negative, this material is a good candidate for very high-Tc superconductivity. Thus, our approach is to elaborate a methodology of ab-initio calculation of the dielectric function of various materials, and then point out appropriate candidates. We used the powerful codes (TDDF with the DP package in conjunction with ABINIT) for computing dielectric responses at finite values of the wave vectors in the reciprocal lattice space. Though our report is concerned with the particular problem of superconductivity, the application range of the data processing methodology is much wider. The ability to compute the dielectric function of existing and still non-existing (though being predicted!) materials will have many more repercussions not only in fundamental sciences but also in technology and industry.
Ab initio calculation of infrared intensities for hydrogen peroxide
NASA Technical Reports Server (NTRS)
Rogers, J. D.; Hillman, J. J.
1982-01-01
Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.
Lead-Chalcogenides Under Pressure: Ab-Initio Study
NASA Astrophysics Data System (ADS)
Gupta, Dinesh C.; Hamid, Idris
ab-initio calculations using fully relativistic pseudo-potential have been performed to investigate the high pressure phase transition, elastic and electronic properties of lead-chalcogenides including the less known lead polonium. The calculated ground state parameters, for the rock-salt structure show good agreement with the experimental data. The enthalpy calculations show that these materials undergo a first-order phase transition from rock-salt to CsCl structure at 19.4, 15.5, 11.5 and 7.3 GPa for PbS, PbSe, PbTe and PbPo, respectively. Present calculations successfully predicted the location of the band gap at L-point of Brillouin zone as well as the value of the band gap in every case at ambient pressure. It is observed that unlike other lead-chalcogenides, PbPo is semi-metal at ambient pressure. The pressure variation of the energy gap indicates that these materials metalized under high pressures. For this purpose, the electronic structure of these materials has also been computed in parent as well as in high pressure phase.
Ab initio calculations of nuclear reactions important for astrophysics
NASA Astrophysics Data System (ADS)
Navratil, Petr; Dohet-Eraly, Jeremy; Calci, Angelo; Horiuchi, Wataru; Hupin, Guillaume; Quaglioni, Sofia
2016-09-01
In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. One of the newly developed approaches is the No-Core Shell Model with Continuum (NCSMC), capable of describing both bound and scattering states in light nuclei simultaneously. We will present NCSMC results for reactions important for astrophysics that are difficult to measure at relevant low energies, such as 3He(α,γ)7Be and 3H(α,γ)7Li and 11C(p,γ)12N radiative capture, as well as the 3H(d,n)4He fusion. We will also address prospects of calculating the 2H(α,γ)6Li capture reaction within the NCSMC formalism. Prepared in part by LLNL under Contract DE-AC52-07NA27344. Supported by the U.S. DOE, OS, NP, under Work Proposal No. SCW1158, and by the NSERC Grant No. SAPIN-2016-00033. TRIUMF receives funding from the NRC Canada.
Ab initio Raman spectroscopy of water under extreme conditions
NASA Astrophysics Data System (ADS)
Rozsa, Viktor; Pan, Ding; Wan, Quan; Galli, Giulia
Water exhibits one of the most complex phase diagrams of any binary compound. Despite extensive studies, the melting lines of high-pressure ice phases remain very controversial, with reports differing by hundreds of Kelvin. The boundary between ice VII and liquid phase is particularly disputed, with recent work exploring plasticity and amorphization mediating the transition. Raman measurements are often used to fingerprint melting, yet their interpretation is difficult without atomistic modeling. Here, we report a study of high P/T water where we computed Raman spectra using a method combining ab initio molecular dynamics and density functional perturbation theory, as implemented in the Qbox code. Spectra were computed for the liquid at 10 and 20 GPa, both at 1000 K, and for solid ice VII (20 GPa, 500 K). Decomposing the spectra into inter and intra molecular contributions provided insight into the dynamics of the hydrogen-bonded network at extreme conditions. The relevance of our simulation results for models of water in Earth, Uranus, and Neptune will be discussed, and an interpretation of existing experiments at high pressure will be presented.
Ab initio predictions of the symmetry energy and recent constraints
NASA Astrophysics Data System (ADS)
Sammarruca, Francesca
2017-01-01
The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.
Ab Initio Study of Covalently Functionalized Graphene and Carbon Nanotubes
NASA Astrophysics Data System (ADS)
Jha, Sanjiv; Hammouri, Mahmoud; Vasiliev, Igor; Magedov, Igor; Frolova, Liliya; Kalugin, Nikolai
2014-03-01
The electronic and structural properties of carbon nanomaterials can be affected by chemical functionalization. We apply ab initio computational methods based on density functional theory to study the properties of graphene and single-walled carbon nanotubes functionalized with benzyne. Our calculations are carried out using the SIESTA electronic structure code combined with the generalized gradient approximation for the exchange correlation functional. The calculated binding energies, densities of states, and band structures of functionalized graphene and carbon nanotubes are analyzed in comparison with the available experimental data. The surfaces of carbon nanotubes are found to be significantly more reactive toward benzyne molecules than the surface of graphene. The strength of interaction between benzyne and carbon nanotubes is affected by the curvature of the nanotube sidewall. The binding energies of benzyne molecules attached to both semiconducting zigzag and metallic armchair nanotubes increase with decreasing the nanotube diameter. Supported by NSF CHE-1112388, NMSU GREG Award, NSF ECCS-0925988, NIH-5P20RR016480-12, and NIH- P20 GM103451.
Local structure analysis in ab initio liquid water
NASA Astrophysics Data System (ADS)
Santra, Biswajit; DiStasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto
2015-09-01
Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyse the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I ), was unimodal with most water molecules characterised by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I ) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high-density- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water. Analysis of the LSI autocorrelation function uncovered a persistence time of ∼ 4 ps - a finding consistent with the fact that natural thermal fluctuations are responsible for transitions between these distinct yet transient local aqueous environments in ambient liquid water.
Local Environment Distribution in Ab Initio Liquid Water
NASA Astrophysics Data System (ADS)
Santra, Biswajit; Distasio, Robert A., Jr.; Car, Roberto
2013-03-01
We have analyzed the distribution of local environments in liquid water at ambient conditions and its inherent potential energy surface (IPES) based on state-of-the-art ab initio molecular dynamics simulations performed on 128 molecules implementing hybrid PBE0 exchange [PRB 79, 085102 (2009)] and van der Waals (vdW) interactions [PRL 102, 073005 (2009)]. The local environments of molecules are characterized in terms of the local structure index (LSI) [JCP 104, 7671 (1996)] which is able to distinguish high- and low-density molecular environments. In agreement with simulations based on model potentials, we find that the distribution of LSI is unimodal at ambient conditions and bimodal in the IPES, consistent with the existence of polymorphism in amorphous phases of water. At ambient conditions spatial LSI fluctuations extend up to ~7 Å and their dynamical correlation decays on a time scale of ~3 ps, as found for density fluctuations in a recent study [PRL 106, 037801 (2011)]. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500
Ab-Initio Molecular Dynamics Simulation of Graphene Sheet
NASA Astrophysics Data System (ADS)
Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.
2017-01-01
The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.
An efficient approach to ab initio Monte Carlo simulation.
Leiding, Jeff; Coe, Joshua D
2014-01-21
We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β(0)), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where-depending on the quality of the reference system potential-acceptance probabilities were enhanced by factors of 1.2-28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.
Electronic structure and conductivity of ferroelectric hexaferrite: Ab initio calculations
NASA Astrophysics Data System (ADS)
Knížek, K.; Novák, P.; Küpferling, M.
2006-04-01
Ba0.5Sr1.5Zn2Fe12O22 is a promising multiferroic compound in which the electric polarization is intimately connected to the magnetic state. In principle, ferroelectrity might exist above the room temperature, but the electrical conductivity that increases with increasing temperature limits it to temperatures below ≈130K . We present results of an ab initio electronic structure calculation of the (BaSr)Zn2Fe12O22 system. To improve the description of strongly correlated 3d electrons of iron, the GGA+U method is used. The results show that the electrical conductivity strongly depends on relative fractions of iron and zinc in the tetrahedral sublattice that belongs to the spinel block of the hexaferrite structure. If this sublattice is fully occupied by zinc, the system is an insulator with a gap of ≈1.5eV . If it is occupied equally by Fe and Zn the gap decreases by a factor of 2, and the system is metallic when this sublattice is filled by iron only.
Ab initio description of the exotic unbound 7He nucleus
Baroni, Simone; Navratil, Petr; Quaglioni, Sofia
2013-01-11
In this study, the neutron-rich unbound 7He nucleus has been the subject of many experimental investigations. While the ground-state 3/2– resonance is well established, there is a controversy concerning the excited 1/2– resonance reported in some experiments as low lying and narrow (ER~1 MeV, Γ≤1 MeV) while in others as very broad and located at a higher energy. This issue cannot be addressed by ab initio theoretical calculations based on traditional bound-state methods. We introduce a new unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model, a bound-state technique, with the no-coremore » shell model combined with the resonating-group method, a nuclear scattering technique. Our calculations describe the ground-state resonance in agreement with experiment and, at the same time, predict a broad 1/2– resonance above 2 MeV.« less
Structure of diamond(100) stepped surfaces from ab initio calculations
NASA Astrophysics Data System (ADS)
Alfonso, Dominic; Drabold, David; Ulloa, Sergio
1996-02-01
We present theoretical studies of relaxations of monoatomic 0953-8984/8/6/005/img6 and 0953-8984/8/6/005/img7 steps on the diamond(100)-(20953-8984/8/6/005/img81) surface employing an ab initio molecular dynamics simulation method that is based on density functional theory. Stable dimer structures are found in the upper and lower planes of the step surfaces in agreement with experiment. Significant atomic relaxations occur near the step edges of 0953-8984/8/6/005/img9 and 0953-8984/8/6/005/img7 stepped surfaces induced by the creation of the steps. Atomic H adsorption on these step surfaces to form monohydride structures is energetically favourable. We also simulate the presence of radical sites near the step edges of 0953-8984/8/6/005/img11, 0953-8984/8/6/005/img7 and 0953-8984/8/6/005/img9 and local reconstruction involving the dimer containing the radical sites is found. Electronic charge density profiles of the filled states near the Fermi level show features associated with the dimer structures.
Ab initio no-core solutions for 6Li
NASA Astrophysics Data System (ADS)
Shin, Ik Jae; Kim, Youngman; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy; Michel, Nicolas
2017-07-01
We solve for properties of 6Li in the ab initio no-core full configuration (NCFC) approach and we separately solve for its ground state and {J}π ={2}2+ resonance with the Gamow shell model (GSM) in the Berggren basis. We employ both the JISP16 and chiral {{NNLO}}{opt} realistic nucleon-nucleon interactions and investigate the ground state energy, excitation energies, point proton root mean square (rms) radius and a suite of electroweak observables. We also extend and test methods to extrapolate the ground state energy, point proton rms radius, and electric quadrupole moment. We attain improved estimates of these observables in the NCFC approach by using basis spaces up through {N}\\max =18 that enable more definitive comparisons with experiment. Using the density matrix renormalization group approach with the JISP16 interaction, we find that we can significantly improve the convergence of the GSM treatment of the 6Li ground state and {J}π ={2}2+ resonance by adopting a natural orbital single-particle basis.
Perovskite transparent conducting oxides: an ab initio study.
Dabaghmanesh, S; Saniz, R; Amini, M N; Lamoen, D; Partoens, B
2013-10-16
We present an ab initio study of the electronic structure and of the formation energies of various point defects in BaSnO3 and SrGeO3. We show that La and Y impurities substituting Ba or Sr are shallow donors with a preferred 1 + charge state. These defects have a low formation energy within all the suitable equilibrium growth conditions considered. Oxygen vacancies behave as shallow donors as well, preferring the 2 + charge state. Their formation energies, however, are higher in most growth conditions, indicating a limited contribution to conductivity. The calculated electron effective mass in BaSnO3, with a value of 0.21 m(e), and the very high mobility reported recently in La-doped BaSnO3 single-crystals, suggest that remarkably low scattering rates can be achieved in the latter. In the case of SrGeO3, our results point to carrier density and mobility values in the low range for typical polycrystalline TCOs, in line with experiment.
Moderate-Cost Ab Initio Thermochemistry with Chemical Accuracy.
Ganyecz, Ádám; Kállay, Mihály; Csontos, József
2017-09-12
A moderate-cost ab initio composite model chemistry including the explicitly correlated CCSD(T*)(F12) and conventional coupled-cluster methods up to perturbative quadruple excitations along with correlation consistent basis sets is developed. The model, named diet-HEAT-F12, is also augmented with diagonal Born-Oppenheimer and scalar relativistic corrections. The methods and basis sets used for the calculation of the individual components are selected to reproduce, as close as possible, without using any fitted parameters, the benchmark HEAT contributions. A well-defined recipe for calculating size-dependent 95% confidence intervals was also worked out for the model. The reliability of the protocol was checked using the W4-11 data set as well as a disjoint set of 23 accurate atomization energies collected from the literature and obtained by the procedure of Feller, Peterson, and Dixon. The best error statistics for the test set was yielded by the diet-HEAT-F12 protocol among the models W3X, W3X-L, and W3-F12 considered.
Ab initio study of MoS2 nanotube bundles
NASA Astrophysics Data System (ADS)
Verstraete, Matthieu; Charlier, Jean-Christophe
2003-07-01
Recently, the synthesis of a new phase of MoS2I1/3 stoichiometry was reported [M. Remskar, A. Mrzel, Z. Skraba, A. Jesih, M. Ceh, J. Demšar, P. Stadelmann, F. Lévy, and D. Mihailovic, Science 292, 479 (2001)]. Electron microscope images and diffraction data were interpreted to indicate bundles of sub-nanometer-diameter single-wall MoS2 nanotubes. After experimental characterization, the structure was attributed to an assembly of “armchair” nanotubes with interstitial iodine. Using first-principles total-energy calculations, bundles of MoS2 nanotubes with different topologies and stoichiometries are investigated. All of the systems are strongly metallic. Configurations with “zigzag” structures are found to be more stable energetically than the “armchair” ones, though all of the structures have similar stabilities. After relaxation, there remain several candidates which give a lattice parameter in relative agreement with experiment. Further, spin-polarized calculations indicate that a structure with armchair tubes iodine atoms in their center acquires a very large spontaneous magnetic moment of 12μB, while the other structures are nonmagnetic. Our ab initio calculations show that in most of the other structures, the tubes are very strongly bound together, and that the compounds should be considered as a crystal, rather than as a bundle of tubes in the habitual sense.
Challenges for large scale ab initio Quantum Monte Carlo
NASA Astrophysics Data System (ADS)
Kent, Paul
2015-03-01
Ab initio Quantum Monte Carlo is an electronic structure method that is highly accurate, well suited to large scale computation, and potentially systematically improvable in accuracy. Due to increases in computer power, the method has been applied to systems where established electronic structure methods have difficulty reaching the accuracies desired to inform experiment without empiricism, a necessary step in the design of materials and a helpful step in the improvement of cheaper and less accurate methods. Recent applications include accurate phase diagrams of simple materials through to phenomena in transition metal oxides. Nevertheless there remain significant challenges to achieving a methodology that is robust and systematically improvable in practice, as well as capable of exploiting the latest generation of high-performance computers. In this talk I will describe the current state of the art, recent applications, and several significant challenges for continued improvement. Supported through the Predictive Theory and Modeling for Materials and Chemical Science program by the Office of Basic Energy Sciences (BES), Department of Energy (DOE).
Accurate ab initio vibrational energies of methyl chloride
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2015-06-28
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup HL}, and CBS-37{sup HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup HL} and CBS-37{sup HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.
Ab initio electronic structure and optical conductivity of bismuth tellurohalides
NASA Astrophysics Data System (ADS)
Schwalbe, Sebastian; Wirnata, René; Starke, Ronald; Schober, Giulio A. H.; Kortus, Jens
2016-11-01
We investigate the electronic structure, dielectric, and optical properties of bismuth tellurohalides BiTe X (X =I , Cl, Br) by means of all-electron density functional theory. In particular, we present the ab initio conductivities and dielectric tensors calculated over a wide frequency range, and compare our results with the recent measurements by Akrap et al. [Phys. Rev. B 90, 035201 (2014), 10.1103/PhysRevB.90.035201], Makhnev et al. [Opt. Spectrosc. 117, 764 (2014), 10.1134/S0030400X14110125], and Rusinov et al. [JETP Lett. 101, 507 (2015), 10.1134/S0021364015080147]. We show how the low-frequency branch of the optical conductivity can be used to identify characteristic intra- and interband transitions between the Rashba spin-split bands in all three bismuth tellurohalides. We further calculate the refractive indices and dielectric constants, which in turn are systematically compared to previous predictions and measurements. We expect that our quantitative analysis will contribute to the general assessment of bulk Rashba materials for their potential use in spintronics devices.
Ab initio liquid water from PBE0 hybrid functional simulations
NASA Astrophysics Data System (ADS)
Li, Zhaofeng; Wu, Xifan; Car, Roberto
2010-03-01
For reasons of computational efficiency, so far most ab initio molecular dynamics simulations of liquid water have been based on semi-local density functional approximations, such as PBE and BLYP. These approaches yield a liquid structure that, albeit qualitatively correct, is overstructured compared to experiment, even after nuclear quantum effects have been taken into account.footnotetextJ. A. Morrone and R. Car, Phys. Rev. Lett. 101, 017801(2008) A major cause of this inaccuracy is the delocalization error associated to semi-local density functional approximations, which, as a consequence, overestimate slightly the hydrogen bond strength in the liquid. In this work we adopt the PBE0 hybrid functional approximation, which, by mixing a fraction of exact (Hartree-Fock) exchange, reduces significantly the delocalization error of semi-local functionals. Our approach is based on a numerically efficient order-N implementation of exact exchange.footnotetextX. Wu, A. Selloni, and R. Car, Phys. Rev. B 79, 085102(2009) We find that PBE0 systematically improves the agreement of the simulated liquid with experiment. Our conclusion is substantiated by the calculated radial distribution functions, H-bond statistics, and molecular dipole distribution.
Ab initio studies of niobium defects in uranium
Xiang, S; Huang, H; Hsiung, L
2007-06-01
Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.
Melting curves of metals by ab initio calculations
NASA Astrophysics Data System (ADS)
Minakov, Dmitry; Levashov, Pavel
2015-06-01
In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).
Ab initio studies of phosphorene island single electron transistor
NASA Astrophysics Data System (ADS)
Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.
2016-05-01
Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.
Ab initio theory of perpendicular magnetotransport in metallic multilayers
NASA Astrophysics Data System (ADS)
Kudrnovský, J.; Drchal, V.; Blaas, C.; Weinberger, P.; Turek, I.; Bruno, P.
2000-12-01
The current-perpendicular-to-plane (CPP) magnetotransport of a metallic sample sandwiched by two ideal leads is described at an ab initio level. The so-called ``active'' part of the system is either a trilayer consisting of two magnetic slabs of finite thickness separated by a nonmagnetic spacer or a multilayer formed by alternating magnetic and nonmagnetic layers. We use a transmission matrix formulation of the conductance based on surface Green's functions as formulated by means of the tight-binding linear muffin-tin orbital method. The formalism is extended to the case of lateral supercells with random arrangements of atoms of two types, which in turn allows to deal with specular and diffusive scattering on equal footing, and which is applicable also to the case of noncollinear alignments of the magnetization in the layers. Applications refer to fcc-based Co/Cu/Co(001) trilayers and multilayers, considering in detail the effect of substitutional alloying in the spacer and in the magnetic layers, as well as interdiffusion at the interfaces.
Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures
NASA Astrophysics Data System (ADS)
Debernardi, Alberto; Marchetti, Luigi
2016-06-01
Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.
Ab initio studies of the passive film formed on iron
NASA Astrophysics Data System (ADS)
Hendy, S.; Walker, B.; Laycock, N.; Ryan, M.
2003-02-01
Passive metals are protected from the environment by a thin (3 5 nm) oxide film that forms on their surface. The corrosion rate of these materials is typically of the order of 0.1 μm/year, and depends on the electronic structure of the oxide layer. Here we present ab initio total-energy calculations of the passive oxide film that forms on iron at anodic potentials in weakly alkaline solutions. Surface x-ray diffraction studies have revealed that this nanocrystalline passive film has a spinel structure with a fully occupied oxygen lattice [M. F. Toney, A. J. Davenport, L. J. Oblonsky, M. P. Ryan, and C. M. Vitus, Phys. Rev. Lett. 79, 4282 (1997)]. However, the octahedral and tetrahedral iron site occupancies are found to be reduced (approximately 80% and 66%, respectively) and partial occupancy of octahedral interstitial sites is also observed (approximately 12%). We have used total-energy pseudopotential calculations to study the energetics and electronic structure of these defects and the interrelationships between site occupancies. The calculations suggest that film is metastable and may be semi-conducting. The calculations also suggest a correlation between octahedral interstitials and tetrahedral vacancies. Finally, an estimation of energy barriers in the film suggests that cation migration through the tetrahedral sublattice dominates film growth.
Ab Initio Multiple Spawning Photochemical Dynamics of DMABN Using GPUs
Curchod, Basile F. E.; Sisto, Aaron; Martinez, Todd J.
2016-12-15
The ultrafast decay dynamics of 4-(N,N-dimethylamino)benzonitrile (DMABN) following photoexcitation was studied with the ab initio multiple spawning (AIMS) method, combined with GPU-accelerated linear-response time-dependent density functional theory (LR-TDDFT). We validate the LR-TDDFT method for this case and then present a detailed analysis of the first ≈200 fs of DMABN excited-state dynamics. Almost complete nonadiabatic population transfer from S_{2} (the initially populated bright state) to S_{1} takes place in less than 50 fs, without significant torsion of the dimethylamino (DMA) group. Significant torsion of the DMA group is only observed after the nuclear wavepacket reaches S_{1} and acquires locally excited electronic character. Here, our results show that torsion of the DMA group is not prerequisite for nonadiabatic transitions in DMABN, although such motion is indeed relevant on the lowest excited state (S_{1}).
Ab initio calculations of correlated electron dynamics in ultrashort pulses
NASA Astrophysics Data System (ADS)
Feist, Johannes
2010-03-01
The availability of ultrashort and intense light pulses on the femtosecond and attosecond timescale promises to allow to directly probe and control electron dynamics on their natural timescale. A crucial ingredient to understanding the dynamics in many-electron systems is the influence of electron correlation, induced by the interelectronic repulsion. In order to study electron correlation in ultrafast processes, we have implemented an ab initio simulation of the two-electron dynamics in helium atoms. We solve the time-dependent Schr"odinger equation in its full dimensionality, with one temporal and five spatial degrees of freedom in linearly polarized laser fields. In our computational approach, the wave function is represented through a combination of time-dependent close coupling with the finite element discrete variable representation, while time propagation is performed using an Arnoldi-Lanczos approximation with adaptive step size. This approach is optimized to allow for efficient parallelization of the program and has been shown to scale linearly using up to 1800 processor cores for typical problem sizes. This has allowed us to perform highly accurate and well- converged computations for the interaction of ultrashort laser pulses with He. I will present some recent results on using attosecond and femtosecond pulses to probe and control the temporal structure of the ionization process. This work was performed in collaboration with Stefan Nagele, Renate Pazourek, Andreas Kaltenb"ack, Emil Persson, Barry I. Schneider, Lee A. Collins, and Joachim Burgd"orfer.
Exploring the free energy surface using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-01
Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.
Ab initio modeling of decomposition in iron based alloys
NASA Astrophysics Data System (ADS)
Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.
2016-12-01
This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.
Volumic omit maps in ab initio dual-space phasing.
Oszlányi, Gábor; Sütő, András
2016-07-01
Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed.
Ab initio molecular dynamics calculations of ion hydration free energies.
Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
Ab Initio Investigation of NH_3-O_2 Exciplex
NASA Astrophysics Data System (ADS)
Haupert, L. M.; Simpson, G.; Slipchenko, L. V.
2010-06-01
In their recent investigation of fluorescence from poly(amido amine) (PAMAM) dendrimers, Chu and Imae suggested an exciplex composed of tertiary amine and oxygen molecules might be responsible for fluorescence in PAMAM dendrimers. In this work, we present an ab initio investigation of the electronic structure of a possible ammonia-oxygen exciplex model system using equation-of-motion coupled cluster techniques. Geometry optimization of the triplet ground state produced a weakly bound state with an equilibrium separation of ˜ 3.5 Å, and an excited state geometry scan revealed a bound, excited triplet state with an equilibrium separation of 2.02 Å, consistent with results of earlier PM3 work by Juranic et al. The energy gap between the triplet ground state and first triplet excited state of the exciplex at 2.02 Å is 412.8 nm, lending support to the exciplex hypothesis. C.-C. Chu, and T. Imae, Macromol. Rapid. Commun., 30, 89-93 (2009). I. Juranic, H. S. Rzepa, and Y. MinYan, J. Chem. Soc. Perkin Trans., 2 (1990)
Ab initio study of the thermopower of biphenyl-based single-molecule junctions
NASA Astrophysics Data System (ADS)
Bürkle, M.; Zotti, L. A.; Viljas, J. K.; Vonlanthen, D.; Mishchenko, A.; Wandlowski, T.; Mayor, M.; Schön, G.; Pauly, F.
2012-09-01
By employing ab initio electronic-structure calculations combined with the nonequilibrium Green's function technique, we study the dependence of the thermopower Q on the conformation in biphenyl-based single-molecule junctions. For the series of experimentally available biphenyl molecules, alkyl side chains allow us to gradually adjust the torsion angle ϕ between the two phenyl rings from 0∘ to 90∘ and to control in this way the degree of π-electron conjugation. Studying different anchoring groups and binding positions, our theory predicts that the absolute values of the thermopower decrease slightly towards larger torsion angles, following an a+bcos2ϕ dependence. The anchoring group determines the sign of Q and a,b simultaneously. Sulfur and amine groups give rise to Q,a,b>0, while for cyano, Q,a,b<0. The different binding positions can lead to substantial variations of the thermopower mostly due to changes in the alignment of the frontier molecular orbital levels and the Fermi energy. We explain our ab initio results in terms of a π-orbital tight-binding model and a minimal two-level model, which describes the pair of hybridizing frontier orbital states on the two phenyl rings. The variations of the thermopower with ϕ seem to be within experimental resolution.
2015-06-28
Charts 3. DATES COVERED (From - To) June 2015-June 2015 4. TITLE AND SUBTITLE AB INITIO QUANTUM CHEMICAL REACTION KINETICS: RECENT APPLICATIONS IN...Unlimited. 13. SUPPLEMENTARY NOTES Briefing Charts presented at 9th Int. Conf. Chemical Kinetics; Ghent, Belgium; 28 Jun 2015. PA#15351. 14. ABSTRACT...ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry Ghanshyam L. Vaghjiani* DISTRIBUTION A
Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.
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.
Ashcraft, Robert W; Raman, Sumathy; Green, William H
2007-10-18
Ab initio molecular orbital calculations were performed and thermochemical parameters estimated for 46 species involved in the oxidation of hydroxylamine in aqueous nitric acid solution. Solution-phase properties were estimated using the several levels of theory in Gaussian03 and using COSMOtherm. The use of computational chemistry calculations for the estimation of physical properties and constants in solution is addressed. The connection between the pseudochemical potential of Ben-Naim and the traditional standard state-based thermochemistry is shown, and the connection of these ideas to computational chemistry results is established. This theoretical framework provides a basis for the practical use of the solution-phase computational chemistry estimates for real systems, without the implicit assumptions that often hide the nuances of solution-phase thermochemistry. The effect of nonidealities and a method to account for them is also discussed. A method is presented for estimating the solvation enthalpy and entropy for dilute aqueous solutions based on the solvation free energy from the ab initio calculations. The accuracy of the estimated thermochemical parameters was determined through comparison with (i) enthalpies of formation in the gas phase and in solution, (ii) Henry's law data for aqueous solutions, and (iii) various reaction equilibria in aqueous solution. Typical mean absolute deviations (MAD) for the solvation free energy in room-temperature water appear to be ~1.5 kcal/mol for most methods investigated. The MAD for computed enthalpies of formation in solution was 1.5-3 kcal/mol, depending on the methodology employed and the type of species (ion, radical, closed-shell) being computed. This work provides a relatively simple and unambiguous approach that can be used to estimate the thermochemical parameters needed to build detailed ab initio kinetic models of systems in aqueous solution. Technical challenges that limit the accuracy of the estimates are
An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry
Matthew Neurock; David A. Walthall
2006-05-07
One of the greatest societal challenges over the next decade is the production of cheap, renewable energy for the 10 billion people that inhabit the earth. This will require the development of various different energy sources potentially including fuels derived from methane, coal, and biomass and alternatives sources such as solar, wind and nuclear energy. One approach will be to synthesize gasoline and other fuels from simpler hydrocarbons such as CO derived from methane or other U.S. based sources such as coal. Syngas (CO and H{sub 2}) can be readily converted into higher molecular weight hydrocarbons through Fischer-Tropsch synthesis. Fischer-Tropsch synthesis involves the initiation or activation of CO and H{sub 2} bonds, the subsequent propagation steps including hydrogenation and carbon-carbon coupling, followed by chain termination reactions. Commercially viable catalysts include supported Co and Co-alloys. Over the first two years of this project we have used ab initio methods to determine the adsorption energies for all reactants, intermediates, and products along with the overall reaction energies and their corresponding activation barriers over the Co(0001) surface. Over the third year of the project we developed and advanced an ab initio-based kinetic Monte Carlo simulation code to simulate Fischer Tropsch synthesis. This report details our work over the last year which has focused on the derivation of kinetic parameters for the elementary steps involved in FT synthesis from ab initio density functional theoretical calculations and the application of the kinetic Monte Carlo algorithm to simulate the initial rates of reaction for FT over the ideal Co(0001) surface. The results from our simulations over Co(0001) indicate the importance of stepped surfaces for the activation of adsorbed CO. In addition, they demonstrate that the dominant CH{sub x}* surface intermediate under steady state conditions is CH*. This strongly suggests that hydrocarbon coupling
Bridging a gap between continuum-QCD and ab initio predictions of hadron observables
Binosi, Daniele; Chang, Lei; Papavassiliou, Joannis; ...
2015-03-01
Within contemporary hadron physics there are two common methods for determining the momentum- dependence of the interaction between quarks: the top-down approach, which works toward an ab initiocomputation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD’s gauge sector coincides with that required in order to describe ground-state hadron observables usingmore » a nonperturbative truncation of QCD’s Dyson–Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.« less
Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.
Martí-Rujas, Javier; Kawano, Masaki
2013-02-19
Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific
An analytical ab initio potential surface and the calculated tunneling energies for the HCl dimer
NASA Astrophysics Data System (ADS)
Bunker, P. R.; Epa, V. C.; Jensen, Per; Karpfen, Alfred
1991-03-01
The six-dimensional potential energy surface of the HCl dimer has been calculated ab initio at 1654 nuclear geometries [A. Karpfen, P. R. Bunker and P. Jensen, Chem. Phys., in press]. In the present paper we have fitted an analytical function to these points; the analytical function is similar to that used previously by us for the potential surface of the HF dimer. The fitted function has 38 adjustable parameters and the standard deviation of the weighted fit is 19.0 cm -1. We have determined the minimum energy path for the trans-bending tunneling motion on this surface, and have calculated the tunneling and K-rotation energies and wavefunctions. Around equilibrium the path is qualitatively similar to that for the HF dimer in that there are two equivalent hydrogen-bonded structures of Cs symmetry (which are approximately L-shaped with a "bound" and a "free" H-atom) that can tunnel through a C2 h saddle point (the "closed" C2 h saddle point). However, away from equilibrium the path is qualitatively different from that found for the HF dimer since the HCl dimer never becomes linear along the path; in fact it passes through a second C2 h saddle point (the "open" C2 h saddle point). As a result the A-rotational constant only varies slightly along the path, and this explains the experimental observation that the tunneling splitting varies little with K-type rotation for the HCl dimer, in contrast to the situation for the HF dimer. Quantitatively it is clear that errors in the ab initio calculation, errors in the fitting of an analytic function to the points, the correction to the path that is caused by the zero point motion in the other vibrations, and the coupling between the four low-frequency modes, will all be relatively more significant than they were for the HF dimer because the full six-dimensional potential is much flatter; the ab initio dissociation energy is only ˜600 cm -1, and the ab initio tunneling barrier is only ˜70 cm -1. Therefore, we modify the
Ab initio molecular dynamics of heme in cytochrome c.
Furlan, Sara; Penna, Giovanni La; Banci, Lucia; Mealli, Carlo
2007-02-08
Ab initio molecular dynamics (AIMD) calculations, based on the Car-Parrinello method, have been carried out for three models of heme c that is present in cytochrome c. Both the reduced (Fe(II)) and oxidized (Fe(III)) forms have been analyzed. The simplest models (1R and 1O, respectively) consist of a unsubstituted porphyrin (with no side chains) and two axially coordinated imidazole and ethylmethylthioether ligands. Density functional theory optimizations of these models confirm the basic electronic features and are the starting point for building more complex derivatives. AIMD simulations were performed after reaching the thermal stability at T = 300 K. The evolution of the Fe-L(ax) bond strengths is examined together with the relative rotations of the imidazole and methionine about the axial vector, which appear rather independent from each other. The next models (2R and 2O) contain side chains at the heme to better simulate the actual active site. It is observed that two adjacent propionate groups induce some important effects. The axial Fe-Sdelta bond is only weakened in 2R but is definitely cleaved in the oxidized species 2O. Also the mobility of the Im ligand seems to be reduced by the formation of a strong hydrogen bond that involves the Im Ndelta1-Hdelta1 bond and one carboxylate group. In 2O the interaction becomes so strong that a proton transfer occurs and the propionic acid is formed. Finally, the models 3 include a free N-methyl-acetamide molecule to mimic a portion of the protein backbone. This influences the orientation of carboxylate groups and limits the amount of their hydrogen bonding with the Im ligand. Residual electrostatic interactions are maintained, which are still able to modulate the dissociation of the methionine from the heme.
Efficient conformational space exploration in ab initio protein folding simulation
Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A. Z. M. Dayem; Rahman, M. Sohel
2015-01-01
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554
Ab initio molecular dynamics of liquid hydrogen chloride
NASA Astrophysics Data System (ADS)
Dubois, Vincent; Pasquarello, Alfredo
2005-03-01
We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (ℓ-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)2 dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in ℓ-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.
The hydration structure of carbon monoxide by ab initio methods
NASA Astrophysics Data System (ADS)
Awoonor-Williams, Ernest; Rowley, Christopher N.
2017-01-01
The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO-H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration using the TIP3P water model is in good agreement with the experiment (9.3 kJ mol-1 expt. vs 10.7 kJ mol-1 calc.). The calculated diffusivity of CO (aq) in TIP3P-model water was 5.1 ×10-5 cm2/s calc., more than double the experimental value of 2.3 ×10-5 cm2/s. The hydration energy calculated using the TIP4P-FB water model is in poorer agreement with the experiment (ΔG = 6.8 kJ/mol) but the diffusivity is in better agreement (D =2.5 ±0.1 ×10-5 cm2/s).
Cosmic-Ray Modulation: an Ab Initio Approach
NASA Astrophysics Data System (ADS)
Engelbrecht, N. E.; Burger, R. A.
2014-10-01
A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three-dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented.
Ab initio valence-space theory for exotic nuclei
NASA Astrophysics Data System (ADS)
Holt, Jason
2015-10-01
Recent advances in ab initio nuclear structure theory have led to groundbreaking predictions in the exotic medium-mass region, from the location of the neutron dripline to the emergence of new magic numbers far from stability. Playing a key role in this progress has been the development of sophisticated many-body techniques and chiral effective field theory, which provides a systematic basis for consistent many-nucleon forces and electroweak currents. Within the context of valence-space Hamiltonians derived from the nonperturbative in-medium similarity renormalization group (IM-SRG) approach, I will discuss the importance of 3N forces in understanding and making new discoveries in the exotic sd -shell region. Beginning in oxygen, we find that the effects of 3N forces are decisive in explaining why 24O is the last bound oxygen isotope, validating first predictions of this phenomenon from several years ago. Furthermore, 3N forces play a key role in reproducing spectroscopy, including signatures of doubly magic 22,24O, and physics beyond the dripline. Similar improvements are obtained in new spectroscopic predictions for exotic fluorine and neon isotopes, where agreement with recent experimental data is competitive with state-of-the-art phenomenology. Finally, I will discuss first applications of the IM-SRG to effective valence-space operators, such as radii and E 0 transitions, as well as extensions to general operators crucial for our future understanding of electroweak processes, such as neutrinoless double-beta decay. This work was supported by NSERC and the NRC Canada.
AN AB INITIO MODEL FOR COSMIC-RAY MODULATION
Engelbrecht, N. E.; Burger, R. A.
2013-07-20
A proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays (CRs) is of vital importance for a better understanding of CR modulation in the heliosphere. This study presents an ab initio model for CR modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for solar minimum heliospheric conditions, utilizing boundary values chosen so that model results are in reasonable agreement with spacecraft observations of turbulence quantities in the solar ecliptic plane and along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modeled slab and two-dimensional (2D) turbulence energy spectra. The modeled 2D spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers. There currently exist no models or observations for the wavenumber where this drop-off occurs, and it is considered to be the only free parameter in this study. The modeled spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on CR drifts are modeled in a self-consistent way, also employing a recently developed model for wavy current sheet drift. The resulting diffusion and drift coefficients are applied to the study of galactic CR protons and antiprotons using a 3D, steady-state CR modulation code, and sample solutions in fair to good agreement with multiple spacecraft observations are presented.
Efficient conformational space exploration in ab initio protein folding simulation.
Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel
2015-08-01
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.
Ab initio calculations of ^12C and neutron drops
NASA Astrophysics Data System (ADS)
Pieper, Steven C.
2009-10-01
Ab initio calculations of nuclei, which treat a nucleus as a system of A nucleons interacting by realistic two- and three-nucleon forces, have made tremendous progress in the last 15 years. This is a result of better Hamiltonians, rapidly increasing computer power, and new or improved many-body methods. Three methods are principally being used: Green's function Monte Carlo (GFMC), no-core shell model, and coupled cluster. In the limit of large computer resources, all three methods produce exact eigenvalues of a given nuclear Hamiltonian. With DOE SciDAC and INCITE support, all three methods are using the largest computers available today. Under the UNEDF SciDAC grant, the Argonne GFMC program was modified to efficiently use more than 2000 processors. E. Lusk (Argonne), R.M. Butler (Middle Tennessee State U.) and I have developed an Asynchronous Dynamic Load-Balancing (ADLB) library. In addition all the cores in a node are used via OpenMP as one ADLB/MPI client. In this way we obtain very good scalability up to 30,000 processors on Argonne's IBM Blue Gene/P. Two systems of particular interest that require this computer power are ^12C and neutron drops. V.R. Pandharipande (UIUC, deceased), J. Carlson (LANL), R.B. Wiringa (Argonne), and I have developed new trial wave functions that explicitly contain the three-alpha particle structure of ^12C. These are being used with the Argonne V18 and Illinois-7 potentials which reproduce the energies of 51 states in 3<=A<=12 nuclei with an rms error of 600,eV. Neutron drops are collections of neutrons confined in an artificial external well and interacting with realistic NN and NNN potentials. Their properties can be used as ``experimental data'' for developing energy-density functionals.
Resonance and aromaticity: an ab initio valence bond approach.
Rashid, Zahid; van Lenthe, Joop H; Havenith, Remco W A
2012-05-17
Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randić's conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.
Uniaxial phase transition in Si: Ab initio calculations
NASA Astrophysics Data System (ADS)
Cheng, C.
2003-04-01
Based on a previously proposed thermodynamic analysis, [C. Cheng, W. H. Huang, and H. J. Li, Phys. Rev. B 63, 153202 (2001)] we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, βSn, simple-hexagonal (sh), simple-cubic, and hexagonal closed-packed structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different contributions to the relative phase stability, we identified the most important factors in reducing the phase-transition pressures at uniaxial compression. We also show that it is possible to have phase transitions occur only when the phases are under uniaxial compression, in spite of no phase transition when under hydrostatic compression. Taking all five phases into consideration, the phase diagram at uniaxial compression was constructed for pressures up to 20 GPa. The stable phases were found to be diamond, βSn, and sh structures, i.e., the same as those when under hydrostatic condition. According to the phase diagram, direct phase transition from the diamond to the sh phase is possible if the applied uniaxial pressures, on increasing, satisfy the condition Px>Pz. Similarly, the sh-to-βSn transition on increasing pressures is also possible if the applied uniaxial pressures are varied from the condition of Px>Pz, on which the phase of sh is stable to the condition Px
Mugnaioli, Enrico; Gemmi, Mauro; Merlini, Marco; Gregorkiewitz, Michele
2016-01-01
(Nax□1 − x)5[MnO2]13 has been synthesized with x = 0.80 (4), corresponding to Na0.31[MnO2]. This well known material is usually cited as Na0.4[MnO2] and is believed to have a romanèchite-like framework. Here, its true structure is determined, ab initio, by single-crystal electron diffraction tomography (EDT) and refined both by EDT data applying dynamical scattering theory and by the Rietveld method based on synchrotron powder diffraction data (χ2 = 0.690, R wp = 0.051, R p = 0.037, R F2 = 0.035). The unit cell is monoclinic C2/m, a = 22.5199 (6), b = 2.83987 (6), c = 14.8815 (4) Å, β = 105.0925 (16)°, V = 918.90 (4) Å3, Z = 2. A hitherto unknown [MnO2] framework is found, which is mainly based on edge- and corner-sharing octahedra and comprises three types of tunnels: per unit cell, two are defined by S-shaped 10-rings, four by egg-shaped 8-rings, and two by slightly oval 6-rings of Mn polyhedra. Na occupies all tunnels. The so-determined structure excellently explains previous reports on the electrochemistry of (Na,□)5[MnO2]13. The trivalent Mn3+ ions concentrate at two of the seven Mn sites where larger Mn—O distances and Jahn–Teller distortion are observed. One of the Mn3+ sites is five-coordinated in a square pyramid which, on oxidation to Mn4+, may easily undergo topotactic transformation to an octahedron suggesting a possible pathway for the transition among different tunnel structures. PMID:27910840
Surface segregation in AuPd alloys: Ab initio analysis of the driving forces
NASA Astrophysics Data System (ADS)
Creuze, Jérôme; Guesmi, Hazar; Mottet, Christine; Zhu, Beien; Legrand, Bernard
2015-09-01
In order to determine the energetic driving forces for surface segregation in AuPd alloys, we use a combined approach coupling ab initio calculations and an analysis via an effective Ising model. Previously, this approach has been used successfully in the framework of N-body interatomic potentials to study the surface segregation in both semi-infinite alloys and nanoparticles, allowing one to determine the relative contributions of the different elementary driving forces. Here, we go beyond the use of N-body interatomic potentials by using ab initio calculations to evaluate the segregation enthalpy and the effective pair interactions, the contribution due to the size difference between the constituants being still obtained by N-body interatomic potentials. We show that the decomposition of the segregation enthalpy into its different elementary contributions is still valid at this level of description. This allows us to analyze the segregation driving forces in the two infinite dilute limits of the Au-Pd system, for both (100) and (111) surfaces. Finally, between the two infinite dilute limits, we find that our results are consistent with existing experimental data.
Ab initio study of hydrous Mg- and Si- vacancies in forsterite: their stability and IR signatures
NASA Astrophysics Data System (ADS)
Qin, T.; Umemoto, K.; Wentzcovitch, R. M.; Hirschmann, M. M.; Kohlstedt, D. L.
2016-12-01
In addition to well-known hydrous phases, water or hydrogen in the mantle can be stored as hydrous defects in major mantle minerals, that is, the nominally anhydrous minerals (NAMs). Though in relatively small amounts, these defects change the physical properties of their hosts, including electrical conductivity and viscosity, properties that affect mantle processes such as convection. To understand the influence of water on mantle properties, the mechanisms of water incorporation in olivine, the most voluminous mineral in the upper mantle, must be determined. Several water incorporation mechanisms in olivine are possible, but the most likely ones are hydrogen ions substituting for Mg and Si cations. In forsterite, the Mg end member, a long-standing debate remains concerning the relative thermodynamic stability of these defects. In this study, we reinvestigate the energetics of two of these defects - (4H·)Six and (2H·)Mgx - in forsterite using ab initio calculations. We conclude that proper identification of the configurations of these defects is essential to determining their entropies and relative stability. We identify several new defect configurations that can resolve the long standing (apparent) paradox regarding their relative stability exposed by previous ab initio calculations. IR frequencies for these new configurations are also computed to help their identification in measured IR spectra.
Ab initio SCF MO study of the chemisorption of methane on Al and La oxide surfaces
Capitan, M.J.; Odriozola, J.A.; Marquez, A.
1995-10-01
A theoretical approach to the rate-determining step for methane activation on Al and La oxides has been performed by means of ab initio quantum mechanical calculations. In a first approach, transition states and products for the heterolytic chemisorption of CH{sub 4} on Al(OH){sub 3} and La(OH){sub 3} molecules have been determined at the RHF-SCF level of theory. Transition-state structures correspond to a four-center interaction with an energy barrier of about 40 kcal/mol. This high activation barrier supports the heterolytic mechanism proposed for this reaction. The products are methyl-metal compounds, CH{sub 3}-Me(Me= Al, La), with the carbon atom negatively charged. Catalytic surfaces have been modeled by introducing the effects due to the lattice through both point charges and ab initio model potentials. The selectivity of these catalysts towards C2 is discussed on the grounds of the differences found for the relative stability of the methy-metal intermediates. 42 refs., 4 figs., 2 tabs.
An investigation of ab initio shell-model interactions derived by no-core shell model
NASA Astrophysics Data System (ADS)
Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing
2016-09-01
The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.
2014-08-20
Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules The focus of this research was to apply efficient...methods for using ab initio potential energy surfaces (PESs) computed with high levels of quantum chemistry theory to predict chemical reaction properties...in non peer-reviewed journals: Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules Report
Ab initio study of weakly bound halogen complexes: RX⋯PH3.
Georg, Herbert C; Fileti, Eudes E; Malaspina, Thaciana
2013-01-01
Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range -4.14 to -11.92 kJ mol(-1) (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27% in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl⋯PH3 and all MeX⋯PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7-6.7 u.a. (about 3-7%).
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.
Han, Huixian; Li, Anyang; Guo, Hua
2014-12-28
A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S{sub 0}) electronic state has been constructed by fitting ∼37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm{sup −1}. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm{sup −1} above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.
A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.
Voss, Neil R; Lyumkis, Dmitry; Cheng, Anchi; Lau, Pick-Wei; Mulder, Anke; Lander, Gabriel C; Brignole, Edward J; Fellmann, Denis; Irving, Christopher; Jacovetty, Erica L; Leung, Albert; Pulokas, James; Quispe, Joel D; Winkler, Hanspeter; Yoshioka, Craig; Carragher, Bridget; Potter, Clinton S
2010-03-01
Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a "toolbox" of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map.
Ab initio study of intrinsic profiles of liquid metals and their reflectivity
NASA Astrophysics Data System (ADS)
del Rio, B. G.; Souto, J.; Alemany, M. M. G.; González, L. E.
2017-08-01
The free surfaces of liquid metals are known to exhibit a stratified profile that, in favourable cases, shows up in experiments as a peak in the ratio between the reflectivity function and that of an ideal step-like profile. This peak is located at a wave-vector related to the distance between the layers of the profile. In fact the surface roughness produced by thermally induced capillary waves causes a depletion of the previous so called intrinsic reflectivity by a damping factor that may hinder the observation of the peak. The behaviour of the intrinsic reflectivity below the layering peak is however far from being universal, with systems as Ga or In where the reflectiviy falls uniformly towards the q → 0 value, others like Sn or Bi where a shoulder appears at intermediate wavevectors, and others like Hg which show a minimum. We have performed extensive ab initio simulations of the free liquid surfaces of Bi, Pb and Hg, that yield direct information on the structure of the profiles and found that the macroscopic capillary wave theory usually employed in order to remove the capillary wave components fails badly in some cases for the typical sample sizes affordable in ab initio simulations. However, a microscopic method for the determination of the intrinsic profile is shown to be succesful in obtaining meaningful intrinsic profiles and corresponding reflectivities which reproduce correctly the qualitative behaviour observed experimentally.
Ab initio simulations of phase stability and martensitic transitions in NiTi
NASA Astrophysics Data System (ADS)
Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.
2016-12-01
For NiTi-based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. We show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing phase transformation temperatures is discussed.
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)
1996-01-01
Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within +/- 8 cm(sup -1) on average, and molecular bond distances are accurate to within +/- 0.001-0.003 A, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as rovibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy win be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.
Optimized unrestricted Kohn-Sham potentials from ab initio spin densities
NASA Astrophysics Data System (ADS)
Boguslawski, Katharina; Jacob, Christoph R.; Reiher, Markus
2013-01-01
The reconstruction of the exchange-correlation potential from accurate ab initio electron densities can provide insights into the limitations of the currently available approximate functionals and provide guidance for devising improved approximations for density-functional theory (DFT). For open-shell systems, the spin density is introduced as an additional fundamental variable in spin-DFT. Here, we consider the reconstruction of the corresponding unrestricted Kohn-Sham (KS) potentials from accurate ab initio spin densities. In particular, we investigate whether it is possible to reconstruct the spin exchange-correlation potential, which determines the spin density in unrestricted KS-DFT, despite the numerical difficulties inherent to the optimization of potentials with finite orbital basis sets. We find that the recently developed scheme for unambiguously singling out an optimal optimized potential [Ch. R. Jacob, J. Chem. Phys. 135, 244102 (2011), 10.1063/1.3670414] can provide such spin potentials accurately. This is demonstrated for two test cases, the lithium atom and the dioxygen molecule, and target (spin) densities from full configuration interaction and complete active space self-consistent field calculations, respectively.
Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.
NASA Astrophysics Data System (ADS)
Yusuf, Muhammad; Sitepu, Deby Elfrinasti Br
2017-01-01
The computational calculation on the acetalization of benzaldehyde using acid catalysts (HCl) with computational method (Ab-Initio) has been done. The aim of this research was to studies the mechanism of benzaldehyde acetalization. The studies focus on the energy changes in the reaction coordinate. All geometry optimizations on the model of acetalization of benzaldehyde were performed with Hyperchem 8.0 (windows version) to the ab initio method using 3-21G and 6-31G* basis set. All optimized structures were also visualized by hyperchem 8.0. Based on the computational calculations, Hemiacetal 3 showed the highest energy among the others due to its lability (1399.6 kJ/mol). This step also could become as the rate determining step due to its rate which is the slowest among the others reaction. In addition, benzaldehyde dimethyl acetal (7) showed the lowest energy among the others(-6.8 kJ/mol) due to its stability which was the highest among the others.
Iyengar, Srinivasan S; Jakowski, Jacek
2005-03-15
A methodology to efficiently conduct simultaneous dynamics of electrons and nuclei is presented. The approach involves quantum wave packet dynamics using an accurate banded, sparse and Toeplitz representation for the discrete free propagator, in conjunction with ab initio molecular dynamics treatment of the electronic and classical nuclear degree of freedom. The latter may be achieved either by using atom-centered density-matrix propagation or by using Born-Oppenheimer dynamics. The two components of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. The quantum wave packet dynamics is made computationally robust by using adaptive grids to achieve optimized sampling. One notable feature of the approach is that important quantum dynamical effects including zero-point effects, tunneling, as well as over-barrier reflections are treated accurately. The electronic degrees of freedom are simultaneously handled at accurate levels of density functional theory, including hybrid or gradient corrected approximations. Benchmark calculations are provided for proton transfer systems and the dynamics results are compared with exact calculations to determine the accuracy of the approach.
Polyatomic ab Initio Complex Potential Energy Surfaces: Illustration of Ultracold Collisions.
Bhattacharya, Debarati; Ben-Asher, Anael; Haritan, Idan; Pawlak, Mariusz; Landau, Arie; Moiseyev, Nimrod
2017-03-29
Resonances are metastable states that decay after a finite period of time. These states play a role in many physical processes. For example, in recent cold collision experiments, autoionization from a resonance state was observed. Complementing such observations with theory provides insight into the reaction dynamics under study. Theoretical investigation of autoionization processes is enabled via complex potential energy surfaces (CPESs), where the real and imaginary parts, respectively, provide the energy and decay rate of the system. Unfortunately, calculation of ab initio polyatomic CPESs are cumbersome; hence, they are not in abundance. Here, we present an ab initio polyatomic CPES utilizing a recently developed approach, which makes such calculations feasible. This CPES helps interpret the autoionization process observed in the He(2(3)S) + H2 collision. From the behavior of the calculated CPES we can conclusively determine the nature of the autoionization process. Moreover, this CPES was used to generate reaction rates for the collision of He with ortho- and para-H2. These reaction rates are obtained from first principles. The results show a remarkable agreement with the cold collision experimental measurements, which demonstrates the robustness of our method. Hereby, we provide a computational tool for designing and interpreting new types of experiments that involve resonance states, e.g., in nucleobase damages (DNA or RNA) or in interatomic (intermolecular) Coulombic decay.
A Toolbox for Ab Initio 3-D Reconstructions in Single-particle Electron Microscopy
Voss, Neil R; Lyumkis, Dmitry; Cheng, Anchi; Lau, Pick-Wei; Mulder, Anke; Lander, Gabriel C; Brignole, Edward J; Fellmann, Denis; Irving, Christopher; Jacovetty, Erica L; Leung, Albert; Pulokas, James; Quispe, Joel D; Winkler, Hanspeter; Yoshioka, Craig; Carragher, Bridget; Potter, Clinton S
2010-01-01
Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a “toolbox” of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map. PMID:20018246
Ab initio structure prediction of the antibody hypervariable H3 loop.
Zhu, Kai; Day, Tyler
2013-06-01
Antibodies have the capability of binding a wide range of antigens due to the diversity of the six loops constituting the complementarity determining region (CDR). Among the six loops, the H3 loop is the most diverse in structure, length, and sequence identity. Prediction of the three-dimensional structures of antibodies, especially the CDR loops, is an important step in the computational design and engineering of novel antibodies for improved affinity and specificity. Although it has been demonstrated that the conformation of the five non-H3 loops can be accurately predicted by comparing their sequences against databases of canonical loop conformations, no such connection has been established for H3 loops. In this work, we present the results for ab initio structure prediction of the H3 loop using conformational sampling and energy calculations with the program Prime on a dataset of 53 loops ranging in length from 4 to 22 residues. When the prediction is performed in the crystal environment and including symmetry mates, the median backbone root mean square deviation (RMSD) is 0.5 Å to the crystal structure, with 91% of cases having an RMSD of less than 2.0 Å. When the prediction is performed in a noncrystallographic environment, where the scaffold is constructed by swapping the H3 loops between homologous antibodies, 70% of cases have an RMSD below 2.0 Å. These results show promise for ab initio loop predictions applied to modeling of antibodies.
Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.
Chen, Chung-De; Huang, Yen-Chieh; Chiang, Hsin-Lin; Hsieh, Yin-Cheng; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Chen, Chun-Jung
2014-09-01
A novel direct phase-selection method to select optimized phases from the ambiguous phases of a subset of reflections to replace the corresponding initial SAD phases has been developed. With the improved phases, the completeness of built residues of protein molecules is enhanced for efficient structure determination. Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ{sub 1} and ϕ{sub 2}) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ{sub DS} list as a criterion to select optimized phases ϕ{sub am} from ϕ{sub 1} or ϕ{sub 2} of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕ{sub SAD} has been developed. Based on this work, reflections with an angle θ{sub DS} in the range 35–145° are selected for an optimized improvement, where θ{sub DS} is the angle between the initial phase ϕ{sub SAD} and a preliminary density-modification (DM) phase ϕ{sub DM}{sup NHL}. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.
Threshold displacement energy in GaN; Ab initio molecular dynamics study
Xiao, H. Y.; Gao, Fei; Zu, Xiaotao T.; Weber, William J.
2009-06-25
Large-scale ab initio molecular dynamics method has been used to determine the threshold displacement energies, Ed, along five specific directions and to determine the defect configurations created during low energy events. The Ed shows a significant dependence on direction. The minimum Ed is determined to be 39 eV along the <-1010> direction for a gallium atom and 17.0 eV along the <-1010> direction for a nitrogen atom, which are in reasonable agreement with the experimental measurements. The average Ed values determined are 73.2 and 32.4 eV for gallium and nitrogen atoms, respectively. The N defects created at low energy events along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed in GaN.
ab initio MD simulations of geomaterials with ~1000 atoms
NASA Astrophysics Data System (ADS)
Martin, G. B.; Kirtman, B.; Spera, F. J.
2009-12-01
In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in
Ab initio computational applications to complex biomolecular systems
NASA Astrophysics Data System (ADS)
Liang, Lei
A series of biomaterial related systems---including water and DNA molecules---have been studied using ab initio (first-principles) methods. By investigating the properties of water as the preliminary step, the hydrogen bond (HB) interactions, which play important roles in biomolecules, were better understood from the quantum mechanical viewpoint. The calculated K-edge x-ray absorption near edge structure (XANES) spectra of all 340 oxygen atoms in the model have been accumulated to reproduce the experimental one. The spectra were shown to be very sensitive to the HB configurations of O atoms, which could be used to elucidate the subtle structural variations in complex biomolecules. The simulation of single-molecule DNA overstretching experiments under torsionally constrained condition has been carried out afterwards. The initial DNA models were stretched stepwisely and eventually gained an extension of 1.5-fold (150% x the original length). The variation of total energy, atomic configuration, and the electronic structure during this process were analyzed in details. At the extension of ˜1.3-fold, the ring opening reactions occurred in the backbones. The backbone nicks appeared at elongations of ˜1.40-fold. The whole process was accompanied by HB breaking and charge transfers. We have proposed an overstretched structure named O-DNA (Opened-DNA) to clarify the confusion in understanding the behavior of DNA under high force load. With more experiences gained, a comprehensive methodology revealing the underlying principles of bioprocesses from the quantum mechanical viewpoint eventually come up. For the purpose of better computational accuracy, the scheme of implementing the generalized gradient approximation (GGA) exchange-correlation functionals into the Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) program suite has been discussed, and the computational efficiency has been analyzed correspondingly. Moreover, the parallel strategy for performing
Ab initio study of the optical properties of carbon nanotubes
NASA Astrophysics Data System (ADS)
Chang, Eric
2006-03-01
We present an ab initio study of the optical properties of carbon nanotubes. We use state-of-the-art electronic structure methods based on many-body perturbation theory to compute the optical absorption and resonance Raman spectra of large tubes which have up to 200 atoms [1,2]. Our symmetry-based method makes the study of large tubes feasible within the many- body framework and also allows us to understand the symmetry properties of the excitons and selection rules. We include a study of the so-called dark excitons which are crucial for understanding luminescence efficiency in carbon nanotubes. The mechanism that explains the dark-bright splitting can be understood within our symmetry-based approach. Finally, we present an analysis of the two-photon spectra for several carbon nanotubes, a theoretical analysis which, in conjunction with combined one- and two-photon experiments, allows one to measure the binding energy of excitons. We find in all cases that the excitonic binding energy is large, ranging from 0.5 to 0.9 eV depending on the diameter of the tube, and that the excitonic wavefunction is Wannier-like and extended over many atoms. Our studies for the one- and two-photon absorption and resonance Raman spectra have been fruitful for understanding the corresponding experiments. In particular, our theoretical results are in good agreement with one- and two-photon absorption experiments [3-5]. The results for resonance Raman show that such a spectroscopic technique is a good alternative to optical absorption since it allows for the selection of tubes of a given diameter while probing the same excited states. 1. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. Lett. 92, 196401 (2004). 2. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. B 72, 195423 (2005). 3. M. Y. Sfeir et al., Science 306, 1540 (2004). 4. J. Maultzsch et al., to be published in Phys. Rev. B, see also cond-mat/0505150. 5. Z. M. Li et. al., Phys. Rev. Lett. 87, 127401 (2001).
NASA Astrophysics Data System (ADS)
Malbon, Christopher L.; Zhu, Xiaolei; Guo, Hua; Yarkony, David R.
2016-12-01
For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian Hd (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the Hd by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding Hd determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.
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.
Autrey, Tom; Brown, Aaron K; Camaioni, Donald M; Dupuis, Michel; Foster, Nancy S; Getty, April
2004-03-31
Photoacoustic signals from dilute ( approximately 30 mM) solutions of H2O2 were measured over the temperature range from 10 to 45 degrees C to obtain the reaction enthalpy and volume change for H2O2(aq) --> 2 OH(aq) from which we ultimately determined DeltafG degrees , DeltafH degrees and partial molal volume, v degrees , of OH (aq). We find DeltarH = 46.8 +/- 1.4 kcal/mol, which is 4 kcal/mol smaller than the gas-phase bond energy, and DeltaVr = 6.5 +/- 0.4 mL/mol. The v degrees for OH in water is 14.4 +/- 0.4 mL/ml: smaller than the v degrees of water. Using ab intio continuum theory, the hydration free energy is calculated to be -3.9 +/- 0.3 kcal/mol (for standard states in number density concentration units) by a novel approach devised to capture in the definition of the solute cavity the strength and specific interactions of the solute with a water solvent molecule. The shape of the cavity is defined by "rolling" a three-dimensional electron density isocontour of water on the ab initio water-OH minimum interaction surface. The value of the contour is selected to reproduce the volume of OH in water. We obtain for OH(aq): DeltafH degrees = -0.2 +/- 1.4 and DeltafG degrees = 5.8 +/- 0.4 kcal/mol that are in agreement with literature values. The results provide confidence in the pulsed PAC technique for measuring aqueous thermochemistry of radicals and open the way to obtaining thermochemistry for most radicals that can be formed by reaction of OH with aqueous substrates while advancing the field of continuum solvation theory toward ab initio-defined solute cavities.
An ab initio-based Er–He interatomic potential in hcp Er
Yang, Li; ye, Yeting; Fan, K. M.; Shen, Huahai; Peng, Shuming; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei
2014-09-01
We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations. The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.
Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening
NASA Astrophysics Data System (ADS)
de Jonge, Marc R.; Vinkers, H. Maarten; van Lenthe, Joop H.; Daeyaert, Frits; Bush, Ian J.; van Dam, Huub J. J.; Sherwood, Paul; Guest, Martyn F.
2007-09-01
We present a new and completely parallel method for protein ligand docking. The potential of the docking target structure is obtained directly from the electron density derived through an ab initio computation. A large subregion of the crystal structure of Isocitrate Lyase, was selected as docking target. To allow the full ab initio treatment of this region special care was taken to assign optimal basis functions. The electrostatic potential is tested by docking a small charged molecule (succinate) into the binding site. The ab initio grid yields a superior result by producing the best binding orientation and position, and by recognizing it as the best. In contrast the same docking procedure, but using a classical point-charge based potential, produces a number of additional incorrect binding poses, and does not recognize the correct pose as the best solution.
Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization
NASA Astrophysics Data System (ADS)
Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng
With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.
Global exploration of the energy landscape of solids on the ab initio level.
Doll, K; Schön, J C; Jansen, M
2007-12-14
Predicting which crystalline modifications can be present in a chemical system requires the global exploration of its energy landscape. Due to the large computational effort involved, in the past this search for sufficiently stable minima has been performed employing a variety of empirical potentials and cost functions followed by a local optimization on the ab initio level. However, this entails the risk of overlooking important modifications that are not modeled accurately using empirical potentials. In order to overcome this critical limitation, we develop an approach to employ ab initio energy functions during the global optimization phase of the structure prediction. As an example, we perform a global exploration of the landscape of LiF on the ab initio level and show that the relevant crystalline modifications are found during the search.
Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.
2015-02-01
Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. 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.
Classical and ab-initio molecular dynamic simulation of an amorphous silica surface
NASA Astrophysics Data System (ADS)
Mischler, C.; Kob, W.; Binder, K.
2002-08-01
We present the results of a classical molecular dynamic simulation as well as of an ab-initio molecular dynamic simulation of an amorphous silica surface. In the case of the classical simulation we use the potential proposed by van Beest et al. (BKS) whereas the ab-initio simulation is done with a Car-Parrinello method (CPMD). We find that the surfaces generated by BKS have a higher concentration of defects (e.g., concentration of two-membered rings) than those generated with CPMD. In addition also the distribution functions of the angles and of the distances are different for the short rings. Hence we conclude that whereas the BKS potential is able to correctly reproduce the surface on the length scale beyond ≈5 Å, it is necessary to use an ab-initio method to reliably predict the structure at small scales.
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.
Ab initio potential energy surfaces describing the interaction of CH(X2Π) with H2
NASA Astrophysics Data System (ADS)
Dagdigian, Paul J.
2016-09-01
We have determined four-dimensional ab initio quasi-diabatic potential energy surfaces describing the interaction of CH(X2Π) with H2, under the assumption of fixed CH and H2 internuclear separations. These calculations employed the multi-reference configuration interaction method [MRCISD+Q(Davidson)]. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants.
Ab Initio Calculations and Synthesis of Sc2InC-Y2InC Solid Solution
2010-02-03
tribological materials. It will study a solid solution of this fascinating new class of nanolaminated materials using both theoretical and experimental means...Sc2InC-Y2InC solid solution using ab initio calculations and 2) to synthesize Sc2InC-Y2InC thin films using magnetron sputtering and to determine the correlation between composition, structure, and mechanical properties thereof.
Ab initio potential energy surface and vibration-rotation energy levels of sulfur dioxide.
Koput, Jacek
2017-05-05
An accurate potential energy surface of sulfur dioxide, SO2 , in its ground electronic state X∼ 1A1 has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent basis sets up to septuple-zeta quality. The results obtained with the conventional and explicitly correlated coupled-cluster methods are compared. The role of the core-electron correlation, higher-order valence-electron correlation, scalar relativistic, and adiabatic effects in determining the structure and dynamics of the SO2 molecule is discussed. The vibration-rotation energy levels of the (32) SO2 and (34) SO2 isotopologues were predicted using a variational approach. It was shown that the inclusion of the aforementioned effects was mandatory to attain the "spectroscopic" accuracy. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules
NASA Astrophysics Data System (ADS)
Zheng, Haoping
The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with precise calculations. Thus the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule has become a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), will be presented in this paper. The reactive sites of the inhibitors are determined and explained. The accuracy of structure determination of the inhibitors are tested theoretically.
Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules
NASA Astrophysics Data System (ADS)
Zheng, Haoping
2003-04-01
The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with unchanged calculation precision. So the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule becomes a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the Ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), are presented. The reactive sites of the inhibitors are determined and explained. The precision of structure determination of inhibitors are tested theoretically.
Quantum fluctuations and isotope effects in ab initio descriptions of water
Wang, Lu; Markland, Thomas E.; Ceriotti, Michele
2014-09-14
Isotope substitution is extensively used to investigate the microscopic behavior of hydrogen bonded systems such as liquid water. The changes in structure and stability of these systems upon isotope substitution arise entirely from the quantum mechanical nature of the nuclei. Here, we provide a fully ab initio determination of the isotope exchange free energy and fractionation ratio of hydrogen and deuterium in water treating exactly nuclear quantum effects and explicitly modeling the quantum nature of the electrons. This allows us to assess how quantum effects in water manifest as isotope effects, and unravel how the interplay between electronic exchange and correlation and nuclear quantum fluctuations determine the structure of the hydrogen bond in water.
Quantum fluctuations and isotope effects in ab initio descriptions of water.
Wang, Lu; Ceriotti, Michele; Markland, Thomas E
2014-09-14
Isotope substitution is extensively used to investigate the microscopic behavior of hydrogen bonded systems such as liquid water. The changes in structure and stability of these systems upon isotope substitution arise entirely from the quantum mechanical nature of the nuclei. Here, we provide a fully ab initio determination of the isotope exchange free energy and fractionation ratio of hydrogen and deuterium in water treating exactly nuclear quantum effects and explicitly modeling the quantum nature of the electrons. This allows us to assess how quantum effects in water manifest as isotope effects, and unravel how the interplay between electronic exchange and correlation and nuclear quantum fluctuations determine the structure of the hydrogen bond in water.
Impact and penetration studies: Simplified models and materials design from ab initio methods
NASA Astrophysics Data System (ADS)
Jiang, Tianci
In recent impact and penetration mechanical tests, steel projectiles (AISI4340) were impacted into targets like concrete with striking velocities (1200 m/s to 1500 m/s). Results indicated a material removal from the nose of the projectile, phase changes of the projectile materials, a reduction in the length of the projectile, and a blunting of the nose shape. These observations cannot be explained by current theories and numerical integration code that are used to study impact and penetration mechanics. Thus, the objectives of the thesis research are to (a) formulate and characterize the mechanisms responsible for the material erosion of the impacting projectile and the mass loss from the nose region; and (b) to determine the physical properties of alloy steels that are important to penetration mechanics from ab initio methods. The results can be used to design new projectile materials that can provide the desired penetration characteristics. These objectives are accomplished by investigating two related problems. The first problem is to formulate simplified models that can explain the penetration mechanics. The new models include the varying cross-section nose, changes of yield stress behind the shock wave and high strain rate phase transitions. Nose erosion effects, and time-dependent penetration path can be determined by integrating ODEs. A cavity expansion theory model is used to obtain the target resistance that is responsible slowing and deforming the penetrating projectile. The second problem concerns the determination of the constitutive relations from ab initio methods. The equation of state (EOS) and magnetic moments for alloy steels are investigated by using a special quasirandom structure technique and ab initio methods. Specifically, EOS for an interstitial disordered alloy Fe1-x-yNixCy is developed. First, the EOS of iron and phase transition of iron are studied and validated. Second, Nickel is considered to investigate the substitutional disordered
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.
Ab Initio Green-Kubo Approach for the Thermal Conductivity of Solids
NASA Astrophysics Data System (ADS)
Carbogno, Christian; Ramprasad, Rampi; Scheffler, Matthias
2017-04-01
We herein present a first-principles formulation of the Green-Kubo method that allows the accurate assessment of the phonon thermal conductivity of solid semiconductors and insulators in equilibrium ab initio molecular dynamics calculations. Using the virial for the nuclei, we propose a unique ab initio definition of the heat flux. Accurate size and time convergence are achieved within moderate computational effort by a robust, asymptotically exact extrapolation scheme. We demonstrate the capabilities of the technique by investigating the thermal conductivity of extreme high and low heat conducting materials, namely, Si (diamond structure) and tetragonal ZrO2 .
Ab initio study of collective excitations in a disparate mass molten salt.
Bryk, Taras; Klevets, Ivan
2012-12-14
Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.
NASA Astrophysics Data System (ADS)
de Boer, K.; Jansen, A. P. J.; van Santen, R. A.
1994-06-01
We have developed a new method for deriving parameters for the shell model of silica polymorphs. All parameters for the shell model are derived in a self-consistent way from ab initio energy surfaces, polarizabilities and dipole moments of small clusters. This yields an ab initio partial charge shell model potential. The predictive power of our potential is demonstrated by presenting predictions for the structure of α-quartz, α-cristobalite, coesite, stishovite and the IR spectrum of α-quartz which are compared with experiment and predictions of the widely used potentials of Jackson and Catlow, and Kramer, Farragher, van Beest and van Santen.
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
Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J
2015-02-01
AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.
Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations
NASA Technical Reports Server (NTRS)
Good, Brian S.
2003-01-01
We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.
Ab initio theory of charge-carrier conduction in ultrapure organic crystals
NASA Astrophysics Data System (ADS)
Hannewald, K.; Bobbert, P. A.
2004-08-01
We present an ab initio description of charge-carrier mobilities in organic molecular crystals of high purity. Our approach is based on Holstein's original concept of small-polaron bands but generalized with respect to the inclusion of nonlocal electron-phonon coupling. By means of an explicit expression for the mobilities as a function of temperature in combination with ab initio calculations of the material parameters, we demonstrate the predictive power of our theory by applying it to naphthalene. The results show a good qualitative agreement with experiment and provide insight into the difference between electron and hole mobilities as well as their peculiar algebraic and anisotropic temperature dependencies.
Khaliullin, Rustam Z; Kühne, Thomas D
2013-10-14
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.
2001-04-01
UNCLASSIFIED Defense Technical Information Center Compilation Part Notice ADP012281 TITLE: Chalcopyrite Magnetic Semiconductors: An Ab-Initio Study...UNCLASSIFIED Mat. Res. Soc. Symp. Proc. Vol. 674 © 2001 Materials Research Society CHALCOPYRITE MAGNETIC SEMICONDUCTORS: AN AB-INITIO STUDY OF THEIR...slight reduction of the total magnetic moment per Mn atom from ’- pB in all the Cd-rich P-based chalcopyrites to -4 p13 in the Mn rich MnGeP 2 and
Ab initio Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions
Goldman, N; Fried, L E; Mundy, C J; Kuo, I W; Curioni, A; Reed, E
2007-07-25
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.
X-ray absorption Debye-Waller factors from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Vila, F. D.; Lindahl, V. E.; Rehr, J. J.
2012-01-01
An ab initio equation of motion method is introduced to calculate the temperature-dependent mean-square vibrational amplitudes σ2 which appear in the Debye-Waller factors in x-ray absorption, x-ray scattering, and related spectra. The approach avoids explicit calculations of phonon modes, and is based instead on calculations of the displacement-displacement time correlation function from ab initio density functional theory molecular dynamics simulations. The method also yields the vibrational density of states and thermal quantities such as the lattice free energy. Illustrations of the method are presented for a number of systems and compared with other methods and experiment.
A density functional and ab initio investigation of the p-aminobenzoic acid molecule
NASA Astrophysics Data System (ADS)
Lago, A. F.; Dávalos, J. Z.; de Brito, A. Naves
2007-08-01
The p-aminobenzoic acid (C 7H 7NO 2) molecule has been investigated at different levels of theory. DFT methods (B3LYP and PBE1PBE), second order Møller-Plesset perturbation theory (MP2) and composite ab initio methods (G3MP2 and CBS) have been employed, in conjunction with large basis sets. Important informations on the electronic structure and thermochemistry of this molecule have been extracted, and the performance of the density functional and ab initio methods has been evaluated, based on the comparison of the calculated and the available experimental data.
NASA Astrophysics Data System (ADS)
Meisel, David D.; Szasz, Csilla; Kero, Johan
2008-06-01
The Arecibo UHF radar is able to detect the head-echos of micron-sized meteoroids up to velocities of 75 km/s over a height range of 80 140 km. Because of their small size there are many uncertainties involved in calculating their above atmosphere properties as needed for orbit determination. An ab initio model of meteor ablation has been devised that should work over the mass range 10-16 kg to 10-7 kg, but the faint end of this range cannot be observed by any other method and so direct verification is not possible. On the other hand, the EISCAT UHF radar system detects micrometeors in the high mass part of this range and its observations can be fit to a “standard” ablation model and calibrated to optical observations (Szasz et al. 2007). In this paper, we present a preliminary comparison of the two models, one observationally confirmable. Among the features of the ab initio model that are different from the “standard” model are: (1) uses the experimentally based low pressure vaporization theory of O’Hanlon (A users’s guide to vacuum technology, 2003) for ablation, (2) uses velocity dependent functions fit from experimental data on heat transfer, luminosity and ionization efficiencies measured by Friichtenicht and Becker (NASA Special Publication 319: 53, 1973) for micron sized particles, (3) assumes a density and temperature dependence of the micrometeoroids and ablation product specific heats, (4) assumes a density and size dependent value for the thermal emissivity and (5) uses a unified synthesis of experimental data for the most important meteoroid elements and their oxides through least square fits (as functions of temperature, density, and/or melting point) of the tables of thermodynamic parameters given in Weast (CRC Handbook of Physics and Chemistry, 1984), Gray (American Institute of Physics Handbook, 1972), and Cox (Allen’s Astrophysical Quantities 2000). This utilization of mostly experimentally determined data is the main reason for
yambo: An ab initio tool for excited state calculations
NASA Astrophysics Data System (ADS)
Marini, Andrea; Hogan, Conor; Grüning, Myrta; Varsano, Daniele
2009-08-01
yambo is an ab initio code for calculating quasiparticle energies and optical properties of electronic systems within the framework of many-body perturbation theory and time-dependent density functional theory. Quasiparticle energies are calculated within the GW approximation for the self-energy. Optical properties are evaluated either by solving the Bethe-Salpeter equation or by using the adiabatic local density approximation. yambo is a plane-wave code that, although particularly suited for calculations of periodic bulk systems, has been applied to a large variety of physical systems. yambo relies on efficient numerical techniques devised to treat systems with reduced dimensionality, or with a large number of degrees of freedom. The code has a user-friendly command-line based interface, flexible I/O procedures and is interfaced to several publicly available density functional ground-state codes. Program summaryProgram title:yambo Catalogue identifier: AEDH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence v2.0 No. of lines in distributed program, including test data, etc.: 149 265 No. of bytes in distributed program, including test data, etc.: 2 848 169 Distribution format: tar.gz Programming language: Fortran 95, C Computer: any computer architecture, running any flavor of UNIX Operating system: GNU/Linux, AIX, Irix, OS/X Has the code been vectorised or parallelized?: Yes RAM: 10-1000 Mbytes Classification: 7.3, 4.4, 7.2 External routines:BLAS ( http://www.netlib.org/blas/) LAPACK ( http://www.netlib.org/lapack/) MPI ( http://www-unix.mcs.anl.gov/mpi/) is optional. BLACS ( http://www.netlib.org/scalapack/) is optional. SCALAPACK ( http://www.netlib.org/scalapack/) is optional. FFTW ( http://www.fftw.org/) is optional. netCDF ( http://www.unidata.ucar.edu/software/netcdf/) is optional. Nature of problem
Parkes, Marie V.; Greathouse, Jeffery A.; Hart, David B.; Sava Gallis, Dorina F.; Nenoff, Tina M.
2016-04-04
The separation of oxygen from nitrogen using metal–organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O_{2} on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O_{2} and N_{2} in the M_{2}(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. Lastly, this unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize the process of multiple guests competitively binding to coordinatively unsaturated metal sites of a MOF.
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: Na9[Ln(W5O18)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 Na9[Ln(W5O18)2] family.
Ab initio study of intrinsic, H and He point defects in hcp-Er
Yang, Li; Peng, SM; Long, XG; Gao, Fei; Heinisch, Howard L.; Kurtz, Richard J.; Zu, Xiaotao T.
2010-03-01
Ab initio calculations based on density functional theory have been performed to determine the properties of self-interstitial atoms (SIAs), vacancies, and single H and He atoms in hcp-Er. The results show that the most stable configuration for an SIA is a basal octahedral (BO) configuration, while the octahedral (O), basal split (BS) and crowdion (C) interstitial configurations are less stable, followed by the split <0001> dumbbell and tetrahedral configurations. For both H and He defects, the formation energy of an interstitial atom is less than that of a substitutional atom in hcp-Er. Furthermore, the tetrahedral interstitial position is more stable than an octahedral position for both He and H interstitials. The hybridization of the He and H defects with Er atoms has been used to explain the relative stabilities of these defects in hcp-Er.
Ab initio study of the anharmonic lattice dynamics of iron at the γ -δ phase transition
NASA Astrophysics Data System (ADS)
Lian, Chao-Sheng; Wang, Jian-Tao; Chen, Changfeng
2015-11-01
We report calculations of phonon dispersions of iron (Fe) at its γ -δ phase transition using a self-consistent ab initio lattice dynamical method in conjunction with an effective magnetic force approach via the antiferromagnetic approximation. Our results show that anharmonic phonon-phonon interactions play a crucial role in stabilizing the δ -Fe phase in the open bcc lattice. In contrast, the lattice dynamics of the close-packed fcc γ -Fe phase are dominated by magnetic interactions. Simultaneous considerations of the lattice anharmonic and magnetic interactions produced temperature-dependent phonon dispersions for δ -Fe and γ -Fe phases in excellent agreement with recent experimental measurements. The present results highlight the key role of lattice anharmonicity in determining the structural stability of iron at high temperatures, which has significant implications for other high-temperature paramagnetic metals like Ce and Pu.
Ab initio potential energy surface and vibration-rotation energy levels of beryllium monohydroxide.
Koput, Jacek
2017-01-05
The accurate potential energy surface of beryllium monohydroxide, BeOH, in its ground electronic state X 2A' has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent core-valence basis sets up to septuple-zeta quality. The higher-order electron correlation, scalar relativistic, and adiabatic effects were taken into account. The BeOH molecule was confirmed to be bent at equilibrium, with the BeOH angle of 141.2° and the barrier to linearity of 129 cm(-1) . The vibration-rotation energy levels of the BeOH and BeOD isotopologues were predicted using a variational approach and compared with recent experimental data. The results can be useful in a further analysis of high-resolution vibration-rotation spectra of these interesting species. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Steinmann, Casper; Fedorov, Dmitri G; Jensen, Jan H
2013-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.
Yu, Kuang; Carter, Emily A
2014-03-28
The density functional theory (DFT)+U method is an efficient and effective way to calculate the ground-state properties of strongly correlated transition metal compounds, with the effective U parameters typically determined empirically. Two ab initio methods have been developed to compute the U parameter based on either constrained DFT (CDFT) or unrestricted Hartree-Fock (UHF) theory. Previous studies have demonstrated the success of both methods in typical open-shell materials such as FeO and NiO. In this Communication we report numerical instability issues that arise for the CDFT method when applied to closed-shell transition metals, by using ZnO and Cu2O as examples. By contrast, the UHF method behaves much more robustly for both closed- and open-shell materials, making it more suitable for treating closed-shell transition metals, as well as main group elements.
Ab Initio Atomic Simulations of Antisite Pair Recovery in Cubic Silicon Carbide
Gao, Fei; Du, Jincheng; Bylaska, Eric J.; Posselt, Matthias; Weber, William J.
2007-05-28
The thermal stability of an antisite pair in 3C-SiC is studied using ab initio molecular dynamics within the framework of density functional theory. The lifetime of the antisite pair configuration is calculated for temperatures between 1800 and 2250 K, and the effective activation energy for antisite pair recombination is determined to be 2.52 eV. The recombination energy path and static energy barrier are also calculated using the nudged elastic band method, along with the dimer method to accurately locate the transition states. The consistency of the results suggests that the antisite pair cannot be correlated with the DI photoluminescence center, as proposed by previously theoretical interpretations. An extended exchange mechanism is found for the antisite pair recombination, and this may be a dominant mechanism for antisite pair recombination and diffusion of impurities in compound semiconductors.
Ab initio simulation of dissolution energy and carbon activity in fcc Fe
NASA Astrophysics Data System (ADS)
Ridnyi, Ya. M.; Mirzoev, A. A.; Mirzaev, D. A.
2017-07-01
The equilibrium structure and properties of fcc iron with a carbon impurity were simulated ab initio using the WIEN2k software package. A procedure is proposed that enables the simulation of the magnetically disordered state of a system within the density functional theory. In the framework of this procedure, the value of the dissolution energy of carbon was calculated, which was 0.25 eV. Interaction energies between carbon atoms in the first, second, and third coordination spheres of each other were also determined, which were E 1 = 0.06 eV, E 2 = 0.1 eV, and E 3 = 0.005 eV. To verify the reliability of the obtained energy values, the activity of carbon was calculated by the Monte Carlo method. A good qualitative agreement of the calculated activity with the experimental data indicates the reliability of the obtained energy parameters.
Ab-initio Study of the Diffusion Mechanisms of Gallium in a Silicon Matrix
NASA Astrophysics Data System (ADS)
Levasseur-Smith, Kevin; Mousseau, Normand
2007-03-01
We present the results of a study into the diffusion mechanisms of Ga defects in crystalline Si. The dominant neutral configurations for single and multi-atom defects are established by ab-initio calculations using the density functional theory in the LDA approximation, with a LCAO basis as implemented in the SIESTA package. We find formation energies of 0.7 eV and 2.9 eV, respectively, for the substitutional and tetrahedral interstitial defects, while the diatomic substitutional-tetrahedral complex has a formation energy of 2.2 eV. Subsequent calculations using this same DFT package in conjunction with the activation relaxation technique (ART nouveau) allow us to determine possible diffusion pathways as well as their corresponding saddle points and energy barriers.
Hydrogen-water mixtures in giant planet interiors studied with ab initio simulations
NASA Astrophysics Data System (ADS)
Soubiran, F.; Militzer, B.
2015-12-01
We study water-hydrogen mixtures under planetary interior conditions using ab initio molecular dynamics simulations. We determine the thermodynamic properties of various water-hydrogen mixing ratios at temperatures of 2000 and 6000 K for pressures of a few tens of GPa. These conditions are relevant for ice giant planets and for the outer envelope of the gas giants. We find that at 2000 K the mixture is in a molecular regime, while at 6000 K the dissociation of hydrogen and water is important and affects the thermodynamic properties. We study the structure of the liquid and analyze the radial distribution function. We provide estimates for the transport properties, diffusion and viscosity, based on autocorrelation functions. We obtained viscosity estimates of the order of a few tenths of mPa s for the conditions under consideration. These results are relevant for dynamo simulations of ice giant planets.
Vibrational infrared spectrum of NH 3 adsorbed on MgO(100). I. Ab initio calculations
NASA Astrophysics Data System (ADS)
Allouche, A.; Corà, F.; Girardet, C.
1995-12-01
The perturbed cluster approach, previously devoted to the calculation of the stable adsorption site and energy for ammonia adsorbed on MgO(100), is used to determine the frequency and the intensity of the main peaks associated with the normal vibrational modes of the admolecule. The ab initio model based on a cluster embedded in an array of point charges is then compared to the perturbed cluster approach and used to investigate different molecular orientations and associations on the surface in order to give an interpretation to the occurrence of the infrared signals. Six normal modes for each admolecule are calculated due to the removing of internal degeneracy by adsorption. The characteristics of the calculated spectrum are compared to the experimental infrared data and it is shown that the set of selected situations is able to explain almost every band in the spectrum without implication of NH 3 dissociation on the surface.
NASA Astrophysics Data System (ADS)
Mazzola, Guglielmo; Sorella, Sandro
2017-01-01
We propose an ab initio molecular dynamics method, capable of dramatically reducing the autocorrelation time required for the simulation of classical and quantum particles at finite temperatures. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix S . Here, we apply this technique to both Lennard-Jones models, to demonstrate the accuracy and speeding-up of the sampling, and within a quantum Monte Carlo based wave function approach, for determining the phase diagram of high-pressure hydrogen with simulations much longer than the autocorrelation time. With the proposed method, we are able to equilibrate in a few hundred steps even close to the liquid-liquid phase transition (LLT). Within our approach, we find that the LLT transition is consistent with recent density functionals predicting a much larger transition pressure when the long range dispersive forces are taken into account.
Ab initio Prediction of Martensitic and Intermartensitic Phase Boundaries in Ni-Mn-Ga.
Dutta, B; Çakır, A; Giacobbe, C; Al-Zubi, A; Hickel, T; Acet, M; Neugebauer, J
2016-01-15
Despite the importance of martensitic transformations of Ni-Mn-Ga Heusler alloys for their magnetocaloric and shape-memory properties, the martensitic part of their phase diagrams is not well determined. Using an ab initio approach that includes the interplay of lattice and vibrational degrees of freedom we identify an intermartensitic transformation between a modulated and a nonmodulated phase as a function of excess Ni and Mn content. Based on an evaluation of the theoretical findings and experimental x-ray diffraction data for Mn-rich alloys, we are able to predict the phase diagram for Ni-rich alloys. In contrast to other mechanisms discussed for various material systems in the literature, we herewith show that the intermartensitic transformation can be understood solely using thermodynamic concepts.
On potential energy models for EA-based ab initio protein structure prediction.
Mijajlovic, Milan; Biggs, Mark J; Djurdjevic, Dusan P
2010-01-01
Ab initio protein structure prediction involves determination of the three-dimensional (3D) conformation of proteins on the basis of their amino acid sequence, a potential energy (PE) model that captures the physics of the interatomic interactions, and a method to search for and identify the global minimum in the PE (or free energy) surface such as an evolutionary algorithm (EA). Many PE models have been proposed over the past three decades and more. There is currently no understanding of how the behavior of an EA is affected by the PE model used. The study reported here shows that the EA behavior can be profoundly affected: the EA performance obtained when using the ECEPP PE model is significantly worse than that obtained when using the Amber, OPLS, and CVFF PE models, and the optimal EA control parameter values for the ECEPP model also differ significantly from those associated with the other models.
Ab initio study of zinc chloride dication ZnCl2+ in the gas phase
NASA Astrophysics Data System (ADS)
Fišer, J.
2014-09-01
Our high-level ab initio calculations show that the ZnCl2+ ground state of 2Π symmetry is metastable with a bond length of 2.242 Å, an effective dissociation energy of 1.66 eV, and an adiabatic double ionization energy of ZnCl of 26.11 eV. Potential energy curves for 18 Λ + S states and ten Ω states of ZnCl2+ are presented as well as the associated spectroscopic constants. Tunneling lifetimes, spin-orbit induced predissociation lifetimes and radiative lifetimes for the vibrational levels in the low-lying electronic states of ZnCl2+ are determined and the metastability of the dication is discussed.
Rafiee, Marjan A; Hadipour, Nasser L; Naderi-manesh, Hossein
2004-03-01
In this paper, ab initio calculated NQR parameters for some quinoline-containing derivatives are presented. The calculations are carried out in a search for the relationships between the charge distribution of these compounds and their ability to interact with haematin. On the basis of NQR parameters, pi-electron density on the nitrogen atom of the quinoline ring plays a dominant role in determining the ability of quinolines to interact with haematin. This point was confirmed with investigation of Fe+3 cation-pi quinoline ring interactions in 2- and 4-aminoquinoline. However, our results do not show any preference for those carbon atoms of the quinoline ring which previous reports have noted. In order to calculate the NQR parameters, the electric field gradient (EFG) should be evaluated at the site of a quadrupolar nucleus in each compound. EFGs are calculated by the Gaussian 98 program using the B3LYP/6-31 G* level of theory.
Electronic and optical properties of K-doped ZnO: Ab initio study
NASA Astrophysics Data System (ADS)
Aimouch, D. E.; Meskine, S.; Hayn, R.; Zaoui, A.; Boukortt, A.
2016-08-01
We present the results of ab initio calculations of K-doped ZnO in the wurtzite structure using a supercell of 32 atoms and density functional theory. A complete analysis of its electronic, optical and magnetic properties is provided. The local spin density approximation (LSDA) has been used to analyze the density of states and to understand the K influence at different concentration values. The material is revealed to become a p-type doped semiconductor. The optical constant or refractive index, the dielectric function, and the absorption coefficient were determined and show a good agreement with available experimental data. Potassium doping leads to an absorption peak at about 380 nm. That peak might improve the absorption characteristics of ZnO for solar cell or optical applications.
Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.
2013-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be kcal mol−1 for MP2/cc-pVDZ and for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively. PMID:23593259
Ab initio based force field and molecular dynamics simulations of crystalline TATB.
Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E
2004-04-15
An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. (c) 2004 American Institute of Physics.
Harding, M. E.; Vazquez, J.; Ruscic, B.; Wilson, A. K.; Gauss, J.; Stanton, J. F.; Chemical Sciences and Engineering Division; Univ. t Mainz; The Univ. of Texas; Univ. of North Texas
2008-01-01
Effects of increased basis-set size as well as a correlated treatment of the diagonal Born-Oppenheimer approximation are studied within the context of the high-accuracy extrapolated ab initio thermochemistry (HEAT) theoretical model chemistry. It is found that the addition of these ostensible improvements does little to increase the overall accuracy of HEAT for the determination of molecular atomization energies. Fortuitous cancellation of high-level effects is shown to give the overall HEAT strategy an accuracy that is, in fact, higher than most of its individual components. In addition, the issue of core-valence electron correlation separation is explored; it is found that approximate additive treatments of the two effects have limitations that are significant in the realm of <1 kJ mol{sup -1} theoretical thermochemistry.
The ideal strength of gold under uniaxial stress: an ab initio study.
Wang, Hao; Li, Mo
2010-07-28
We employ an ab initio calculation based on density functional theory to investigate the ideal strength of face-centered cubic crystal Au under uniaxial stress along the [100] direction. We show that the stability of the perfect Au crystal under tensile stress is determined by the tetragonal shear stiffness modulus, with an ideal tensile strength of 4.2 GPa and the corresponding Lagrangian tensile strain of ∼ 0.07. The potential bifurcation from the primary uniaxial loading path is along the tetragonal shear. Under compressive stress, there is a stress-free body-centered cubic phase, which is unstable and ready to transform to a stress-free body-centered tetragonal phase with lower internal energy. The stable region is from - 1.6 to 4.2 GPa in the ideal strength, or from - 0.07 to 0.07 in the Lagrangian strain.
Ab initio calculations in the symplectic no-core configuration interaction framework
NASA Astrophysics Data System (ADS)
McCoy, Anna; Caprio, Mark; Dytrych, Tomas
2016-09-01
A major challenge in quantitatively predicting nuclear structure directly from realistic nucleon-nucleon interactions, i.e., ab initio, arises due to an explosion in the dimension of the traditional Slater determinant basis as the number of nucleons and included shells increases. The need for including highly excited configurations arises, in large part, because the kinetic energy induces strong coupling across shells. However, the kinetic energy conserves symplectic symmetry. By combining this symplectic symmetry with the no-core configuration interaction (NCCI) framework, we reduce the size of basis necessary to obtain accurate results for p-shell nuclei. Supported by the US DOE under Grants DE-AC05-06OR23100 and DE-FG02-95ER-40934, and the Czech Science Foundation under Grant No. 16-16772S.
Autrey, Thomas; Brown, Aaron K.; Camaioni, Donald M.; Dupuis, Michel; Foster, Nancy S.; Getty, April D.
2004-03-31
Photoacoustic signals from dilute ({approx}30 mM) solutions of H{sub 2}O{sub 2} were measured over the temperature range from 10-45 C to obtain the reaction enthalpy and volume change for H{sub 2}O{sub 2}(aq) {yields} 2 OH(aq) from which we ultimately determined {Delta}{sub f}G{sup o}, {Delta}{sub f}H{sup o} and partial molal volume, v{sup o}, of OH (aq). We find {Delta}{sub r}H = 46.8 {+-} 1.4 kcal/mol, which is 4 kcal/mol smaller than the gas phase bond energy, and {Delta}V{sub r} = 6.5 {+-} 0.4 mL/mol. The v{sup o} for OH in water is 14.4 {+-} 0.4 mL/ml: smaller than the v{sup o} of water. Using ab initio continuum theory, the hydration free energy is calculated to be -3.9 {+-} 0.3 kcal/mol (for standard states in number density concentration units) by a novel approach devised to capture in the definition of the solute cavity the strength and specific interactions of the solute with a water solvent molecule. The shape of the cavity is defined by ''rolling'' a 3 dimensional electron density isocontour of water on the ab initio water-OH minimum interaction surface. The value of the contour is selected to reproduce the volume of OH in water. We obtain for OH(aq): {Delta}{sub f}H{sup o} = -0.2 {+-} 1.4 and {Delta}{sub f}G{sup o} = 5.8 {+-} 0.4 kcal/mol that are in agreement with literature values. The results provide confidence in the pulsed PAC technique for measuring aqueous thermochemistry of radicals and open the way to obtaining thermochemistry for most radicals that can be formed by reaction of OH with aqueous substrates while advancing the field of continuum solvation theory towards ab initio-defined solute cavities.
Kostadinova, O.; Chrissanthopoulos, A.; Petkova, T.; Petkov, P.; Yannopoulos, S.N.
2011-02-15
We report an investigation of the structure and vibrational modes of (AgI){sub x} (AsSe){sub 100-x}, bulk glasses using Raman spectroscopy and first principles calculations. The short- and medium-range structural order of the glasses was elucidated by analyzing the reduced Raman spectra, recorded at off-resonance conditions. Three distinct local environments were revealed for the AsSe glass including stoichiometric-like and As-rich network sub-structures, and cage-like molecules (As{sub 4}Se{sub n}, n=3, 4) decoupled from the network. To facilitate the interpretation of the Raman spectra ab initio calculations are employed to study the geometric and vibrational properties of As{sub 4}Se{sub n} molecular units that are parts of the glass structure. The incorporation of AgI causes appreciable structural changes into the glass structure. AgI is responsible for the population reduction of molecular units and for the degradation of the As-rich network-like sub-structure via the introduction of As-I terminal bonds. Ab initio calculations of mixed chalcohalide pyramids AsSe{sub m}I{sub 3-m} provided useful information augmenting the interpretation of the Raman spectra. -- Graphical abstract: Raman scattering and ab initio calculations are employed to study the structure of AgI-AsSe superionic glasses. The role of mixed chalcohalide pyramidal units as illustrated in the figure is elucidated. Display Omitted Research highlights: {yields} Doping binary As-Se glasses with AgI cause dramatic changes in glass structure. {yields} Raman scattering and ab initio calculations determine changes in short- and medium-range order. {yields} Three local environments exist in AsSe glass including a network sub-structure and cage-like molecules. {yields} Mixed chalcohalide pyramids AsSe{sub m}I{sub 3-m} dominate the AgI-doped glass structure.
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. As a firstmore » 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
NASA Astrophysics Data System (ADS)
Raimondi, Francesco; Hupin, Guillaume; Navrátil, Petr; Quaglioni, Sofia
2016-05-01
Background: 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. Ab initio approaches have been successfully applied to describe the 3H (d ,n )4He and 3He(d ,p )4He fusion processes. Purpose: 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. As 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. Methods: 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. Results: 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. Conclusions: Deuteron stripping reactions with p -shell targets can now be computed ab initio, but calculations are very demanding. 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.
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.
NASA Astrophysics Data System (ADS)
Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.
2016-07-01
Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.
An efficient and accurate molecular alignment and docking technique using ab initio quality scoring
Füsti-Molnár, László; Merz, Kenneth M.
2008-01-01
An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561
Ab initio molecular dynamics simulations of a binary system of ionic liquids.
Brüssel, Marc; Brehm, Martin; Voigt, Thomas; Kirchner, Barbara
2011-08-14
This work presents first insights into the structural properties of a binary mixture of ionic liquids from the perspective of ab initio molecular dynamics simulations. Simulations were carried out for a one-to-one mixture of 1-ethyl-3-methyl-imidazolium thiocyanate and 1-ethyl-3-methyl-imidazolium chloride and compared to pure 1-ethyl-3-methyl-imidazolium thiocyanate.
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.
Ab initio prediction of vacancy properties in concentrated alloys: The case of fcc Cu-Ni
NASA Astrophysics Data System (ADS)
Zhang, Xi; Sluiter, Marcel H. F.
2015-05-01
Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total energies in a consistent manner without a statistical model. Essential features of such a model are knowledge of the chemical potential and imposition of invariants. In the present work, we derive the simplest model that satisfies these requirements and we compare it with models in the literature. As illustration we compute ab initio vacancy properties of fcc Cu-Ni alloys as a function of composition and temperature. Ab initio density functional calculations were performed for SQS supercells at various compositions with and without vacancies. Various methods of extracting alloy vacancy properties were examined. A ternary cluster expansion yielded effective cluster interactions (ECIs) for the Cu-Ni-Vac system. Composition and temperature dependent alloy vacancy concentrations were obtained using statistical thermodynamic models with the ab initio ECIs. An Arrhenius analysis showed that the heat of vacancy formation was well represented by a linear function of temperature. The positive slope of the temperature dependence implies a negative configurational entropy contribution to the vacancy formation free energy in the alloy. These findings can be understood by considering local coordination effects.
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…
Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)
NASA Astrophysics Data System (ADS)
Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang
2001-01-01
Semiempirical PM3, ab initio HF/3-21g ∗, and DFT B3LYP/6-31g ∗ calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.
Ab initio charge-carrier mobility model for amorphous molecular semiconductors
NASA Astrophysics Data System (ADS)
Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.
2016-05-01
Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.
An efficient method for electron-atom scattering using ab-initio calculations
NASA Astrophysics Data System (ADS)
Xu, Yuan; Yang, Yonggang; Xiao, Liantuan; Jia, Suotang
2017-02-01
We present an efficient method based on ab-initio calculations to investigate electron-atom scatterings. Those calculations profit from methods implemented in standard quantum chemistry programs. The new approach is applied to electron-helium scattering. The results are compared with experimental and other theoretical references to demonstrate the efficiency of our method.
Computer simulation of acetonitrile and methanol with ab initio-based pair potentials
NASA Astrophysics Data System (ADS)
Hloucha, M.; Sum, A. K.; Sandler, S. I.
2000-10-01
This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.
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…
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.
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.
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.
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.
Ab-initio kinetics and thermodynamics studies of ammonia-borane for hydrogen storage
NASA Astrophysics Data System (ADS)
Miranda, Caetano R.; Ceder, Gerbrand
2007-03-01
Ammonia-borane (BH3NH3) is a promising chemical hydrogen storage material given its high gravimetry and volumetric properties. However, the ammonia-borane (AB) thermal hydrogen release is not very efficient, being mainly limited by the kinetics of hydrogenation. Using ab initio calculations, we have investigated the thermodynamics and kinetics of hydrogen release on AB by calculating the free energies of the H2 release reactions for different possible decomposition products. Our results indicate that AB regeneration through the ammonia-borane polymeric and borazine-cyclotriborazane cycles is very unlikely due to the strong exothermic character of the reactions. The kinetics of hydrogen release is further investigated with the recently developed metadynamics method. This method allows us to calculate the multidimensional free energy surface of hydrogen release on AB. Our simulations reveal the atomistic mechanism of hydrogenation and provide the free energies barriers and transition states involved in inter and intramolecule H2 release on AB.
High-throughput ab initio screening for two-dimensional electride materials.
Tada, Tomofumi; Takemoto, Seiji; Matsuishi, Satoru; Hosono, Hideo
2014-10-06
High-throughput ab initio screening of approximately 34000 materials in the Materials Project was conducted to identify two-dimensional (2D) electride materials, which are composed of cationic layers and anionic electrons confined in a 2D empty space. The screening was based on three indicators: (1) a positive total formal charge per formula unit; (2) layered structures for two-dimensionality; (3) empty spaces between the layer units. Three nitrides, Ca2N, Sr2N, and Ba2N, and the carbide Y2C were identified as 2D electrides, where Ca2N is the only experimentally confirmed 2D electride (Lee, K.; et al. Nature 2013, 494, 336-341). Electron density analysis using ionic radii revealed a smaller number of anionic electrons in Y2C than those in the three nitrides as a result of the partial occupation of the anionic electrons in the d orbitals of Y. In addition, no candidates were identified from the p-block elements, and thus the ab initio screening indicates that the s-block elements (i.e., alkali or alkaline-earth metals) are highly preferable as cation elements. To go beyond the database screening, a tailored modeling was conducted to determine unexplored compounds including the s-block elements that are suitable for 2D electrides. The tailored modeling found that (1) K2Cl, K2Br, Rb2Cl, and Rb2Br dialkali halides are highly plausible candidates, (2) Li2F and Na2Cl dialkali halides are highly challenging candidates, and (3) the Cs2O(1-x)F(x) halogen-doped dialkali oxide is a promising candidate.
SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles.
Elmlund, Dominika; Elmlund, Hans
2012-12-01
The open source software suite SIMPLE: Single-particle IMage Processing Linux Engine provides data analysis methods for single-particle cryo-electron microscopy (cryo-EM). SIMPLE addresses the problem of obtaining 3D reconstructions from 2D projections only, without using an input reference volume for approximating orientations. The SIMPLE reconstruction algorithm is tailored to asymmetrical and structurally heterogeneous single-particles. Its basis is global optimization with the use of Fourier common lines. The advance that enables ab initio reconstruction and heterogeneity analysis is the separation of the tasks of in-plane alignment and projection direction determination via bijective orientation search - a new concept in common lines-based strategies. Bijective orientation search divides the configuration space into two groups of paired parameters that are optimized separately. The first group consists of the rotations and shifts in the plane of the projection; the second group consists of the projection directions and state assignments. In SIMPLE, ab initio reconstruction is feasible because the 3D in-plane alignment is approximated using reference-free 2D rotational alignment. The subsequent common lines-based search hence searches projection directions and states only. Thousands of class averages are analyzed simultaneously in a matter of hours. Novice SIMPLE users get a head start via the well documented front-end. The structured, object-oriented back-end invites advanced users to develop new alignment and reconstruction algorithms. An overview of the package is presented together with benchmarks on simulated data. Executable binaries, source code, and documentation are available at http://simple.stanford.edu.
High pressure behaviour of uranium dicarbide (UC2): Ab-initio study
NASA Astrophysics Data System (ADS)
Sahoo, B. D.; Mukherjee, D.; Joshi, K. D.; Kaushik, T. C.
2016-08-01
The structural stability of uranium dicarbide has been examined under hydrostatic compression employing evolutionary structure search algorithm implemented in the universal structure predictor: evolutionary Xtallography (USPEX) code in conjunction with ab-initio electronic band structure calculation method. The ab-initio total energy calculations involved for this purpose have been carried out within both generalized gradient approximations (GGA) and GGA + U approximations. Our calculations under GGA approximation predict the high pressure structural sequence of tetragonal → monoclinic → orthorhombic for this material with transition pressures of ˜8 GPa and 42 GPa, respectively. The same transition sequence is predicted by calculations within GGA + U also with transition pressures placed at ˜24 GPa and ˜50 GPa, respectively. Further, on the basis of comparison of zero pressure equilibrium volume and equation of state with available experimental data, we find that GGA + U approximation with U = 2.5 eV describes this material better than the simple GGA approximation. The theoretically predicted high pressure structural phase transitions are in disagreement with the only high experimental study by Dancausse et al. [J. Alloys. Compd. 191, 309 (1993)] on this compound which reports a tetragonal to hexagonal phase transition at a pressure of ˜17.6 GPa. Interestingly, during lowest enthalpy structure search using USPEX, we do not see any hexagonal phase to be closer to the predicted monoclinic phase even within 0.2 eV/f. unit. More experiments with varying carbon contents in UC2 sample are required to resolve this discrepancy. The existence of these high pressure phases predicted by static lattice calculations has been further substantiated by analyzing the elastic and lattice dynamic stability of these structures in the pressure regimes of their structural stability. Additionally, various thermo-physical quantities such as equilibrium volume, bulk modulus, Debye
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.
NASA Astrophysics Data System (ADS)
Timko, Jeff; Kuyucak, Serdar
2012-11-01
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.
Combined electron beam imaging and ab initio modeling of T{sub 1} precipitates in Al-Li-Cu alloys
Dwyer, C.; Weyland, M.; Chang, L. Y.; Muddle, B. C.
2011-05-16
Among the many considerable challenges faced in developing a rational basis for advanced alloy design, establishing accurate atomistic models is one of the most fundamental. Here we demonstrate how advanced imaging techniques in a double-aberration-corrected transmission electron microscope, combined with ab initio modeling, have been used to determine the atomic structure of embedded 1 nm thick T{sub 1} precipitates in precipitation-hardened Al-Li-Cu aerospace alloys. The results provide an accurate determination of the controversial T{sub 1} structure, and demonstrate how next-generation techniques permit the characterization of embedded nanostructures in alloys and other nanostructured materials.
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
NASA Astrophysics Data System (ADS)
Mullaney, John C.; Zaleski, Daniel P.; Tew, David Peter; Walker, Nick; Legon, Anthony
2016-06-01
An isolated, gas-phase dimer of imidazole is generated through laser vaporisation of a solid rod containing a 1:1 mixture of imidazole and copper in the presence of an argon buffer gas undergoing supersonic expansion. The complex is characterised through broadband rotational spectroscopy and is shown to have a twisted, hydrogen-bonded geometry. Calculations at the CCSD(T)(F12*)/cc-pVDZ-F12 level of theory confirm this to be the lowest-energy conformer of the imidazole dimer. The distance between the respective centres of mass of the imidazole monomer subunits is determined to be 5.2751(1) Å, and the twist angle γ describing rotation of one monomer with respect to the other about a line connecting the centres of mass of the monomers is determined to be 87.9(4)o. Four out of six intermolecular parameters in the model geometry are precisely determined from the experimental rotational constants and are consistent with results calculated ab initio.
An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.
1995-01-01
A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.
An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.
1995-01-01
A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.
Jacob, Rebecca; Tate, Margaret; Banti, Yididya; Rix, Colin; Mainwaring, David E
2008-01-17
Despite the complex phenomena involved in encoding template molecule information within stable synthetic polymers to yield selective and efficient molecular recognition processes, molecularly imprinted polymers (MIP) are increasingly finding broad areas of application. Molecular interactions, both during the polymerization of the functional monomers in the presence of the template and during the processes of specific recognition after template removal, are key determinants of an effective MIP. Covalent and noncovalent template imprinting have been employed to achieve specific recognition sites. In the present study, a molecularly imprinted biocompatible polymer, having a high capacity and affinity for the dye template, nickel(II) phthalocyanine tetrasulfonic acid, has been prepared. UV-visible spectroscopy, FTIR spectroscopy, and ICP analysis were used to investigate the aspects of the synthesis, binding capacity, and adsorption kinetics of the system. Poly(allylamine) cross-linked with epichlorohydrin has been used to represent an amino-functional receptor. Binding isotherms and capacities were correlated with the degree of template removal. Kinetic studies of binding allowed diffusion mechanisms to be evaluated for the fine particulate MIP. Ab initio molecular orbital calculations were performed using Hartree-Fock, MP2, and density functional theory methods to determine the most likely mechanisms of molecular imprinting. Suitable theoretical models have been constructed to mimic the interactions between the template molecule and the polymer. Simulation of the vibrational spectra was also undertaken to make meaningful assignments to experimentally determined spectral bands resulting from these template MIP receptor interactions.
Ab initio phasing of X-ray powder diffraction patterns by charge flipping.
Wu, Jinsong; Leinenweber, Kurt; Spence, John C H; O'Keeffe, Michael
2006-08-01
Determining crystal structures from powder X-ray diffraction data remains a challenging problem in materials science. By embedding a Le-Bail-like procedure within the recently discovered charge-flipping phasing algorithm, an extremely simple, fast and effective ab initio method has been developed to determine phases directly from indexed powder diffraction patterns. The algorithm solves the degeneracy problem by applying spherical averaging for overlapping Bragg reflections, while solving the phase problem by using the Oszlányi-Süto charge-flipping algorithm. The processes of peak decomposition and phasing are integrated within the same iteration, and a dynamic support is used. The Fienup hybrid input-output algorithm is also incorporated to minimize stagnation. The ability of the algorithm to find structure-factor phases rapidly is found to assist with the fundamental problem of degeneracy (overlapping reflections) which is intrinsic to powder diffraction data. Space-group and chemical-composition information are not needed as inputs, and can be determined from the result. The method is illustrated using several experimental powder patterns of indifferent quality.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo.
Zen, Andrea; Luo, Ye; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Melting of sodium under high pressure. An ab-initio study
González, D. J.; González, L. E.
2015-08-17
We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.
Ab initio simulation of atomic-scale imaging in noncontact atomic force microscopy.
Caciuc, V; Hölscher, H
2009-07-01
In this paper, we summarize some results of our ab initio simulations aimed at investigating the mechanism of the NC-AFM image contrast on semiconductor and metallic surfaces. We start with an introduction into the basic ideas behind the ab initio simulation process of the NC-AFM experimental results. Our simulations reveal that the interaction of a clean silicon tip with a semiconductor surface like InAs(110) might lead to bond-formation and bond-breaking processes during the approach and retraction of the tip. This imaging mechanism is very similar to that observed on a metallic surface like Ag(110). Interestingly, a clean silicon tip can become contaminated with Ag surface atoms. On both types of surface we observe a significant energy dissipation which is caused by a hysteresis in the tip-sample force curves calculated on the approach and retraction path.
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.
Siddick, M M; Ackland, G J; Morrison, C A
2006-08-14
We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.
[Photoelectron Spectra of CCl2-: Ab Initio Calculation and Franck-Condon Analysis].
Wu, Jun
2015-12-01
Geometry optimization and harmonic vibrational frequency calculations were performed on the X¹A₁ state of CCl₂ and X²B₁ state of CCl₂⁻ at the B3LYP, MP2, CCSD levels. Franck-Condon analysis and spectral simulations were carried out on the photoelectron band of CCl₂⁻ including Duschinsky effects. The simulated spectra obtained are in excellent agreement with the experiment. Note that Duschinsky effect between bending vibration and the symmetric stretch modes should be considered in the CCl₂ (X¹A₁)-CCl₂⁻ (X²B₁) photodetachment process. By combining ab initio calculations with Franck-Condon analyses, the assignment of spectrum observed is firmly established to the X¹A₁-X²B₁ photodetachment process of the CCl₂⁻ radical, and the recommended geometric parameters of which in the literature are confirmed again base on ab initio theory and IFCA process.
Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study
Rio, B. G. del; González, L. E.
2015-08-17
Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.
NASA Astrophysics Data System (ADS)
Shibuta, Yasushi; Shimamura, Kohei; Oguri, Tomoya; Arifin, Rizal; Shimojo, Fuyuki; Yamaguchi, Shu
2015-03-01
The growth mechanism of carbon nanotubes (CNT) has been widely discussed both from experimental and computational studies. Regarding the computational studies, most of the studies focuses on the aggregation of isolate carbon atoms on the catalytic metal nanoparticle, whereas the initial dissociation of carbon source molecules should affect the yield and quality of the products. On the other hand, we have studied the dissociation process of carbon source molecules on the metal surface by the ab initio molecular dynamics simulation. In the study, we investigate the ethanol dissociation on Pt and Ni clusters by ab initio MD simulations to discuss the initial stage of CNT growth by alcohol CVD technique. Part of this research is supported by the Grant-in-Aid for Young Scientists (a) (No. 24686026) from MEXT, Japan.
Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation
NASA Astrophysics Data System (ADS)
Correa, J. D.; Cisternas, E.
2016-09-01
By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.
Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.
2015-02-27
The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.
Infrared spectra and tautomerism of isocytosine; an ab initio and matrix isolation study
NASA Astrophysics Data System (ADS)
Vranken, Hertwig; Smets, Johan; Maes, Guido; Lapinski, Leszek; Nowak, Maciej J.; Adamowicz, Ludwik
1994-05-01
Prototropic tautomerism of isocytosine has been investigated using both theoretical ab initio and experimental matrix isolation IR methods. The coexistence of the amino-hydroxy and amino-oxo N(3)H forms, with a clear predominance of the hydroxy form, was observed. The tautomerization constant [oxo]/[hydroxy] obtained from experimental and calculated IR intensities was 0.11 at the micro-oven temperature of 400 K. The ab initio prediction of the relative energies of the tautomers is in reasonable agreement with the experimental estimation. The change of the tautomeric form oxo→hydroxy upon UV irradiation was used to separate the IR spectra of both tautomers. A theoretically assisted interpretation of the IR spectra of both observed tautomers is proposed.
B28: the smallest all-boron cage from an ab initio global search
NASA Astrophysics Data System (ADS)
Zhao, Jijun; Huang, Xiaoming; Shi, Ruili; Liu, Hongsheng; Su, Yan; King, R. Bruce
2015-09-01
Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures.Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures. Electronic supplementary information (ESI) available: Planar isomer structures of B28 and spatial distributions of front molecular orbitals. See DOI: 10.1039/c5nr04034e
Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.
Yang, Jianjun; Tse, John S
2011-11-17
The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.
Ab initio study of AlxMoNbTiV high-entropy alloys.
Cao, Peiyu; Ni, Xiaodong; Tian, Fuyang; Varga, Lajos K; Vitos, Levente
2015-02-25
The Al(x)MoNbTiV (x = 0-1.5) high-entropy alloys (HEAs) adopt a single solid-solution phase, having the body centered cubic (bcc) crystal structure. Here we employ the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to investigate the equilibrium volume, elastic constants, and polycrystalline elastic moduli of Al(x)MoNbTiV HEAs. A comparison between the ab initio and experimental equilibrium volumes demonstrates the validity and accuracy of the present approach. Our results indicate that Al addition decreases the thermodynamic stability of the bcc structure with respect to face-centered cubic and hexagonal close packed lattices. For the elastically isotropic Al(0.4)MoNbTiV HEAs, the valence electron concentration (VEC) is about 4.82, which is slightly different from VEC ∼ 4.72 obtained for the isotropic Gum metals and refractory--HEAs.
The Pu-U-Am system: An ab initio informed CALPHAD thermodynamic study
NASA Astrophysics Data System (ADS)
Perron, A.; Turchi, P. E. A.; Landa, A.; Söderlind, P.; Ravat, B.; Oudot, B.; Delaunay, F.
2015-03-01
Phase diagram and thermodynamic properties of the Am-U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu-U and Am-Pu thermodynamic assessments are combined to build a Pu-U-Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies.
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.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
Zen, Andrea; Luo, Ye Mazzola, Guglielmo Sorella, Sandro; Guidoni, Leonardo
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Point defect modeling in materials: Coupling ab initio and elasticity approaches
NASA Astrophysics Data System (ADS)
Varvenne, Céline; Bruneval, Fabien; Marinica, Mihai-Cosmin; Clouet, Emmanuel
2013-10-01
Modeling point defects at an atomic scale requires careful treatment of the long-range atomic relaxations. This elastic field can strongly affect point defect properties calculated in atomistic simulations because of the finite size of the system under study. This is an important restriction for ab initio methods which are limited to a few hundred atoms. We propose an original approach coupling ab initio calculations and linear elasticity theory to obtain the properties of an isolated point defect for reduced supercell sizes. The reliability and benefit of our approach are demonstrated for three problematic cases: the self-interstitial in zirconium, clusters of self-interstitials in iron, and the neutral vacancy in silicon.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil
2015-05-15
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.
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.
Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy
NASA Astrophysics Data System (ADS)
Chen, Xi H.; Zhang, John Z. H.
2004-06-01
In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.
Ab initio studies of equations of state and chemical reactions of reactive structural materials
NASA Astrophysics Data System (ADS)
Zaharieva, Roussislava
subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated
Pierce, Levi C T; Markwick, Phineus R L; McCammon, J Andrew; Doltsinis, Nikos L
2011-05-07
A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate.
Ab initio electron mobility and polar phonon scattering in GaAs
NASA Astrophysics Data System (ADS)
Zhou, Jin-Jian; Bernardi, Marco
2016-11-01
In polar semiconductors and oxides, the long-range nature of the electron-phonon (e -ph ) interaction is a bottleneck to compute charge transport from first principles. Here, we develop an efficient ab initio scheme to compute and converge the e -ph relaxation times (RTs) and electron mobility in polar materials. We apply our approach to GaAs, where by using the Boltzmann equation with state-dependent RTs, we compute mobilities in excellent agreement with experiment at 250 -500 K . The e -ph RTs and the phonon contributions to intravalley and intervalley e -ph scattering are also analyzed. Our work enables efficient ab initio computations of transport and carrier dynamics in polar materials.
Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations.
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.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study
Sharma, Nalini 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 local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.
Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions
Navratil, P; Ormand, W E; Forssen, C; Caurier, E
2004-11-30
There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.
Pierce, Levi C. T.; Markwick, Phineus R. L.; McCammon, J. Andrew; Doltsinis, Nikos L.
2011-01-01
A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate. PMID:21548673
Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2014-04-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and lead (l-Pb). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2015-05-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2016-05-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.
Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective
NASA Astrophysics Data System (ADS)
Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge
2013-03-01
Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at < 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ~300 K across the entire pressure range considered.
NASA Astrophysics Data System (ADS)
Whitfield, T. W.; Crain, J.; Martyna, G. J.
2006-03-01
In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.
Ab initio large unit cell calculations of the electronic structure of diamond nanocrystals
NASA Astrophysics Data System (ADS)
Abdulsattar, Mudar A.
2011-05-01
In order to reduce computational efforts, and separate surface and core properties, diamond nanocrystals in the present model is represented by a heterojunction between the surface and the core in which the surface represents the outer most four layers and the core by the rest of the internal region of nanocrystal. Ab initio restricted Hartree-Fock (RHF) method coupled with the large unit cell method (LUC) is used to determine the electronic structure and physical properties of diamond nanocrystals core part with different sizes. The use of STO-3G basis choice is made to be able to compare to semiempirical methods using the complete neglect of differential overlap (CNDO) that uses Slater type orbitals (STO). The oxygenated (001)-(1 × 1) facet that expands with larger sizes of nanocrystals is also investigated to determine the rule of the surface in nanocrystals electronic structure. The results show that the present method agrees with semiempirical method contraction of lattice constant with increasing nanocrystal size but disagrees with energy gap variation with nanocrystal size in some regions. After nearly 1.4 nm the energy gap which is controlled by surface states begins to rise. The lowest unoccupied molecular orbital (LUMO) is attributed to surface states that largely reduce the value of energy gap. The sources of disagreement between semiempirical and ab initio results are discussed. The present method shows a maximum increment of the lattice constant by 3.3% over the calculated bulk for the smallest diamond nanocrystals. The surface states are found mostly non-degenerated because of the effect of surface discontinuity and oxygen atoms. Valance and conduction bands are wider on the surface due to splitting and oxygen atoms. The method also shows fluctuations in the converged energy gap, valence band width and cohesive energy of the core part of nanocrystal. These fluctuations might partially explain the controversial experimental results for diamond
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.
Ab initio calculations of the H centers in MgF2 crystals
NASA Astrophysics Data System (ADS)
Abuova, F. U.; Akilbekov, A. T.; Kotomin, E. A.
2012-08-01
MgF2 with rutile structure is important wide-gap optical material with numerous applications. We present and discuss the results of calculations for basic hole defects - interstitial F atoms (called also the colour H centres). This study is based on the large scale ab initio DFT calculations using hybrid B3PW exchange-correlation functional as implemented into CRYSTAL computer code. The electronic structure, atomic geometry, charge density distribution are calculated and discussed.