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.
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 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.
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.
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.
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
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).
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.
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 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.
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 Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method
NASA Astrophysics Data System (ADS)
Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori
2009-10-01
We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.
Ab-initio method for X-ray absorption spectra simulation of hydride molecular ions
NASA Astrophysics Data System (ADS)
Puglisi, Alessandra; Sisourat, Nicolas; Carniato, Stéphane
2017-03-01
Soft X-ray absorption spectra of molecular ions are important data for the modeling and understanding of laboratory and astrophysical plasma. In this work, we present an ab-initio method, based on the Configuration Interaction (CI) approach, for the calculations of energy positions and oscillator strengths of X-ray absorption spectra. Furthermore, we investigate the effects of the choice of the nature and number of spin-orbitals used in the CI expansion on the spectra. The method is applied on three hydride molecular ions, namely CH+, OH+ and SiH+. However, the approach proposed here is general and may thus be applied to any kind of molecular ions.
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.
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.
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
Jursic, B.S.
1996-12-31
Up to four ionization potentials of elements from the second-row of the periodic table were computed using the ab initio (HF, MP2, MP3, MP4, QCISD, GI, G2, and G2MP2) and DFT (B3LY, B3P86, B3PW91, XALPHA, HFS, HFB, BLYP, BP86, BPW91, BVWN, XAPLY, XAP86, XAPW91, XAVWN, SLYR SP86, SPW91 and SVWN) methods. In all of the calculations, the large 6-311++G(3df,3pd) gaussian type of basis set was used. The computed values were compared with the experimental results and suitability of the ab initio and DFF methods were discussed, in regard to reproducing the experimental data. From the computed ionization potentials of the second-row elements, it can be concluded that the HF ab initio computation is not capable of reproducing the experimental results. The computed ionization potentials are too low. However, by using the ab initio methods that include electron correlation, the computed IPs are becoming much closer to the experimental values. In all cases, with the exception of the first ionization potential for oxygen, the G2 computation result produces ionization potentials that are indistinguishable from the experimental results.
Physical properties and spectra of IO, IO- and HOI studied by ab initio methods.
Minaev, Boris; Loboda, Oleksandr; Vahtras, Olav; Agren, Hans; Bilan, Elena
2002-03-15
Structure and properties of the IO, IO- and HOI species, which are of potential importance for the ozone destruction catalytic cycle in the troposphere, have been calculated together with the EPR, NMR and UV-visible spectra by ab initio methodology with account of spin-orbit coupling (SOC) effects. Multi-configuration self-consistent field calculations with linear and quadratic response techniques and the multi-reference configuration interaction method have been employed. Photodissociation of these species, crucial for the catalytic ozone-destruction cycle, is critically reviewed and analyzed. Calculations predict that the singlet-triplet (S-T) transition to the lowest triplet state (X1 A' --> 3A'') should be responsible for the weak long-wavelength tail absorption (approximately 450-560 nm) and photodissociation of the HOI molecule. The second, more intense, band around 400 nm is produced by two overlapping S-S and S-T transitions. In order to check this assignment of the HOI photodissociation the isoelectronic IO- anion and IO radical have been studied by the same methods. Comparison with the EPR spectrum of the IO radical indicates that the methods are reliable which gives credit to the accuracy of the HOI spectral interpretation. NMR spectra of HOI and IO- molecules and some other properties are calculated for the first time.
Benchmark comparison of ab initio microRNA identification methods and software.
Hu, L L; Huang, Y; Wang, Q C; Zou, Q; Jiang, Y
2012-12-19
MicroRNAs (miRNAs) are short, non-coding RNA molecules that play an important role in the world of genes, especially in regulating the gene expression of target messenger RNAs through cleavage or translational repression of messenger RNA. Ab initio methods have become popular in computational miRNA detection. Most software tools are designed to distinguish miRNA precursors from pseudo-hairpins, but a few can mine miRNA from genome or expressed sequence tag sequences. We prepared novel testing datasets to measure and compare the performance of various software tools. Furthermore, we summarized the miRNA mining methods that study next-generation sequencing data for bioinformatics researchers who are analyzing these data. Because secondary structure is an important feature in the identification of miRNA, we analyzed the influence of various secondary structure prediction software tools on miRNA identification. MiPred was the most effective for classifying real-/pseudo-pre-miRNA sequences, and miRAbela performed relatively better for mining miRNA precursors from genome or expressed sequence tag sequences. RNA-fold performed better than m-fold for extracting secondary structure features of miRNA precursors.
NASA Astrophysics Data System (ADS)
Philipp, Dean Michael
Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree-Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by ``breaking'' bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. The mixed modeling presented here can be used for single point energy calculations and geometry optimizations. Results from tests of the method to find relative conformational energies and geometries of alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations.
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)
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).
The ab initio model potential method. Second series transition metal elements
Barandiaran, Z.; Seijo, L. ); Huzinaga, S. )
1990-10-15
The {ital ab} {ital initio} core method potential model (AIMP) has already been presented in its nonrelativistic version and applied to the main group and first series transition metal elements (J. Chem. Phys. {bold 86}, 2132 (1987); {bold 91}, 7011 (1989)). In this paper we extend the AIMP method to include relativistic effects within the Cowan--Griffin approximation and we present relativistic Zn-like core model potentials and valence basis sets, as well as their nonrelativistic Zn-like core and Kr-like core counterparts. The pilot molecular calculations on YO, TcO, AgO, and AgH reveal that the 4{ital p} orbital is indeed a core orbital only at the end part of the series, whereas the 4{ital s} orbital can be safely frozen from Y to Cd. The all-electron and model potential results agree in 0.01--0.02 A in {ital R}{sub {ital e}} and 25--50 cm{sup {minus}1} in {bar {nu}}{sub {ital e}} if the same type of valence part of the basis set is used. The comparison of the relativistic results on AgH with those of the all-electron Dirac--Fock calculations by Lee and McLean is satisfactory: the absolute value of {ital R}{sub {ital e}} is reproduced within the 0.01 A margin and the relativistic contraction of 0.077 A is also very well reproduced (0.075 A). Finally, the relative magnitude of the effects of the core orbital change, mass--velocity potential, and Darwin potential on the net relativistic effects are analyzed in the four molecules studied.
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.
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.
Ab initio infrared and Raman spectra
NASA Astrophysics Data System (ADS)
Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.
1983-06-01
We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum
NASA Astrophysics Data System (ADS)
Liang, Wenkel
This dissertation consists of two general parts: (I) developments of optimization algorithms (both nuclear and electronic degrees of freedom) for time-independent molecules and (II) novel methods, first-principle theories and applications in time dependent molecular structure modeling. In the first part, we discuss in specific two new algorithms for static geometry optimization, the eigenspace update (ESU) method in nonredundant internal coordinate that exhibits an enhanced performace with up to a factor of 3 savings in computational cost for large-sized molecular systems; the Car-Parrinello density matrix search (CP-DMS) method that enables direct minimization of the SCF energy as an effective alternative to conventional diagonalization approach. For the second part, we consider the time dependence and first presents two nonadiabatic dynamic studies that model laser controlled molecular photo-dissociation for qualitative understandings of intense laser-molecule interaction, using ab initio direct Ehrenfest dynamics scheme implemented with real-time time-dependent density functional theory (RT-TDDFT) approach developed in our group. Furthermore, we place our special interest on the nonadiabatic electronic dynamics in the ultrafast time scale, and presents (1) a novel technique that can not only obtain energies but also the electron densities of doubly excited states within a single determinant framework, by combining methods of CP-DMS with RT-TDDFT; (2) a solvated first-principles electronic dynamics method by incorporating the polarizable continuum solvation model (PCM) to RT-TDDFT, which is found to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. (3) applications of the PCM-RT-TDDFT method to study the intramolecular charge-transfer (CT) dynamics in a C60 derivative. Such work provides insights into the
NASA Astrophysics Data System (ADS)
Brown, David F. R.; Gibbs, Mark N.; Clary, David C.
1996-11-01
We describe a new method to calculate the vibrational ground state properties of weakly bound molecular systems and apply it to (HF)2 and HF-HCl. A Bayesian Inference neural network is used to fit an analytic function to a set of ab initio data points, which may then be employed by the quantum diffusion Monte Carlo method to produce ground state vibrational wave functions and properties. The method is general and relatively simple to implement and will be attractive for calculations on systems for which no analytic potential energy surface exists.
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.
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.
The many-body Wigner Monte Carlo method for time-dependent ab-initio quantum simulations
Sellier, J.M. Dimov, I.
2014-09-15
The aim of ab-initio approaches is the simulation of many-body quantum systems from the first principles of quantum mechanics. These methods are traditionally based on the many-body Schrödinger equation which represents an incredible mathematical challenge. In this paper, we introduce the many-body Wigner Monte Carlo method in the context of distinguishable particles and in the absence of spin-dependent effects. Despite these restrictions, the method has several advantages. First of all, the Wigner formalism is intuitive, as it is based on the concept of a quasi-distribution function. Secondly, the Monte Carlo numerical approach allows scalability on parallel machines that is practically unachievable by means of other techniques based on finite difference or finite element methods. Finally, this method allows time-dependent ab-initio simulations of strongly correlated quantum systems. In order to validate our many-body Wigner Monte Carlo method, as a case study we simulate a relatively simple system consisting of two particles in several different situations. We first start from two non-interacting free Gaussian wave packets. We, then, proceed with the inclusion of an external potential barrier, and we conclude by simulating two entangled (i.e. correlated) particles. The results show how, in the case of negligible spin-dependent effects, the many-body Wigner Monte Carlo method provides an efficient and reliable tool to study the time-dependent evolution of quantum systems composed of distinguishable particles.
Slavíček, Petr; Fárník, Michal
2011-07-14
In this perspective article, we focus on the photochemistry of five-membered nitrogen containing heterocycles (pyrrole, imidazole and pyrazole) in clusters. These heterocycles represent paradigmatic structures for larger biologically active heterocyclic molecules and complexes. The dimers of the three molecules are also archetypes of different bonding patterns: N-H···π interaction, N-H···N hydrogen bond and double hydrogen bond. We briefly review available data on photochemistry of the title molecules in the gas phase, but primarily we focus on the new reaction channels opened upon the complexation with other heterocycles or solvent molecules. Based on ab initio calculations we discuss various possible reactions in the excited states of the clusters: (1) hydrogen dissociation, (2) hydrogen transfer between the heterocyclic units, (3) molecular ring distortion, and (4) coupled electron-proton transfer. The increasing photostability with complexity of the system can be inferred from experiments with photodissociation in these clusters. A unified view on photoinduced processes in five-membered N-heterocycles is provided. We show that even though different deactivation channels are energetically possible for the complexed heterocycles, in most cases the major result is a fast reconstruction of the ground state. The complexed or solvated heterocycles are thus inherently photostable although the stability can in principle be achieved via different reaction routes.
Engineering superconductors with ab initio methods: the example of LiB
NASA Astrophysics Data System (ADS)
Curtarolo, Stefano
2007-03-01
The identification of novel crystal structures is a fundamental step for predicting new stable compounds in alloys. While performing ab initio data mining of intermetallic compounds [1], we discover a new family of layered metal borides [2], of which MgB2 is one particular element (the new phases are called Metal Sandwich (MS)). Thermodynamic stability and electronic properties of these MS phases are investigated in details, leading to the prediction of a hypothetical novel superconductor MS-LiB [2,3]. Calculations show that the MS phases in the Li-B system exhibit electronic features similar to those of MgB2 [2,3] and CaC6 [4]. Although the predicted critical temperature of LiB is lower than that of MgB2 (references [4] and [5] for MS2-LiB and MS1-LiB, respectively), the peculiarities of MS-LiB in terms of electronic structure, layer arrangements and doping capabilities allow a lot of freedom in the search for higher Tc systems [5]. We acknowledge the San Diego Supercomputer Center for computational resources. [1] S. Curtarolo et al., Phys. Rev. Lett. 91, 135503 (2003). [2] A.N. Kolmogorov, S. Curtarolo, Phys. Rev. B 73, 180501(R) (2006). [3] A.N. Kolmogorov, S. Curtarolo, in press, Phys. Rev B 74 (2006), condmat/0607654. [4] A.Y. Liu, I.I. Mazin, cond-mat/0610057. [5] M. Calandra, A.N. Kolmogorov, S. Curtarolo, submitted (2006).
NASA Astrophysics Data System (ADS)
Chibotaru, Liviu; Ungur, Liviu
2012-02-01
A large amount of data concerning the blocking barriers of reversal of magnetization in various complexes with strongly anisotropic metal ions (Ln^III, Co^II) became recently available. Understanding the mechanisms of formation of these barriers is of primary importance for an efficient design of Ln-based single-molecule magnet (SMM) and represents a challenging task for the theory. Here an ab initio based approach for the investigation of blocking barriers will be presented. The methodology will be applied for the construction of the blocking barriers and the understanding of the variation of SMM properties in the series of mixed 3d-4f trinuclear complexes Co-Ln-Co, Ln=Gd, Tb, Dy. In particular, the reasons for a more pronounced SMM behavior manifested by the gadolinium complex will be elucidated. Another example is a recently synthesized Dy3 complex, for which the origin of magnetization steps in the hysteresis loops will be explained. [4pt] [1] T. Yamaguchi, J.-P. Costes, Y. Kishima, M. Kojima, Y. Sunatsuki, N. Br'efuel, J.-P. Tuchagues, L. Vendier, W. Wernsdorfer Inorg. Chem. 2010, 49, 9125--9135.
Kinetic approach with ab initio MO method on ionic selectivity and size in sodium channel.
Tani, S; Imamura, A; Kanda, K
1989-10-23
Three kinds of models for ionic selectivity and size of the filter in sodium channel have been treated by using ab initio molecular orbital (MO) calculations with MINI-3 and MIDI-3* basis sets. A three-components system, HCO2M-H2O (M = Li+, Na+ or K+), is acceptable for describing experimental facts well. Thermochemical parameters obtained from harmonic vibrational analysis with MINI-3 basis sets, for the translocation of the permeant metal cations in the HCO2M-H2O system, are that the activation enthalpies for Li+, Na+ and K+ are 7.0, 6.4 and 23.4 kJ/mol, and also the free energies of activation are 10.6, 1.5 and 19.0 kJ/mol, respectively. These results are qualitatively in good correspondence with experimental facts of the ion selectivity of the channel. One of water molecule was found to have a key role in the translocation of the permeant cations.
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
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
Molecular associations from ab initio pair potentials
NASA Astrophysics Data System (ADS)
Iglesias, E.; Sordo, T. L.; Sordo, J. A.
1991-12-01
A method of building up stable molecular associations by using pair potentials from ab initio calculations is presented. The Matsuoka-Clementi-Yoshimine potential has been chosen to emulate the water-water interactions while 1-6-12 potentials are used to compute both solute-solvent and solute-solute interactions. Parameters for neutral-amino-acid-water and neutral- amino-acid-neutral-amino-acid interactions are provided by the program. Supermolecules are constructed by minimization of the interaction energy of the molecules involved. Both steepest-decent and Fletcher-Powell algorithms are available to carry out such a minimization.
Ab-initio Studies Of Lithium Oxide
NASA Astrophysics Data System (ADS)
Gupta, M. K.; Goel, Prabhatasree; Mittal, R.; Chaplot, S. L.
2010-12-01
Lithium oxide is an important material because of its high thermal conductivity and superionic behavior at high temperature. It behaves like a superionic conductor above 1200 K. Phonon frequencies have been calculated using ab-initio method. The calculations of phonon dispersion relation near unit cell volume corresponding to the superionic transition indicate softening of zone boundary transverse acoustic phonon mode along (110). The instability of phonon mode could lead to the dynamical disorder of lithium sub lattice. Thermal expansion and equation of states are also computed. The results compare well with our previous semi-empirical potential calculations.
Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; ...
2014-10-20
This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitationmore » on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.« less
NASA Astrophysics Data System (ADS)
John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.
2016-04-01
We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.
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.
Lu, Zhenyu; Zhang, Yingkai
2009-01-01
In order to further improve the accuracy and applicability of combined quantum mechanical/molecular mechanical (QM/MM) methods, we have interfaced the ab initio QM method with the classical Drude oscillator polarizable MM force field (ai-QM/MM-Drude). Different coupling approaches have been employed and compared: 1. the conventional dual self-consistent-field (SCF) procedure; 2. the direct SCF scheme, in which QM densities and MM Drude positions are converged simultaneously; 3. the micro-iterative SCF scheme, in which the Drude positions of the polarizable model are fully converged during each self-consistent field (SCF) step of QM calculations; 4. the one-step-Drude-update scheme, in which the MM Drude positions are updated only once instead of fully converged during each molecular dynamics (MD) step. The last three coupling approaches are found to be efficient and can achieve the desired convergence in a similar number of QM SCF steps comparing with the corresponding QM method coupled to a non-polarizable force field. The feasibility and applicability of the implemented ai-QM/MM-Drude approach have been demonstrated by carrying out Born-Oppenheimer molecular dynamics simulations with the umbrella sampling method to determine potentials of mean force for both the methyl transfer reaction of the methyl chlorine-chlorine ion system and the glycine intra-molecular proton transfer reaction in aqueous solution. Our results indicate that the ai-QM/MM-Drude approach is very promising, which provides a better description of QM/MM interactions while can achieve quite similar computational efficiency in comparison with the corresponding conventional ab initio QM/MM method. PMID:19221605
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.
Grid-based methods for biochemical ab initio quantum chemical applications
Colvin, M.E.; Nelson, J.S.; Mori, E.
1997-01-01
A initio quantum chemical methods are seeing increased application in a large variety of real-world problems including biomedical applications ranging from drug design to the understanding of environmental mutagens. The vast majority of these quantum chemical methods are {open_quotes}spectral{close_quotes}, that is they describe the charge distribution around the nuclear framework in terms of a fixed analytic basis set. Despite the additional complexity they bring, methods involving grid representations of the electron or solvent charge can provide more efficient schemes for evaluating spectral operators, inexpensive methods for calculating electron correlation, and methods for treating the electrostatic energy of salvation in polar solvents. The advantage of mixed or {open_quotes}pseudospectral{close_quotes} methods is that they allow individual non-linear operators in the partial differential equations, such as coulomb operators, to be calculated in the most appropriate regime. Moreover, these molecular grids can be used to integrate empirical functionals of the electron density. These so-called density functional methods (DFT) are an extremely promising alternative to conventional post-Hartree Fock quantum chemical methods. The introduction of a grid at the molecular solvent-accessible surface allows a very sophisticated treatment of a polarizable continuum solvent model (PCM). Where most PCM approaches use a truncated expansion of the solute`s electric multipole expansion, e.g. net charge (Born model) or dipole moment (Onsager model), such a grid-based boundary-element method (BEM) yields a nearly exact treatment of the solute`s electric field. This report describes the use of both DFT and BEM methods in several biomedical chemical applications.
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.
Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W
2016-08-25
Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and
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 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.
Ab initio alpha-alpha scattering.
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-12-03
Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Ab initio study of cyanoguanidine isomers
NASA Astrophysics Data System (ADS)
Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.
1995-06-01
An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers ('cyanioime' and 'cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.
Ab initio study of cyanoguanidine isomers
NASA Astrophysics Data System (ADS)
Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.
1995-06-01
An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers (‘cyanioime' and ‘cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.
NASA Astrophysics Data System (ADS)
Bacca, Sonia
2016-04-01
A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.
Ab initio 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
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.
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.
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.
Kim, B.
1990-10-01
This report discusses the following topics: molecular structure of NO{sub 3} radical studied by laser induced fluorescence; photodissociation and fluorescence spectroscopy of NO{sub 3} in molecular beam; vertical electronic spectrum of NO{sub 3}:{sup 2}A{prime}{sub 2}, {sup 2}E{double prime}({sup 2}A{sub 2}{sup 2}B{sub 1}), and {sup 2}E{prime} states; and Ab initio study of the vibrational spectra of NO{sub 3}.
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 phase diagram of iridium
NASA Astrophysics Data System (ADS)
Burakovsky, L.; Burakovsky, N.; Cawkwell, M. J.; Preston, D. L.; Errandonea, D.; Simak, S. I.
2016-09-01
The phase diagram of iridium is investigated using the Z methodology. The Z methodology is a technique for phase diagram studies that combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. In the direct Z method, the solid phases along the melting curve are determined by comparing the solid-liquid equilibrium boundaries of candidate crystal structures. The inverse Z method involves quenching the liquid into the most stable solid phase at various temperatures and pressures to locate a solid-solid boundary. Although excellent agreement with the available experimental data (to ≲65 GPa) is found for the equation of state (EOS) of Ir, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes our ab initio data to higher pressure (P ) . Our results suggest the existence of a random-stacking hexagonal close-packed structure of iridium at high P . We offer an explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.
Ab Initio 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).
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.
Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi
2014-02-01
The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine.
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.
Multiscale Design of Advanced Materials based on Hybrid Ab Initio and Quasicontinuum Methods
Luskin, Mitchell
2014-03-12
This project united researchers from mathematics, chemistry, computer science, and engineering for the development of new multiscale methods for the design of materials. Our approach was highly interdisciplinary, but it had two unifying themes: first, we utilized modern mathematical ideas about change-of-scale and state-of-the-art numerical analysis to develop computational methods and codes to solve real multiscale problems of DOE interest; and, second, we took very seriously the need for quantum mechanics-based atomistic forces, and based our methods on fast solvers of chemically accurate methods.
Ab initio modeling of carbohydrates: on the proper selection of computational methods and basis sets
Technology Transfer Automated Retrieval System (TEKTRAN)
With the development of faster computer hardware and quantum mechanical software it has become more feasible to study large carbohydrate molecules via quantum mechanical methods. In the past, studies of carbohydrates were restricted to empirical/semiempirical methods and Hartree Fock. In the last ...
Orimoto, Yuuichi; Xie, Peng; Liu, Kai; Yamamoto, Ryohei; Imamura, Akira; Aoki, Yuriko
2015-03-14
An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs’ inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligibly small energy error in the total energy calculations (in the order of 10{sup −7}–10{sup −8} hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. −290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for
NASA Astrophysics Data System (ADS)
Orimoto, Yuuichi; Yamamoto, Ryohei; Xie, Peng; Liu, Kai; Imamura, Akira; Aoki, Yuriko
2015-03-01
An Elongation-counterpoise (ELG-CP) method was developed for performing accurate and efficient interaction energy analysis and correcting the basis set superposition error (BSSE) in biosystems. The method was achieved by combining our developed ab initio O(N) elongation method with the conventional counterpoise method proposed for solving the BSSE problem. As a test, the ELG-CP method was applied to the analysis of the DNAs' inter-strands interaction energies with respect to the alkylation-induced base pair mismatch phenomenon that causes a transition from G⋯C to A⋯T. It was found that the ELG-CP method showed high efficiency (nearly linear-scaling) and high accuracy with a negligibly small energy error in the total energy calculations (in the order of 10-7-10-8 hartree/atom) as compared with the conventional method during the counterpoise treatment. Furthermore, the magnitude of the BSSE was found to be ca. -290 kcal/mol for the calculation of a DNA model with 21 base pairs. This emphasizes the importance of BSSE correction when a limited size basis set is used to study the DNA models and compare small energy differences between them. In this work, we quantitatively estimated the inter-strands interaction energy for each possible step in the transition process from G⋯C to A⋯T by the ELG-CP method. It was found that the base pair replacement in the process only affects the interaction energy for a limited area around the mismatch position with a few adjacent base pairs. From the interaction energy point of view, our results showed that a base pair sliding mechanism possibly occurs after the alkylation of guanine to gain the maximum possible number of hydrogen bonds between the bases. In addition, the steps leading to the A⋯T replacement accompanied with replications were found to be unfavorable processes corresponding to ca. 10 kcal/mol loss in stabilization energy. The present study indicated that the ELG-CP method is promising for
NASA Astrophysics Data System (ADS)
Kurz, Ph.; Förster, F.; Nordström, L.; Bihlmayer, G.; Blügel, S.
2004-01-01
The massively parallelized full-potential linearized augmented plane-wave bulk and film program FLEUR for first-principles calculations in the context of density functional theory was adapted to allow calculations of materials with complex magnetic structures—i.e., with noncollinear spin arrangements and incommensurate spin spirals. The method developed makes no shape approximation to the charge density and works with the continuous vector magnetization density in the interstitial and vacuum region and a collinear magnetization density in the spheres. We give an account of the implementation. Important technical aspects, such as the formulation of a constrained local moment method in a full-potential method that works with a vector magnetization density to deal with specific preselected nonstationary-state spin configurations, the inclusion of the generalized gradient approximation in a noncollinear framework, and the spin-relaxation method are discussed. The significance and validity of different approximations are investigated. We present examples to the various strategies to explore the magnetic ground state, metastable states, and magnetic phase diagrams by relaxation of spin arrangements or by performing calculations for constraint spin configurations to invest the functional dependence of the total energy and magnetic moment with respect to external parameters.
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.
Intrinsic errors in several ab initio methods. The dissociation energy of N{sub 2}
Peterson, K.A. |; Dunning, T.H. Jr.
1995-03-23
Using sequences of correlation consistent basis sets, complete basis set (CBS) limits for the dissociation energy D{sub c} of N{sub 2} have been estimated for a variety of commonly used electron correlation methods. After extrapolation to the CBS limit, the difference between theory and experiment corresponds to the error intrinsic to the chosen theoretical method. Correlated wave functions (valence electrons correlated only) for which intrinsic errors have been estimated include internally contracted multireference configuration interaction (CMRCI), singles and doubles coupled cluster theory with and without perturbative triple excitations [CCSD, CCSD(T)], and second-, third-, and fourth-order Moller-Plesset perturbation theory (MP2, MP3, MP4). For CMRCI and CCSD(T), D{sub c} converges smoothly from below the experimental value and yields the smallest intrinsic errors, -0.8 and -1.6 kcal/mol, respectively. In contrast, for MP2 and MP4, D{sub c} exhibits fortuitously good agreement with experiment for small basis sets but leads to CBS limits that are 11.6 and 3.4 kcal/mol larger than experiment, respectively. Correlation of the 1s core electrons is predicted to yield intrinsic errors of less than 1 kcal/mol for CMRCI and CCSD(T), while those for MP2 and MP4 increase still further. 38 refs., 1 fig., 1 tab.
Probing gas adsorption in MOFs using an efficient ab initio widom insertion Monte Carlo method.
Lee, Youhan; Poloni, Roberta; Kim, Jihan
2016-12-15
We propose a novel biased Widom insertion method that can efficiently compute the Henry coefficient, KH , of gas molecules inside porous materials exhibiting strong adsorption sites by employing purely DFT calculations. This is achieved by partitioning the simulation volume into strongly and weakly adsorbing regions and selectively biasing the Widom insertion moves into the former region. We show that only few thousands of single point energy calculations are necessary to achieve accurate statistics compared to many hundreds of thousands or millions of such calculations in conventional random insertions. The methodology is used to compute the Henry coefficient for CO2 , N2 , CH4 , and C2 H2 in M-MOF-74(M = Zn and Mg), yielding good agreement with published experimental data. Our results demonstrate that the DFT binding energy and the heat of adsorption are not accurate enough indicators to rank the guest adsorption properties at the Henry regime. © 2016 Wiley Periodicals, Inc.
Accurate treatment of total photoabsorption cross sections by an ab initio time-dependent method
NASA Astrophysics Data System (ADS)
Daud, Mohammad Noh
2014-09-01
A detailed discussion of parallel and perpendicular transitions required for the photoabsorption of a molecule is presented within a time-dependent view. Total photoabsorption cross sections for the first two ultraviolet absorption bands of the N2O molecule corresponding to transitions from the X1 A' state to the 21 A' and 11 A'' states are calculated to test the reliability of the method. By fully considering the property of the electric field polarization vector of the incident light, the method treats the coupling of angular momentum and the parity differently for two kinds of transitions depending on the direction of the vector whether it is: (a) situated parallel in a molecular plane for an electronic transition between states with the same symmetry; (b) situated perpendicular to a molecular plane for an electronic transition between states with different symmetry. Through this, for those transitions, we are able to offer an insightful picture of the dynamics involved and to characterize some new aspects in the photoabsorption process of N2O. Our calculations predicted that the parallel transition to the 21 A' state is the major dissociation pathway which is in qualitative agreement with the experimental observations. Most importantly, a significant improvement in the absolute value of the total cross section over previous theoretical results [R. Schinke, J. Chem. Phys. 134, 064313 (2011), M.N. Daud, G.G. Balint-Kurti, A. Brown, J. Chem. Phys. 122, 054305 (2005), S. Nanbu, M.S. Johnson, J. Phys. Chem. A 108, 8905 (2004)] was obtained.
Accurate treatment of total photoabsorption cross sections by an ab initio time-dependent method
NASA Astrophysics Data System (ADS)
Noh Daud, Mohammad
2014-09-01
A detailed discussion of parallel and perpendicular transitions required for the photoabsorption of a molecule is presented within a time-dependent view. Total photoabsorption cross sections for the first two ultraviolet absorption bands of the N2O molecule corresponding to transitions from the X1A' state to the 21A' and 11A'' states are calculated to test the reliability of the method. By fully considering the property of the electric field polarization vector of the incident light, the method treats the coupling of angular momentum and the parity differently for two kinds of transitions depending on the direction of the vector whether it is: (a) situated parallel in a molecular plane for an electronic transition between states with the same symmetry; (b) situated perpendicular to a molecular plane for an electronic transition between states with different symmetry. Through this, for those transitions, we are able to offer an insightful picture of the dynamics involved and to characterize some new aspects in the photoabsorption process of N2O. Our calculations predicted that the parallel transition to the 21A' state is the major dissociation pathway which is in qualitative agreement with the experimental observations. Most importantly, a significant improvement in the absolute value of the total cross section over previous theoretical results [R. Schinke, J. Chem. Phys. 134, 064313 (2011), M.N. Daud, G.G. Balint-Kurti, A. Brown, J. Chem. Phys. 122, 054305 (2005), S. Nanbu, M.S. Johnson, J. Phys. Chem. A 108, 8905 (2004)] was obtained.
NASA Astrophysics Data System (ADS)
Kanan, Dalal K.
Photoelectrochemical cells (PECs) use sunlight to drive endoergic reactions such as carbon dioxide reduction to fuels or water-splitting for renewable hydrogen production. However, materials that combine both the efficiency and low cost needed to make solar-powered catalysis a practical reality have yet to be discovered. This thesis presents methods and new design strategies for developing novel, efficient, robust, and inexpensive photocatalysts based on transition metal oxides (TMOs). Quantum mechanics methodologies are developed and tested for their ability to predict the properties of known materials and then used to predict how altering the composition by alloying and doping with abundant elements affects optical, electronic, transport, and catalytic properties. The first material considered for photocatalysis is MnO, the bio-inspired solid state analogue of the photosystem II active site. GW theory with input from hybrid DFT and ab initio DFT+U capably predicts the photoemission/inverse photoemission (PE/IPE) band gap and dielectric properties. An ab initio value of U-J = 3.5 eV for Mn2+ was determined using unrestricted Hartree-Fock theory on cluster-size-converged electrostatically embedded clusters. The lowest-lying excitations in MnO, studied using ECW theory, are found to be single Mn d → d ligand field excitations (~2.5 eV, ~108 s lifetime), followed by double d → d excitations (~5.2 eV, ~106 s lifetime), Mn 3d-4s excitations (~6.3 eV, ~10-3 s lifetime), and higher-lying O 2p → Mn 3d ligand-to-metal charge-transfer (LMCT) excitations (~10.1 eV, ~10-4 s lifetime). The longer-lived transitions should exhibit better electron-hole pair separation and enhance photoconductivity depending on ease of carrier transport. While MnO possesses suitable band edge energies, its band gap is too large for efficient sunlight absorption. We predict alloying MnO with ZnO in varying amounts reduces the PE/IPE band gap (to 2.6 eV for the 1:1 alloy) while preserving
Heats of Segregation of BCC Metals Using Ab Initio and Quantum Approximate Methods
NASA Technical Reports Server (NTRS)
Good, Brian; Chaka, Anne; Bozzolo, Guillermo
2003-01-01
Many multicomponent alloys exhibit surface segregation, in which the composition at or near a surface may be substantially different from that of the bulk. A number of phenomenological explanations for this tendency have been suggested, involving, among other things, differences among the components' surface energies, molar volumes, and heats of solution. From a theoretical standpoint, the complexity of the problem has precluded a simple, unified explanation, thus preventing the development of computational tools that would enable the identification of the driving mechanisms for segregation. In that context, we investigate the problem of surface segregation in a variety of bcc metal alloys by computing dilute-limit heats of segregation using both the quantum-approximate energy method of Bozzolo, Ferrante and Smith (BFS), and all-electron density functional theory. In addition, the composition dependence of the heats of segregation is investigated using a BFS-based Monte Carlo procedure, and, for selected cases of interest, density functional calculations. Results are discussed in the context of a simple picture that describes segregation behavior as the result of a competition between size mismatch and alloying effects
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.
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.
NASA Astrophysics Data System (ADS)
Szalay, Péter G.; Holka, Filip; Fremont, Julien; Rey, Michael; Tyuterev, Vladimir G.
2011-06-01
The aim of the study was to explore the limits of initio methods towards the description of excited vibrational levels up to the dissociation limit for molecules having more than two electrons. To this end a high level ab initio potential energy function was constructed for the four-electron LiH molecule in order to accurately predict a complete set of bound vibrational levels corresponding to the electronic ground state. It was composed from: a) an ab initio non-relativistic potential obtained at the MR-CISD level including size-extensivity corrections and quintuple-sextuple ζ extrapolation of the basis, b) MVD (Mass-velocity-Darwin) relativistic corrections obtained at icMR-CISD/cc-pwCV5Z level, and c) DBOC (Diagonal Born-Oppenheimer correction) obtained at the MR-CISD/cc-pwCVTZ level. Finally, the importance of non-adiabatic effects was also tested by using atomic masses in the vibrational kinetic energy operator and by calculation of non-adiabatic coupling by ab initio methods. The calculated vibrational levels were compared with those obtained from experimental data [J.A. Coxon and C.S. Dickinson, J. Chem. Phys., 2004, 121, 9378]. Our best estimate of the potential curve results in vibrational energies with a RMS deviation of only ˜1 wn\\ for the entire set of all empirically determined vibrational levels known so far. These results represent a drastic improvement over previous theoretical predictions of vibrational levels of ^7LiH up to dissociation, D_0, which was predicted to be 19594 Cm-1. In addition, rotational levels have also been calculated. The RMS deviation between our ab initio calculations and empirical results by Coxon and Dickinson for rotational spacings Δ E = E(v, J = 1)-E(v, J = 0) over all available vibrational states of ^7LiH from v = 0 to v= 20 is 0.010 wn (with nuclear masses) and 0.006 wn (with atomic masses). Note that for high vibrational states with v > 6 this falls within the uncertainty of the measurements.
Application of ab-initio Methods to Grain Boundaries and Point Defects for Poly-CdTe Solar Cells
NASA Astrophysics Data System (ADS)
Buurma, Christopher
CdTe is a material well-suited to solar cell applications due to its 1.5 eV direct bandgap and high optical absorption. To meet energy demands, CdTe solar cells must be produced at a low-cost and with high throughput which often demands the use of non-ideal polycrystalline CdTe. As a result of careful process control, current thin-film poly-CdTe cells have been shown to be somewhat defect tolerant with proven industry success. Yet despite this success poly-CdTe cells are still far from their predicted Shockley-Queisser theoretical limits. The next generation cells must demonstrate higher open-circuit voltages, fill factors, and longer minority carrier lifetimes. Playing a major role in doping, defect migration, carrier recombination, and current transport are 2D extended defects both within grains and between grains as grain boundaries (GBs). A further understanding of these defects is needed which exhibit either high symmetry such as the CSL structures or those mixed or random GBs with low symmetry. Their corresponding formation and electronic behavior will be needed to develop methods to mitigate their effects and instead promote higher doping with less minority carrier recombination. Predictions and guidance on electronic and thermodynamic properties can be obtained from model atomic structures within the framework of ab-initio density-functional theory. Bulk point defect formation energies were determined for comparison to calculations of point defects along GB structures. Model atomic structures of GBs can also be created rapidly and over a wide parameter space using the Grain Boundary Genie code developed for this project. Commonly observed low-angle and special coincident grain boundaries structures were created and a subset relaxed to determine their local strain environment and interfacial energy with for comparison to STEM observations. Additionally, a series of random angle or 'mixed' grain boundaries were created and investigated corresponding to
Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations
NASA Technical Reports Server (NTRS)
Good, Brian S.
2003-01-01
We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.
Ab initio 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).
Towards Accurate Ab Initio Predictions of the Spectrum of Methane
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Kwak, Dochan (Technical Monitor)
2001-01-01
We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.
Ab initio 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 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.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.
Discovering chemistry with an ab initio nanoreactor
NASA Astrophysics Data System (ADS)
Martinez, Todd
Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.
Ab Initio Calculation of the Hoyle State
Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.
2011-05-13
The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.
Guiding ab initio calculations by alchemical derivatives
NASA Astrophysics Data System (ADS)
to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.
2016-03-01
We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-01-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less
NASA Astrophysics Data System (ADS)
Jayaprakash, A.; Arjunan, V.; Jose, Sujin P.; Mohan, S.
2011-12-01
The energy, geometrical parameters and vibrational wavenumbers of crotonaldehyde were calculated by using ab initio and B3LYP with 6-31G(d,p) and 6-311G(d,p) basis sets. The FT-IR and FT-Raman spectra for liquid state crotonaldehyde have been recorded in the region 3400-400 cm -1 and 3400-100 cm -1, respectively and compared with the theoretical spectrographs constructed from the scaled harmonic vibrational frequencies calculated at HF and DFT levels. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Detailed interpretations on vibrational modes have been made on the observed and theoretical spectra and PED for each mode was also reported more precisely. HOMO and LUMO energy levels are constructed and the corresponding theoretical frontier energy gaps are calculated to realise the charge transfer occurring in the molecule. The thermodynamic properties of the title compound have been calculated at different temperatures and the results reveals the standard heat capacities ( C0p), standard entropies ( S0) and standard enthalpy changes (Δ H0) increases with rise in temperature.
da Silva, F Ferreira; Duflot, D; Hoffmann, S V; Jones, N C; Rodrigues, F N; Ferreira-Rodrigues, A M; de Souza, G G B; Mason, N J; Eden, S; Limão-Vieira, P
2015-08-06
We present the first set of ab initio calculations (vertical energies and oscillator strengths) of the valence and Rydberg transitions of the anaesthetic compound halothane (CF3CHBrCl). These results are complemented by high-resolution vacuum ultraviolet photoabsorption measurements over the wavelength range 115-310 nm (10.8-4.0 eV). The spectrum reveals several new features that were not previously reported in the literature. Spin-orbit effects have been considered in the calculations for the lowest-lying states, allowing us to explain the broad nature of the 6.1 and 7.5 eV absorption bands assigned to σ*(C-Br) ← nBr and σ*(C-Cl) ← n(Cl) transitions. Novel absolute photoabsorption cross sections from electron scattering data were derived in the 4.0-40.0 eV range. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of halothane in the upper stratosphere (20-50 km).
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.
E. Bohm A. Bhatele L. V. Kale M. E. Tuckerman S. Kumar J. A. Gunnels G. J. Martyna; Bohm, E.; Bhatele, A.; Kale, L. V.; Tuckerman, M. E.; Kumar, S.; Gunnels, J. A.; Martyna, G. J.
2008-01-01
Important scientific problems can be treated via ab initio-based molecular modeling approaches, wherein atomic forces are derived from an energy Junction that explicitly considers the electrons. The Car-Parrinello ab initio molecular dynamics (CPAIMD) method is widely used to study small systems containing on the order of 10 to 103 atoms. However, the impact of CPAIMD has been limited until recently because of difficulties inherent to scaling the technique beyond processor numbers about equal to the number of electronic states. CPAIMD computations involve a large number of interdependent phases with high interprocessor communication overhead. These phases require the evaluation of various transforms and non-square matrix multiplications that require large interprocessor data movement when efficiently parallelized. Using the Charm++ parallel programming language and runtime system, the phases are discretized into a large number of virtual processors, which are, in turn, mapped flexibly onto physical processors, thereby allowing interleaving of work. Algorithmic and IBM Blue Gene/L(tm) system-specific optimizations are employed to scale the CPAIMD method to at least 30 times the number of electronic states in small systems consisting of 24 to 768 atoms (32 to 1,024 electronic states) in order to demonstrate fine-grained parallelism. The largest systems studied scaled well across the entire machine (20,480 nodes).
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 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.
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.
Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; Martínez, Todd J.; Gordon, Mark S.
2014-10-20
This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitation on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.
NASA Astrophysics Data System (ADS)
Duguet, T.; Bender, M.; Ebran, J.-P.; Lesinski, T.; Somà, V.
2015-12-01
This programmatic paper lays down the possibility to reconcile the necessity to resum many-body correlations into the energy kernel with the fact that safe multi-reference energy density functional (EDF) calculations cannot be achieved whenever the Pauli principle is not enforced, as is for example the case when many-body correlations are parametrized under the form of empirical density dependencies. Our proposal is to exploit a newly developed ab initio many-body formalism to guide the construction of safe, explicitly correlated and systematically improvable parametrizations of the off-diagonal energy and norm kernels that lie at the heart of the nuclear EDF method. The many-body formalism of interest relies on the concepts of symmetry breaking and restoration that have made the fortune of the nuclear EDF method and is, as such, amenable to this guidance. After elaborating on our proposal, we briefly outline the project we plan to execute in the years to come.
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 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 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)
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.
NASA Astrophysics Data System (ADS)
Xu, Shuang; Zhao, Dong-xia; Gong, Li-dong; Liu, Cui; Yang, Zhong-Zhi
2015-01-01
ABEEMσπ polarizable force field (PFF) with fluctuating charges works well for searching stable conformations of Val-dipeptide and Val-tripeptide, showing importance of the polarization. The results demonstrate that ABEEMσπ PFF is able to search out all the 6 types of stable conformations of Val-dipeptide and 34 types of stable conformations of Val-tripeptide that are just all exactly found by the calculations of ab initio B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) methods. In contrast, the force fields with the fixed-charges (FC), such as ABEEMσπ-FC, AMBER-FC 99sb and OPLS/AA-FC force fields can only search out less or much less numbers of stable conformations for them.
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.
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.
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 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.
Bochevarov, Arteum D; Temelso, Berhane; Sherrill, C David
2006-08-07
Moller-Plesset second-order (MP2) perturbation theory remains the least expensive standard ab initio method that includes electron correlation, scaling as O(N5) with the number of molecular orbitals N. Unfortunately, when restricted Hartree-Fock orbitals are employed, the potential energy curves calculated with this method are of little use at large interatomic separations because of the divergent behavior of MP2 in these regions. In our previous study [J. Chem. Phys. 122, 234110 (2005)] we combined the MP2 method with the singles and doubles coupled cluster (CCSD) method to produce a hybrid method that retains the computational scaling of MP2 and improves dramatically the shape of the MP2 curves. In this work we expand the hybrid methodology to several other schemes. We investigate a new, improved MP2-CCSD method as well as a few other O(N5) methods related to the Epstein-Nesbet pair correlation theory. Nonparallelity errors across the dissociation curve as well as several spectroscopic constants are computed for BH, HF, H2O, CH+, CH4, and Li2 molecules with the 6-31G* basis set and compared with the corresponding full configuration interaction results. We show that among the O(N5) methods considered, our new hybrid MP2-CCSD method is the most accurate and significantly outperforms MP2 not only at large interatomic separations, but also near equilibrium geometries.
Barrett, Bruce R.; Navrátil, Petr; Vary, James P.
2012-11-17
A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN
Ab Initio 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.
NASA Astrophysics Data System (ADS)
Réal, Florent; Vallet, Valérie; Flament, Jean-Pierre; Schamps, Joël
2006-11-01
Ab initio study of excitation energies and oscillator strengths for absorption towards the P13 and P11 states of the Bi3+ ion has been performed for the Bi3+ ion in gas phase and as a dopant of the cubic elpasolite Cs2NaYCl6 and the yttria Y2O3 crystal using the ab initio embedded-cluster method. The ground and excited states were computed with a relativistic spin-orbit configuration interaction approach suited for heavy elements. Electron correlation was treated in the scalar relativistic scheme with perturbative, variational, and coupled-cluster methods. Intermediate coupling is included via an effective-Hamiltonian based spin-orbit configuration interaction approach. Small-core (60 electrons) and large-core (78 electrons) relativistic effective core potentials (ECPs) have been used to describe the bismuth ion. The best match with experiment was obtained with the small-core ECP. The accuracy of excitation energies strongly depends on the electron correlation method used. The agreement between experimental data and the results obtained using second-order multiconfigurational perturbation theory is greatly improved with the shifted zeroth-order Hamiltonian proposed by Ghido et al. [Chem. Phys. Lett. 396, 142 (2004)]. Although quite time consuming, coupled-cluster and variational methods yield good agreement with experimental data. The first absorption band recorded for the doped elpasolite crystal is positioned with an excellent accuracy while the computed energy of the second absorbing manifold is in poorer agreement with experimental data. This suggests that interactions with neglected close-lying excited states with a ligand-to-metal charge transfer character may be significant. Calculations of the spectrum of Bi3+ doping yttria in both the S6 and C2 site symmetries indicate that the absorbing manifold arises from electronic excitations localized on the Bi3+ doping ion with main triplet 6s6p character. Our results predict the first absorbing peak to lie about 0
NASA Astrophysics Data System (ADS)
Nishioka, Hirotaka; Ando, Koji
2011-05-01
By making use of an ab initio fragment-based electronic structure method, fragment molecular orbital-linear combination of MOs of the fragments (FMO-LCMO), developed by Tsuneyuki et al. [Chem. Phys. Lett. 476, 104 (2009)], 10.1016/j.cplett.2009.05.069, we propose a novel approach to describe long-distance electron transfer (ET) in large system. The FMO-LCMO method produces one-electron Hamiltonian of whole system using the output of the FMO calculation with computational cost much lower than conventional all-electron calculations. Diagonalizing the FMO-LCMO Hamiltonian matrix, the molecular orbitals (MOs) of the whole system can be described by the LCMOs. In our approach, electronic coupling TDA of ET is calculated from the energy splitting of the frontier MOs of whole system or perturbation method in terms of the FMO-LCMO Hamiltonian matrix. Moreover, taking into account only the valence MOs of the fragments, we can considerably reduce computational cost to evaluate TDA. Our approach was tested on four different kinds of model ET systems with non-covalent stacks of methane, non-covalent stacks of benzene, trans-alkanes, and alanine polypeptides as their bridge molecules, respectively. As a result, it reproduced reasonable TDA for all cases compared to the reference all-electron calculations. Furthermore, the tunneling pathway at fragment-based resolution was obtained from the tunneling current method with the FMO-LCMO Hamiltonian matrix.
Fedorov, Dmitry A; Pruitt, Spencer R; Keipert, Kristopher; Gordon, Mark S; Varganov, Sergey A
2016-05-12
Dynamics at intersystem crossings are fundamental to many processes in chemistry, physics, and biology. The ab initio multiple spawning (AIMS) method was originally developed to describe internal conversion dynamics at conical intersections where derivative coupling is responsible for nonadiabatic transitions between electronic states with the same spin multiplicity. Here, the applicability of the AIMS method is extended to intersystem crossing dynamics in which transitions between electronic states with different spin multiplicities are mediated by relativistic spin-orbit coupling. In the direct AIMS dynamics, the nuclear wave function is expanded in the basis of frozen multidimensional Gaussians propagating on the coupled electronic potential energy surfaces calculated on the fly. The AIMS method for intersystem crossing is used to describe the nonadiabatic transitions between the (3)B1 and (1)A1 states of GeH2. The potential energies and gradients were obtained at the CASSCF(6,6)/6-31G(d) level of theory. The spin-orbit coupling matrix elements were calculated with the configuration interaction method using the two-electron Breit-Pauli Hamiltonian. The excited (3)B1 state lifetime and intersystem crossing rate constants were estimated by fitting the AIMS state population with the first-order kinetics equation for a reversible unimolecular reaction. The obtained rate constants are compared with the values predicted by the statistical nonadiabatic transition state theory with transition probabilities calculated using the Landau-Zener and weak coupling formulas.
Nishioka, Hirotaka; Ando, Koji
2011-05-28
By making use of an ab initio fragment-based electronic structure method, fragment molecular orbital-linear combination of MOs of the fragments (FMO-LCMO), developed by Tsuneyuki et al. [Chem. Phys. Lett. 476, 104 (2009)], we propose a novel approach to describe long-distance electron transfer (ET) in large system. The FMO-LCMO method produces one-electron Hamiltonian of whole system using the output of the FMO calculation with computational cost much lower than conventional all-electron calculations. Diagonalizing the FMO-LCMO Hamiltonian matrix, the molecular orbitals (MOs) of the whole system can be described by the LCMOs. In our approach, electronic coupling T(DA) of ET is calculated from the energy splitting of the frontier MOs of whole system or perturbation method in terms of the FMO-LCMO Hamiltonian matrix. Moreover, taking into account only the valence MOs of the fragments, we can considerably reduce computational cost to evaluate T(DA). Our approach was tested on four different kinds of model ET systems with non-covalent stacks of methane, non-covalent stacks of benzene, trans-alkanes, and alanine polypeptides as their bridge molecules, respectively. As a result, it reproduced reasonable T(DA) for all cases compared to the reference all-electron calculations. Furthermore, the tunneling pathway at fragment-based resolution was obtained from the tunneling current method with the FMO-LCMO Hamiltonian matrix.
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.
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.
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.
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 theory of spin fluctuations in magnets
NASA Astrophysics Data System (ADS)
Antropov, Vladimir; Ke, Liqin; van Schilfgaarde, Mark; Katsnelson, Mikhael
2011-03-01
We propose a framework for a true ab initio theory of magnetism, based on many-body perturbation theory (MPBT). It fits in naturally with methods based MPBT such as the GW approximation; but the approach can be implemented as an extension to any existing static method for electronic structure such as the local spin density approximation to density functional theory, to include spin fluctuations. Initially we calculated the spin fluctuation contributions using random phase approximation. The self consistency procedure similar to the one used in Moryia-Kawabata theory can be naturally implemented. The fluctuation dissipation theorem is used to calculate the reduction of the mean field magnetic moment in itinerant magnets. The applications of the technique includes traditional 3d ferromagnetic metals, their alloys and compounds and 5f systems.
Ab initio 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.
NASA Astrophysics Data System (ADS)
H., Michael; | Isobel C., Palmer; Walker
2010-08-01
The electronic vertical excitation energies for singlet and triplet valence, and Rydberg states of trans-buta-1,3-diene have been computed using ab initio multi-reference multi-root CI procedures with a [4s3p3d3f] set of Rydberg functions. Close numerical agreement between theory and experiment was found for a number of low-lying electronic states. The present CI and CASSCF [8MO,8e] calculations suggest that both the vertical and adiabatic order of the valence (ππ∗) states is: A˜1Amethods are generally in good agreement with each other. The C 1C 2 to C 2C 3 bond length ratio in the excited states varies widely, and is discussed.
NASA Astrophysics Data System (ADS)
Palmer, Michael H.; Ganzenmüller, Georg; Walker, Isobel C.
2007-04-01
The oxazole VUV absorption spectrum over the range 5-12 eV shows intense bands centred near 6.3, 7.5, 8.3, 9.6 and 10.8 eV. The electron energy-loss (EEL) spectrum shows additional structure with a strong peak (˜1.4 eV) arising from resonant vibrational excitation of the molecule via a shape resonance, and a spin-forbidden 3ππ ∗ state at 4.6 eV. Electronic excitation energies for valence and Rydberg-type states have been computed using ab initio multi-reference multi-root CI methods. The CI studies used a triple zeta + polarisation basis set, augmented by diffuse (Rydberg) orbitals, to generate the theoretical singlet and triplet energy manifolds. The correlation of theory and experiment shows the nature of the more intense Rydberg state types, and identification of the main valence and Rydberg bands. Calculated energies for low-lying Rydberg states are relatively close (SD 0.38) to those expected, and there is generally a good correlation between the theoretical and experimental envelopes. Two of the three lowest electronic states arise from ππ ∗ excitation of the outer (3a″ and 2a″) π-orbitals, with one state (LP Nπ ∗) originating from the lone pair on nitrogen (15a') between them.
NASA Astrophysics Data System (ADS)
Arslan, Hakan; Algül, Öztekin
2008-06-01
The room temperature attenuated total reflection Fourier transform infrared spectrum of the 2-(4-methoxyphenyl)-1 H-benzo[ d]imidazole has been recorded with diamond/ZnSe prism. The conformational behaviour, structural stability of optimized geometry, frequency and intensity of the vibrational bands of the title compound were investigated by utilizing ab initio calculations with 6-311G** basis set at HF, B3LYP, BLYP, B3PW91 and mPW1PW91 levels. The harmonic vibrational frequencies were calculated and scaled values have been compared with experimental IR spectrum. The observed and the calculated frequencies are found to be in good agreement. The theoretical vibrational spectra of the title compound were interpreted by means of potential energy distributions using VEDA 4 program. Furthermore, the optimal uniform scaling factors calculated for the title compound are 0.9120, 0.9596, 0.9660, 0.9699, and 0.9993 for HF, mPW1PW91, B3PW91, B3LYP and BLYP methods, respectively.
Mayhall, Nicholas J
2016-09-13
Due to the promise of significantly enhanced photovoltaic efficiencies, significant effort has been directed toward understanding and controlling the singlet fission mechanism. Although accurate quantum chemical calculations would provide a detail-rich view of the singlet fission mechanism, this is complicated by the multiexcitonic nature of one of the key intermediates, the (1)(TT) state. Being described as two simultaneous and singlet-coupled triplet excitations on a pair of nearest neighbor monomers, the (1)(TT) state is inherently a multielectronic excitation. This fact renders most single-reference ab initio quantum chemical methods incapable of providing accurate results. This paper serves two purposes: (1) to demonstrate that the multiexciton states in singlet fission materials can be described using a spin-only Hamiltonian and with each monomer treated as a biradical and (2) to propose a very simple procedure for extracting the values for this Hamiltonian from single-reference calculations. Numerical examples are included for a number of different systems, including dimers, trimers, tetramers, and a cluster comprised of seven chromophores.
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.
Reactive Monte Carlo sampling with an ab initio potential
Leiding, Jeff; Coe, Joshua D.
2016-05-04
Here, we present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We also discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH3 to those of ab initio molecular dynamics (AIMD). Furthermore, we find that there are regions of state space formore » which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.« less
Ab initio 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 Study of KCl and NaCl Clusters
NASA Astrophysics Data System (ADS)
Brownrigg, Clifton; Hira, Ajit; Pacheco, Jose; Salazar, Justin
2013-03-01
We continue our interest in the theoretical study of molecular clusters to examine the chemical properties of small KnCln and NanCln clusters (n = 2 - 15). The potentially important role of these molecular species in biochemical and medicinal processes is well known. This work applies the hybrid ab initio methods of quantum chemistry to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations have been performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. The potential for design of new medicinal drugs is explored.
High-throughput ab-initio dilute solute diffusion database
NASA Astrophysics Data System (ADS)
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-07-01
We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.
Khaliullin, Rustam Z; Kühne, Thomas D
2013-10-14
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.
A density functional and ab initio investigation of the p-aminobenzoic acid molecule
NASA Astrophysics Data System (ADS)
Lago, A. F.; Dávalos, J. Z.; de Brito, A. Naves
2007-08-01
The p-aminobenzoic acid (C 7H 7NO 2) molecule has been investigated at different levels of theory. DFT methods (B3LYP and PBE1PBE), second order Møller-Plesset perturbation theory (MP2) and composite ab initio methods (G3MP2 and CBS) have been employed, in conjunction with large basis sets. Important informations on the electronic structure and thermochemistry of this molecule have been extracted, and the performance of the density functional and ab initio methods has been evaluated, based on the comparison of the calculated and the available experimental data.
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
Towards SiC Surface Functionalization: An Ab Initio Study
Cicero, G; Catellani, A
2005-01-28
We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.
The application of ab initio calculations to molecular spectroscopy
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.
1989-01-01
The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.
The application of ab initio calculations to molecular spectroscopy
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.
1989-01-01
The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.
Hao, Xiao-Hu; Zhang, Gui-Jun; Zhou, Xiao-Gen; Yu, Xu-Feng
2016-01-01
To address the searching problem of protein conformational space in ab-initio protein structure prediction, a novel method using abstract convex underestimation (ACUE) based on the framework of evolutionary algorithm was proposed. Computing such conformations, essential to associate structural and functional information with gene sequences, is challenging due to the high-dimensionality and rugged energy surface of the protein conformational space. As a consequence, the dimension of protein conformational space should be reduced to a proper level. In this paper, the high-dimensionality original conformational space was converted into feature space whose dimension is considerably reduced by feature extraction technique. And, the underestimate space could be constructed according to abstract convex theory. Thus, the entropy effect caused by searching in the high-dimensionality conformational space could be avoided through such conversion. The tight lower bound estimate information was obtained to guide the searching direction, and the invalid searching area in which the global optimal solution is not located could be eliminated in advance. Moreover, instead of expensively calculating the energy of conformations in the original conformational space, the estimate value is employed to judge if the conformation is worth exploring to reduce the evaluation time, thereby making computational cost lower and the searching process more efficient. Additionally, fragment assembly and the Monte Carlo method are combined to generate a series of metastable conformations by sampling in the conformational space. The proposed method provides a novel technique to solve the searching problem of protein conformational space. Twenty small-to-medium structurally diverse proteins were tested, and the proposed ACUE method was compared with It Fix, HEA, Rosetta and the developed method LEDE without underestimate information. Test results show that the ACUE method can more rapidly and more
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.
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.
Simeon, Tomekia M; Ratner, Mark A; Schatz, George C
2013-08-22
The design and assembly of mechanically interlocked molecules, such as catenanes and rotaxanes, are dictated by various types of noncovalent interactions. In particular, [C-H···O] hydrogen-bonding and π-π stacking interactions in these supramolecular complexes have been identified as important noncovalent interactions. With this in mind, we examined the [3]catenane 2·4PF6 using molecular mechanics (MM3), ab initio methods (HF, MP2), several versions of density functional theory (DFT) (B3LYP, M0X), and the dispersion-corrected method DFT-D3. Symmetry adapted perturbation theory (DFT-SAPT) provides the highest level of theory considered, and we use the DFT-SAPT results both to calibrate the other electronic structure methods, and the empirical potential MM3 force field that is often used to describe larger catenane and rotaxane structures where [C-H···O] hydrogen-bonding and π-π stacking interactions play a role. Our results indicate that the MM3 calculated complexation energies agree qualitatively with the energetic ordering from DFT-SAPT calculations with an aug-cc-pVTZ basis, both for structures dominated by [C-H···O] hydrogen-bonding and π-π stacking interactions. When the DFT-SAPT energies are decomposed into components, we find that electrostatic interactions dominate the [C-H···O] hydrogen-bonding interactions, while dispersion makes a significant contribution to π-π stacking. Another important conclusion is that DFT-D3 based on M06 or M06-2X provides interaction energies that are in near-quantitative agreement with DFT-SAPT. DFT results without the D3 correction have important differences compared to DFT-SAPT, while HF and even MP2 results are in poor agreement with DFT-SAPT.
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.
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.
Chikayama, Eisuke; Shimbo, Yudai; Komatsu, Keiko; Kikuchi, Jun
2016-04-14
NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites.
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.
Agrawal, Paras M; Raff, Lionel M; Hagan, Martin T; Komanduri, Ranga
2006-04-07
The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO(2) system. Unlike other similar NN studies, here, we studied the dissociation of SiO(2) without the initial use of any empirical potential. During the dissociation of SiO(2) into Si+O or Si+O(2), the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process.
NASA Astrophysics Data System (ADS)
Agrawal, Paras M.; Raff, Lionel M.; Hagan, Martin T.; Komanduri, Ranga
2006-04-01
The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO2 system. Unlike other similar NN studies, here, we studied the dissociation of SiO2 without the initial use of any empirical potential. During the dissociation of SiO2 into Si +O or Si +O2, the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process.
Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao
2009-04-28
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
NASA Astrophysics Data System (ADS)
Banerjee, Debi; Ghosh, Anirban; Chattopadhyay, Sudip; Ghosh, Pradipta; Chaudhuri, Rajat K.
2014-12-01
The relative stabilities of cis- and trans- isomers of 1,2-difluoroethylene and 1,2-difluorodiazene have been studied via the state-specific multireference coupled cluster (SS-MRCC) method and its perturbative counterpart through the computation of the optimised structures and corresponding energies. Despite the existence of several cis-destabilising mechanisms, present calculations reveal the energetic preference of the cis- isomer (the cis-effect) for the systems considered here. Differences in structural parameters and vibrational frequencies among cis- and trans- isomers have been discussed. Very good agreement of our estimates has been found with the benchmark theoretical and experimental results. The SS-MRCC methods produce a smooth and consistent behaviour across the entire torsional surface for the cis-trans isomerisation indicating that the method has sufficient flexibility to model large changes in electronic structure that accompany chemical changes.
NASA Astrophysics Data System (ADS)
Corral, Inés; González, Leticia
2007-10-01
The vertical excited spectrum of a model endoperoxide (cyclohexadieneendoperoxide) has been calculated using time dependent density functional theory (TD-DFT), resolution of the identity second order approximate coupled-cluster theory (RI-CC2), multiconfigurational complete active space self consistent field (CASSCF) and second order multi-state perturbation theory (MS-CASPT2). All theoretical methods predict the charge transfer πOO∗→πCC∗, and the πOO∗→σOO∗ excitation to be the lowest absorbing excited states. CASSCF optimized geometries for these states provide some hints about the photodissociation mechanisms as well as the emission spectrum of the molecule.
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.
Feller, D.F.
1993-07-01
This collection of benchmark timings represents a snapshot of the hardware and software capabilities available for ab initio quantum chemical calculations at Pacific Northwest Laboratory`s Molecular Science Research Center in late 1992 and early 1993. The ``snapshot`` nature of these results should not be underestimated, because of the speed with which both hardware and software are changing. Even during the brief period of this study, we were presented with newer, faster versions of several of the codes. However, the deadline for completing this edition of the benchmarks precluded updating all the relevant entries in the tables. As will be discussed below, a similar situation occurred with the hardware. The timing data included in this report are subject to all the normal failures, omissions, and errors that accompany any human activity. In an attempt to mimic the manner in which calculations are typically performed, we have run the calculations with the maximum number of defaults provided by each program and a near minimum amount of memory. This approach may not produce the fastest performance that a particular code can deliver. It is not known to what extent improved timings could be obtained for each code by varying the run parameters. If sufficient interest exists, it might be possible to compile a second list of timing data corresponding to the fastest observed performance from each application, using an unrestricted set of input parameters. Improvements in I/O might have been possible by fine tuning the Unix kernel, but we resisted the temptation to make changes to the operating system. Due to the large number of possible variations in levels of operating system, compilers, speed of disks and memory, versions of applications, etc., readers of this report may not be able to exactly reproduce the times indicated. Copies of the output files from individual runs are available if questions arise about a particular set of timings.
Tang, Mei; Hu, Cui-E; Lv, Zhen-Long; Chen, Xiang-Rong; Cai, Ling-Cang
2016-12-01
The structures of cationic water clusters (H2O)8(+) have been globally explored by the particle swarm optimization method in combination with quantum chemical calculations. Geometry optimization and vibrational analysis for the 15 most interesting clusters were computed at the MP2/aug-cc-pVDZ level and infrared spectrum calculation at MPW1K/6-311++G** level. Special attention was paid to the relationships between their configurations and energies. Both MP2 and B3LYP-D3 calculations revealed that the cage-like structure is the most stable, which is different from a five-membered ring lowest energy structure but agrees well with a cage-like structure in the literature. Furthermore, our obtained cage-like structure is more stable by 0.87 and 1.23 kcal/mol than the previously reported structures at MP2 and B3LYP-D3 levels, respectively. Interestingly, on the basis of their relative Gibbs free energies and the temperature dependence of populations, the cage-like structure predominates only at very low temperatures, and the most dominating species transforms into a newfound four-membered ring structure from 100 to 400 K, which can contribute greatly to the experimental infrared spectrum. By topological analysis and reduced density gradient analysis, we also investigated the structural characteristics and bonding strengths of these water cluster radical cations.
NASA Astrophysics Data System (ADS)
Latha, B.; Gunasekaran, S.; Srinivasan, S.; Ramkumaar, G. R.
2014-11-01
The solid phase FTIR and FT-Raman spectra of Losartan have been recorded in the region 400-4000 cm-1. The spectra were interpreted in terms of fundamental modes, combination and overtone bands. The structure of the molecule was optimized and the structural characteristics were determined by Quantum chemical methods. The vibrational frequencies yield good agreement between observed and calculated values. The infrared and Raman spectra were also predicted from the calculated intensities. (1)H and (13)C NMR spectra were recorded and resonance chemical shifts of the molecule were calculated. UV-Visible spectrum of the compound was recorded in the region 200-600 nm and the electronic properties HOMO and LUMO energies calculated by TD-HF approach. NBO atomic charges of the molecules and second order perturbation theory analysis of Fock matrix also calculated and interpreted. The geometrical parameters, energies, harmonic vibrational frequencies, IR intensities, Raman intensities, and absorption wavelengths were compared with experimental and theoretical data of the molecule.
Liu, Cong; Assary, Rajeev S; Curtiss, Larry A
2014-06-26
Upgrading furan and small oxygenates obtained from the decomposition of cellulosic materials via formation of carbon-carbon bonds is critical to effective conversion of biomass to liquid transportation fuels. Simulation-driven molecular level understanding of carbon-carbon bond formation is required to design efficient catalysts and processes. Accurate quantum chemical methods are utilized here to predict the reaction energetics for conversion of furan (C4H4O) to C5-C8 ethers and the transformation of furfural (C5H6O2) to C13-C26 alkanes. Furan can be coupled with various C1 to C4 low molecular weight carbohydrates obtained from the pyrolysis via Diels-Alder type reactions in the gas phase to produce C5-C8 cyclic ethers. The computed reaction barriers for these reactions (∼25 kcal/mol) are lower than the cellulose activation or decomposition reactions (∼50 kcal/mol). Cycloaddition of C5-C8 cyclo ethers with furans can also occur in the gas phase, and the computed activation energy is similar to that of the first Diels-Alder reaction. Furfural, obtained from biomass, can be coupled with aldehydes or ketones with α-hydrogen atoms to form longer chain aldol products, and these aldol products can undergo vapor phase hydrocycloaddition (activation barrier of ∼20 kcal/mol) to form the precursors of C26 cyclic hydrocarbons. These thermochemical studies provide the basis for further vapor phase catalytic studies required for upgrading of furans/furfurals to longer chain hydrocarbons.
Separable metamaterials: analytical ab-initio homogenization and chirality
NASA Astrophysics Data System (ADS)
Ciattoni, Alessandro; Rago, Domenico; Rizza, Carlo
2016-11-01
We investigate the ab-initio homogenization of separable metamaterials with factorized dielectric permittivity profiles, which can be achieved through suitable grey-scale permittivity design techniques. Separability allows such metamaterials to be physically regarded as the superposition of three fictitious 1D generating media. We prove that, in the long-wavelength limit, separable metamaterials admit a simple and analytical description of their electromagnetic bi-anisotropic response, which can be reconstructed from the properties of the 1D generating media. Our approach provides a strategy that allows the full ab-initio and flexible design of a complex bianisotropic response by using the simple and well-known properties of 1D metamaterials.
High Level Ab Initio Kinetics as a Tool for Astrochemistry
NASA Astrophysics Data System (ADS)
Klippenstein, Stephen
2015-05-01
We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.
Spin-orbit decomposition of ab initio nuclear wave functions
NASA Astrophysics Data System (ADS)
Johnson, Calvin W.
2015-03-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.
NASA Astrophysics Data System (ADS)
Kurashige, Yuki; Yanai, Takeshi
2009-06-01
This article presents an efficient and parallelized implementation of the density matrix renormalization group (DMRG) algorithm for quantum chemistry calculations. The DMRG method as a large-scale multireference electronic structure model is by nature particularly efficient for one-dimensionally correlated systems, while the present development is oriented toward applications for polynuclear transition metal compounds, in which the macroscopic one-dimensional structure of electron correlation is absent. A straightforward extension of the DMRG algorithm is proposed with further improvements and aggressive optimizations to allow its application with large multireference active space, which is often demanded for metal compound calculations. Special efficiency is achieved by making better use of sparsity and symmetry in the operator and wave function representations. By accomplishing computationally intensive DMRG calculations, the authors have found that a large number of renormalized basis states are required to represent high entanglement of the electron correlation for metal compound applications, and it is crucial to adopt auxiliary perturbative correction to the projected density matrix during the DMRG sweep optimization in order to attain proper convergence to the solution. Potential energy curve calculations for the Cr2 molecule near the known equilibrium precisely predicted the full configuration interaction energies with a correlation space of 24 electrons in 30 orbitals [denoted by (24e,30o)]. The energies are demonstrated to be accurate to 0.6mEh (the error from the extrapolated best value) when as many as 10 000 renormalized basis states are employed for the left and right DMRG block representations. The relative energy curves for [Cu2O2]2+ along the isomerization coordinate were obtained from DMRG and other correlated calculations, for which a fairly large orbital space (32e,62o) is modeled as a full correlation space. The DMRG prediction nearly overlaps
Ab Initio Atomistic Thermodynamics for Surfaces: A Primer
2006-02-01
Ab Initio Atomistic Thermodynamics for Surfaces: A Primer Jutta Rogal and Karsten Reuter Fritz - Haber -Institut der Max-Planck-Gesellschaft... Fritz - Haber -Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING...of the Fritz - Haber -Institut, in particular Wei-Xue Li, Cathy Stampfl and Mira Todorova. Particular thanks go to Matthias Scheffler for his continued
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.
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.
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).
Ab initio calculations for industrial materials engineering: successes and challenges.
Wimmer, Erich; Najafabadi, Reza; Young, George A; Ballard, Jake D; Angeliu, Thomas M; Vollmer, James; Chambers, James J; Niimi, Hiroaki; Shaw, Judy B; Freeman, Clive; Christensen, Mikael; Wolf, Walter; Saxe, Paul
2010-09-29
Computational materials science based on ab initio calculations has become an important partner to experiment. This is demonstrated here for the effect of impurities and alloying elements on the strength of a Zr twist grain boundary, the dissociative adsorption and diffusion of iodine on a zirconium surface, the diffusion of oxygen atoms in a Ni twist grain boundary and in bulk Ni, and the dependence of the work function of a TiN-HfO(2) junction on the replacement of N by O atoms. In all of these cases, computations provide atomic-scale understanding as well as quantitative materials property data of value to industrial research and development. There are two key challenges in applying ab initio calculations, namely a higher accuracy in the electronic energy and the efficient exploration of large parts of the configurational space. While progress in these areas is fueled by advances in computer hardware, innovative theoretical concepts combined with systematic large-scale computations will be needed to realize the full potential of ab initio calculations for industrial applications.
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Draayer, Jerry P.
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Diffusion in liquid Germanium using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.
1996-03-01
We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.
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.
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 calculation of the potential bubble nucleus 34Si
NASA Astrophysics Data System (ADS)
Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.
2017-03-01
Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to
Ab-initio kinetics and thermodynamics studies of ammonia-borane for hydrogen storage
NASA Astrophysics Data System (ADS)
Miranda, Caetano R.; Ceder, Gerbrand
2007-03-01
Ammonia-borane (BH3NH3) is a promising chemical hydrogen storage material given its high gravimetry and volumetric properties. However, the ammonia-borane (AB) thermal hydrogen release is not very efficient, being mainly limited by the kinetics of hydrogenation. Using ab initio calculations, we have investigated the thermodynamics and kinetics of hydrogen release on AB by calculating the free energies of the H2 release reactions for different possible decomposition products. Our results indicate that AB regeneration through the ammonia-borane polymeric and borazine-cyclotriborazane cycles is very unlikely due to the strong exothermic character of the reactions. The kinetics of hydrogen release is further investigated with the recently developed metadynamics method. This method allows us to calculate the multidimensional free energy surface of hydrogen release on AB. Our simulations reveal the atomistic mechanism of hydrogenation and provide the free energies barriers and transition states involved in inter and intramolecule H2 release on AB.
Ab-Initio Study of Incongruent Melting in Silicates
NASA Astrophysics Data System (ADS)
Pinilla, C.; Stixrude, L. P.
2014-12-01
Knowledge of the multi-component thermodynamics and phase equilibria of silicate melts at Earth's interior conditions are key to understand the chemical and thermal evolution of the planet. Yet they remain poorly constrained with a wide uncertainty on the eutectic composition and temperature. In this work we present results from ab-initio molecular dynamics in combination with the two-phase coexistance method to study properties of a system of MgSiO3 liquid coexisting with crystalline MgO at conditions of the deep lower mantle. During incongruent melting the crystal may either grow via partial freezing of the liquid or shrink via partial melting at a given temperature and pressure. The melting process can be studied using the two-phases method where liquid and solid are in contact at a given temperature and pressure and so under thermodynamic equilibrium. We characterise the composition and densities of the resultant solid and liquid phases, provide chemical potentials of the liquid phase and study the structural and dynamical properties of the melt. In addition, we discuss the performance of alternative computational methods applied to the study of incongruent melting in silicate systems where long simulation times and a large number of atoms are usually needed. Finally, we discuss the implication of our findings for the evolution of the Earth's interior.
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
NASA Astrophysics Data System (ADS)
Bogdanov, Nikolay A.; Bisogni, Valentina; Kraus, Roberto; Monney, Claude; Zhou, Kejin; Schmitt, Thorsten; Geck, Jochen; Mitrushchenkov, Alexander O.; Stoll, Hermann; van den Brink, Jeroen; Hozoi, Liviu
2017-01-01
In existing theoretical approaches to core-level excitations of transition-metal ions in solids relaxation and polarization effects due to the inner core hole are often ignored or described phenomenologically. Here we set up an ab initio computational scheme that explicitly accounts for such physics in the calculation of x-ray absorption and resonant inelastic x-ray scattering spectra. Good agreement is found with experimental transition-metal L-edge data for the strongly correlated d 9 cuprate Li2CuO2, for which we determine the absolute scattering intensities. The newly developed methodology opens the way for the investigation of even more complex d n electronic structures of group VI B to VIII B correlated oxide compounds.
Thermochemistry of molecules in the B-N-Cl-H system: Ab initio predictions using the BAC-MP4 method
Allendorf, M.D.; Melius, C.F.
1997-04-03
A self-consistent set of thermochemical data for 33 molecules in the B-N-Cl-H system are obtained from a combination of ab initio electronic structure calculations and empirical corrections. Calculations were performed for both stable and radical species. Good agreement is found between the calculations and experimental heats of formation for most molecules containing B, H, and Cl. In addition, the BAC-MP4 and experimental heats of formation for H{sub 3}B:NH{sub 3} are also in reasonable agreement, suggesting that the bond additivity parameters chosen for B-N bonds will provide reasonably accurate heats of formation for compounds containing this type of bond. Transition-state energies for two reactions involving BCl{sub 3} and NH{sub 3} are also predicted. Polynomial fits of the predicted thermodynamic data over the 300-4000 K temperature range are included in the Supporting Information. 68 refs., 2 figs., 6 tabs.
Mahalakshmi, G; Balachandran, V
2015-01-25
Experimental FTIR and FT-Raman spectroscopic analysis of 1-Amino-4-methylpiperazine (1A4MP) have been performed. A detailed quantum chemical calculations have been carried out using ab initio HF and density functional theory calculations (B3LYP) with 6-311+G(d,p) basis set. The atomic charges, electronic exchange interaction and charge delocalization of the molecule have been performed by natural bond orbital (NBO) analysis. Electron density distribution and frontier molecular orbitals (FMOs) have been constructed at B3LYP/6-311+G(d,p) level to understand the electronic properties. The charge density distribution and site of chemical reactivity of the molecule have been obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). The electronic properties, HOMO and LUMO energies were measured by time-dependent TD-DFT approach. The dipole moment (μ), polarizability (α), anisotropy polarizability (Δα) and hyperpolarizability (β) of the molecule have been reported.
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
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 molecular dynamics calculations of ion hydration free energies.
Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
Ab initio prediction of 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.
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
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).
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 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.
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.
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 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 Studies of Surfaces and Interfaces
NASA Astrophysics Data System (ADS)
Garrity, Kevin F.
2011-12-01
Over the past 50 years, our ability to design and fabricate materials and devices with ever-smaller components has improved to the point that many technologies are crucially dependent on surfaces and interfaces. As this process continues, the atomic details of these surfaces and interfaces will take on increasing importance, both in understanding the behavior of existing structures as well as proposing and testing new materials and devices. First principles techniques are especially well-suited for exploring these systems, as they have the predictive capability required to understand the new phenomena which emerge at atomic length scales. In this work, we use first principles density functional theory to explore the properties of a variety of interesting surfaces and interfaces. First, we consider the thermodynamics and kinetics of Sr and La deposition on semiconductor surfaces, which is the first step in epitaxial oxide growth on semiconductors. Using this knowledge, we propose a method for growing LaAlO3 on epitaxially on Si. In addition, we explore the surface chemistry of a ferroelectric (PbTiO3) as a function a polarization in order to understand its applications to advanced catalysis. Finally, we investigate the coupling of phonons through an epitaxial interface between SrTiO3 and La 1-xSrxMnO 3, where an interfacial coupling of atomic motion is used to dynamically modulate the conductivity of a La1-xSr xMnO3 thin film.
Ab initio molecular simulations with numeric atom-centered orbitals
NASA Astrophysics Data System (ADS)
Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias
2009-11-01
We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.
Ab Initio Study of 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.
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.
Morphing ab initio potential energy curve of beryllium monohydride
NASA Astrophysics Data System (ADS)
Špirko, Vladimír
2016-12-01
Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.
Ab initio evidence for nonthermal characteristics in ultrafast laser melting
NASA Astrophysics Data System (ADS)
Lian, Chao; Zhang, S. B.; Meng, Sheng
2016-11-01
Laser melting of semiconductors has been observed for almost 40 years; surprisingly, it is not well understood where most theoretical simulations show a laser-induced thermal process. Ab initio nonadiabatic simulations based on real-time time-dependent density functional theory reveal intrinsic nonthermal melting of silicon, at a temperature far below the thermal melting temperature of 1680 K. Both excitation threshold and time evolution of diffraction intensity agree well with experiment. Nonthermal melting is attributed to excitation-induced drastic changes in bonding electron density, and the subsequent decrease in the melting barrier, rather than lattice heating as previously assumed in the two-temperature models.
Communication: Ab initio Joule-Thomson inversion data for argon
NASA Astrophysics Data System (ADS)
Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter
2013-02-01
The Joule-Thomson coefficient μH(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.
Ab-Initio 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 Calculations Applied to Problems in Metal Ion Chemistry
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)
1994-01-01
Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.
Electric field response in bilayer graphene: Ab initio investigation
NASA Astrophysics Data System (ADS)
Mori, Yutaro; Minamitani, Emi; Ando, Yasunobu; Kasamatsu, Shusuke; Watanabe, Satoshi
2016-11-01
Stimulated by quantum capacitance measurements, we have investigated the electric properties of bilayer graphene (BLG) with carrier doping under an external electric field using ab initio calculations. We found that the relative permittivity of BLG depends weakly on the applied electric field, and that the BLG can be regarded as a dielectric material rather than a pair of metallic films. We also found that carrier doping affects the band gap of BLG under electric fields, although carrier doping has a much smaller effect on the band gap and density of states than the application of electric fields.
Communication: Ab initio Joule-Thomson inversion data for argon.
Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter
2013-02-21
The Joule-Thomson coefficient μ(H)(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.
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
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 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.
NASA Astrophysics Data System (ADS)
Mo, Yuxiang; Gao, Shuming; Dai, Zuyang; Li, Hua
2013-06-01
We report a combined experimental and theoretical study on the vibronic structure of CH_3F^+. The results show that the tunneling splittings of vibrational energy levels occur in CH_3F^+ due to the Jahn-Teller effect. Experimentally, we have measured a high resolution ZEKE spectrum of CH_3F up to 3500 cm^-^1 above the ground state. Theoretically, we performed an ab initio calculation based on the diabatic model. The adiabatic potential energy surfaces (APES) of CH_3F^+ have been calculated at the MRCI/CAS/avq(t)z level and expressed by Taylor expansions with normal coordinates as variables. The energy gradients for the lower and upper APES, the derivative couplings between them and also the energies of the APES have been used to determine the coefficients in the Taylor expansion. The spin-vibronic energy levels have been calculated by accounting all six vibrational modes and their couplings. The experimental ZEKE spectra were assigned based on the theoretical calculations. W. Domcke, D. R. Yarkony, and H. Köpple (Eds.), Conical Intersections: Eletronic Structure, Dynamics and Spectroscopy (World Scientific, Singapore, 2004). M. S. Schuurman, D. E. Weinberg, and D. R. Yarkony, J. Chem. Phys. 127, 104309 (2007).
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
Ab initio study of hot electrons in GaAs.
Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B; Louie, Steven G
2015-04-28
Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron-phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron-phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron-phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials.
Emission Spectroscopy and Ab Initio Calculations for TaN
NASA Astrophysics Data System (ADS)
Ram, R. S.; Liévin, J.; Bernath, P. F.
2002-10-01
The emission spectra of TaN have been investigated in the region 3000-35 000 cm -1 using a Fourier transform spectrometer. The spectra were observed in a tantalum hollow-cathode lamp by discharging a mixture of 1.5 Torr of Ne and about 6 mTorr of N 2. In addition to previously known bands, numerous additional bands were observed and assigned to a number of new transitions. The spectroscopic properties of the low-lying electronic states of TaN were also predicted by ab initio calculations. A 1Σ + state, with equilibrium constants of Be=0.457 852 1(48) cm -1, α e=0.002 235 9(67) cm -1, and Re=1.683 099 9(88) Å, has been identified as the ground state of TaN based on our experimental observations supported by the ab initio results. The first excited state has been identified as the a3Δ 1 spin component at 2827 cm -1 above the ground state. To higher energies, the states become difficult to assign because of their Hund's case (c) behavior and extensive interactions between the spin components of the electronic terms.
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-01-01
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906
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 SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT
French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes
2012-09-15
We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.
Ab initio study of hot electrons in GaAs
Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B.; Louie, Steven G.
2015-01-01
Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron–phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron–phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron–phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials. PMID:25870287
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-02-14
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
Ab initio molecular dynamics simulation of pressure-induced phase transformation in BeO
Xiao, Haiyan; Duan, G; Zu, X T; Weber, William J
2011-01-01
Ab initio molecular dynamics (MD) method has been used to study high pressure-induced phase transformation in BeO based on the local density approximation (LDA) and the generalized gradient approximation (GGA). Both methods show that the wurtzite (WZ) and zinc blende (ZB) BeO transforms to the rocksalt (RS) structure smoothly at high pressure. The transition pressures obtained from the LDA method are about 40 GPa larger than the GGA result for both WZ {yields} RS and ZB {yields} RS phase transformations, and the phase transformation mechanisms revealed by the LDA and GGA methods are different. For WZ {yields} RS phase transformations both mechanisms obtained from the LDA and GGA methods are not comparable to the previous ab initio MD simulations of WZ BeO at 700 GPa based on the GGA method. It is suggested that the phase transformation mechanisms of BeO revealed by the ab initio MD simulations are affected remarkably by the exchange-correlation functional employed and the way of applying pressure.
Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions
Navratil, P; Ormand, W E; Forssen, C; Caurier, E
2004-11-30
There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.
Ab initio 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
Geng, Hua Y.
2015-02-15
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.
NASA Astrophysics Data System (ADS)
Geng, Hua Y.
2015-02-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.
Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule
Párraga, H.; Arranz, F. J. Benito, R. M.; Borondo, F.
2013-11-21
An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system.
Optical and other material properties of SiO2 from ab initio studies
NASA Astrophysics Data System (ADS)
Warmbier, Robert; Mohammed, Faris; Quandt, Alexander
2014-07-01
The optical properties of photonic devices largely depend on the dielectric properties of the underlying materials. We apply modern ab initio methods to study crystalline SiO2 phases, which serve as toy models for amorphous glass. We discuss the dielectric response from the infrared to the VIS/UV, which is crucial for glass based photonic applications. Low density silica, like cristobalite, may provide a good basis for high transmission optical devices.
Ab initio study of optical absorption spectra of semiconductors and conjugated polymers
Tiago, M.L.; Chang, Eric K.; Rohlfing, Michael; Louie, Steven G.
2000-04-30
The effects of electron-hole interaction on the optical properties of a variety of materials have been calculated using an ab initio method based on solving the Bethe-Salpeter equation. Results on selected semiconductors, insulators, and semiconducting polymers are presented. In the cases of alpha-quartz (SiO2) and poly-phenylene-vinylene, resonant excitonic states qualitatively alter the absorption spectra.
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.
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.
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
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.
Point defect modeling in materials: Coupling ab initio and elasticity approaches
NASA Astrophysics Data System (ADS)
Varvenne, Céline; Bruneval, Fabien; Marinica, Mihai-Cosmin; Clouet, Emmanuel
2013-10-01
Modeling point defects at an atomic scale requires careful treatment of the long-range atomic relaxations. This elastic field can strongly affect point defect properties calculated in atomistic simulations because of the finite size of the system under study. This is an important restriction for ab initio methods which are limited to a few hundred atoms. We propose an original approach coupling ab initio calculations and linear elasticity theory to obtain the properties of an isolated point defect for reduced supercell sizes. The reliability and benefit of our approach are demonstrated for three problematic cases: the self-interstitial in zirconium, clusters of self-interstitials in iron, and the neutral vacancy in silicon.
Ab initio 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.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
Zen, Andrea; Luo, Ye Mazzola, Guglielmo Sorella, Sandro; Guidoni, Leonardo
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Effects of Mg II and Ca II ionization on ab-initio solar chromosphere models
NASA Technical Reports Server (NTRS)
Rammacher, W.; Cuntz, M.
1991-01-01
Acoustically heated solar chromosphere models are computed considering radiation damping by (non-LTE) emission from H(-) and by Mg II and Ca II emission lines. The radiative transfer equations for the Mg II k and Ca II K emission lines are solved using the core-saturation method with complete redistribution. The Mg II k and Ca II K cooling rates are compared with the VAL model C. Several substantial improvements over the work of Ulmschneider et al. (1987) are included. It is found that the rapid temperature rises caused by the ionization of Mg II are not formed in the middle chromosphere, but occur at larger atmospheric heights. These models represent the temperature structure of the 'real' solar chromosphere much better. This result is a major precondition for the study of ab-initio models for solar flux tubes based on MHD wave propagation and also for ab-initio models for the solar transition layer.
NASA Astrophysics Data System (ADS)
Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.
2015-02-01
The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.
Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study
Rio, B. G. del; González, L. E.
2015-08-17
Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.
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.
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.
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.
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.
Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna
2016-01-01
Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo.
Zen, Andrea; Luo, Ye; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
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.
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
Ab initio study of the optical properties of carbon nanotubes
NASA Astrophysics Data System (ADS)
Chang, Eric
2006-03-01
We present an ab initio study of the optical properties of carbon nanotubes. We use state-of-the-art electronic structure methods based on many-body perturbation theory to compute the optical absorption and resonance Raman spectra of large tubes which have up to 200 atoms [1,2]. Our symmetry-based method makes the study of large tubes feasible within the many- body framework and also allows us to understand the symmetry properties of the excitons and selection rules. We include a study of the so-called dark excitons which are crucial for understanding luminescence efficiency in carbon nanotubes. The mechanism that explains the dark-bright splitting can be understood within our symmetry-based approach. Finally, we present an analysis of the two-photon spectra for several carbon nanotubes, a theoretical analysis which, in conjunction with combined one- and two-photon experiments, allows one to measure the binding energy of excitons. We find in all cases that the excitonic binding energy is large, ranging from 0.5 to 0.9 eV depending on the diameter of the tube, and that the excitonic wavefunction is Wannier-like and extended over many atoms. Our studies for the one- and two-photon absorption and resonance Raman spectra have been fruitful for understanding the corresponding experiments. In particular, our theoretical results are in good agreement with one- and two-photon absorption experiments [3-5]. The results for resonance Raman show that such a spectroscopic technique is a good alternative to optical absorption since it allows for the selection of tubes of a given diameter while probing the same excited states. 1. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. Lett. 92, 196401 (2004). 2. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. B 72, 195423 (2005). 3. M. Y. Sfeir et al., Science 306, 1540 (2004). 4. J. Maultzsch et al., to be published in Phys. Rev. B, see also cond-mat/0505150. 5. Z. M. Li et. al., Phys. Rev. Lett. 87, 127401 (2001).
Ab initio electronic and lattice dynamical properties of cerium dihydride
NASA Astrophysics Data System (ADS)
Gurel, Tanju; Eryigit, Resul
2007-03-01
The rare-earth metal hydrides are interesting systems because of the dramatic structural and electronic changes due to the hydrogen absorption and desorption. Among them, cerium dihydride (CeH2) is one of the less studied rare-earth metal-hydride. To have a better understanding, we have performed an ab initio study of electronic and lattice dynamical properties of CeH2 by using pseudopotential density functional theory within local density approximation (LDA) and a plane-wave basis. Electronic band structure of CeH2 have been obtained within LDA and as well as GW approximation. Lattice dynamical properties are calculated using density functional perturbation theory. The phonon spectrum is found to contain a set of high-frequency (˜ 850-1000 cm-1) optical bands, mostly hydrogen related, and low frequency cerium related acoustic modes climbing to 160 cm^ -1 at the zone boundary.
Approximate ab initio calculations of electronic structure of amorphous silicon
NASA Astrophysics Data System (ADS)
Durandurdu, M.; Drabold, D. A.; Mousseau, N.
2000-12-01
We report on ab initio calculations of electronic states of two large and realistic models of amorphous silicon generated using a modified version of the Wooten-Winer-Weaire algorithm and relaxed, in both cases, with a Keating and a modified Stillinger-Weber potentials. The models have no coordination defects and a very narrow bond-angle distribution. We compute the electronic density-of-states and pay particular attention to the nature of the band-tail states around the electronic gap. All models show a large and perfectly clean optical gap and realistic Urbach tails. Based on these results and the extended quasi-one-dimensional stringlike structures observed for certain eigenvalues in the band tails, we postulate that the generation of model a-Si without localized states might be achievable under certain circumstances.
The ab-initio density matrix renormalization group in practice
Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic; Nakatani, Naoki
2015-01-21
The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.
Ab initio engineering of materials with stacked hexagonal tin frameworks
Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.
2016-01-01
The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140
Quantum plasmonics: from jellium models to ab initio calculations
NASA Astrophysics Data System (ADS)
Varas, Alejandro; García-González, Pablo; Feist, Johannes; García-Vidal, F. J.; Rubio, Angel
2016-08-01
Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT) calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.
Ab initio electronic stopping power of protons in bulk materials
NASA Astrophysics Data System (ADS)
Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia
2016-01-01
The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.
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 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 study of helium behavior in titanium tritides
Liang, J. H.; Dai, Yunya; Yang, Li; Peng, SM; Fan, K. M.; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei
2013-03-01
Ab initio calculations based on density functional theory have been performed to investigate the relative stability of titanium tritides and the helium behavior in stable titanium tritides. The results show that the β-phase TiT1.5 without two tritium along the [100] direction (TiT1.5[100]) is more stable than other possible structures. The stability of titanium tritides decrease with the increased generation of helium in TiT1.5[100]. In addition, helium generated by tritium decay prefers locating at a tetrahedral site, and favorably migrates between two neighbor vacant tetrahedral sites through an intermediate octahedral site in titanium tritides, with a migration energy of 0.23 eV. Furthermore, helium is easily accumulated on a (100) plane in β-phase TiT1.5[100].
Ab initio electron propagator theory of molecular wires. I. Formalism.
Dahnovsky, Yu; Zakrzewski, V G; Kletsov, A; Ortiz, J V
2005-11-08
Ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical approach is developed for the calculation of the retarded and advanced Green functions in terms of the electron propagator matrix for the bridge molecule. The calculation of the current requires integration in a complex half plane for a trace that involves terminal and Green's-function matrices. Because the Green's-function matrices have complex poles represented by matrices, a special scheme is developed to express these "matrix poles" in terms of ordinary poles. An expression for the current is derived for a terminal matrix of arbitrary rank. For a single terminal orbital, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator. It is shown that Dyson orbitals with high pole strengths and overlaps with terminal orbitals are most responsible for the conduction of electrical current.
Ab initio simulations of liquid carbon monoxide at high pressure
NASA Astrophysics Data System (ADS)
Leonhardi, Tanis C.; Militzer, Burkhard
2017-03-01
Carbon monoxide occurs as a volatile species in the interiors of terrestrial planets, and as a disequilibrium atmospheric constituent in the giant planets. It plays an important role during the accretionary stages of planet formation reacting with gases to form compounds such as CH4 and H2O. The structure of carbon monoxide is unknown over the majority of the temperature and pressure regime in giant planet interiors. Here we perform ab initio molecular dynamics simulations to characterize CO to 140 GPa and 5,000 K. We find that CO is stable as a molecular liquid at lower P-T conditions, as a polymeric liquid at higher P-T conditions found in ice giant interiors, and as a plasma at high-T.
Ab initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
An ab initio study on anionic aerogen bonds
NASA Astrophysics Data System (ADS)
Esrafili, Mehdi D.; Mohammadian-Sabet, Fariba
2017-01-01
An ab initio study is carried out to investigate the anionic aerogen bonds in complexes of KrO3, XeO3 and XeOF2 with F-, Cl-, Br-, CN-, NC-, N3-, SH-, SCN-, NCS-, OH- and OCH3- anions. All of the anionic aerogen bonds analyzed here have a partial covalent character. Charge transfer from the anion to the Kr-O or Xe-O σ∗ orbital stabilizes these complexes and leads to a sizable redshift in the corresponding stretching frequencies. The J(Kr-O) or J(Xe-O) spin-spin coupling constants can be regarded as a useful tool for the characterization of strength of the anionic aerogen-bonded complexes.
Ab initio 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.
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).
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.
Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation
NASA Astrophysics Data System (ADS)
Yang, Lina; Minnich, Austin J.
2017-03-01
Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.
Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation
Yang, Lina; Minnich, Austin J.
2017-01-01
Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials. PMID:28290484
Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.
Yang, Lina; Minnich, Austin J
2017-03-14
Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.
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
Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W
2015-01-28
X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.
Liu, Hanchao; Wang, Yimin; Bowman, Joel M
2015-05-21
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.
Liu, Hanchao; Wang, Yimin; Bowman, Joel M.
2015-05-21
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.
NASA Astrophysics Data System (ADS)
Liu, Hanchao; Wang, Yimin; Bowman, Joel M.
2015-05-01
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.
NASA Astrophysics Data System (ADS)
Curchod, Basile F. E.; Rauer, Clemens; Marquetand, Philipp; González, Leticia; Martínez, Todd J.
2016-03-01
Full multiple spawning is a formally exact method to describe the excited-state dynamics of molecular systems beyond the Born-Oppenheimer approximation. However, it has been limited until now to the description of radiationless transitions taking place between electronic states with the same spin multiplicity. This Communication presents a generalization of the full and ab initio multiple spawning methods to both internal conversion (mediated by nonadiabatic coupling terms) and intersystem crossing events (triggered by spin-orbit coupling matrix elements) based on a spin-diabatic representation. The results of two numerical applications, a model system and the deactivation of thioformaldehyde, validate the presented formalism and its implementation.
Synthesis and Ab Initio/DFT Studies on 2-(4-methoxyphenyl)benzo[d]thiazole
Arslan, Hakan; Algül, Öztekin
2007-01-01
2-aminothiophenol and 4-methoxybenzaldehyde were cyclized under microwave irridation and solvent free conditions to synthesize 2-(4-methoxyphenyl)benzo[d]thiazole. The molecular structure and vibrational frequencies of the title compound in the ground state have been investigated with ab initio (HF) and density functional theory methods (BLYP, B3LYP, B3PW91 and mPW1PW91) implementing the standard 6–311G(d,p) basis set. Comparison of the observed fundamental vibrational frequencies of title compound and calculated results by HF and DFT methods indicate that B3LYP is superior to the scaled HF approach for molecular problems.
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.
Karamanis, Panaghiotis; Maroulis, George; Pouchan, Claude
2006-02-21
We have calculated molecular geometries and electric polarizabilities for small cadmium selenide clusters. Our calculations were performed with conventional ab initio and density functional theory methods and Gaussian-type basis sets especially designed for (CdSe)(n). We find that the dipole polarizability per atom converges rapidly to the bulk value.
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.
Ab initio electronic structure and optical conductivity of bismuth tellurohalides
NASA Astrophysics Data System (ADS)
Schwalbe, Sebastian; Wirnata, René; Starke, Ronald; Schober, Giulio A. H.; Kortus, Jens
2016-11-01
We investigate the electronic structure, dielectric, and optical properties of bismuth tellurohalides BiTe X (X =I , Cl, Br) by means of all-electron density functional theory. In particular, we present the ab initio conductivities and dielectric tensors calculated over a wide frequency range, and compare our results with the recent measurements by Akrap et al. [Phys. Rev. B 90, 035201 (2014), 10.1103/PhysRevB.90.035201], Makhnev et al. [Opt. Spectrosc. 117, 764 (2014), 10.1134/S0030400X14110125], and Rusinov et al. [JETP Lett. 101, 507 (2015), 10.1134/S0021364015080147]. We show how the low-frequency branch of the optical conductivity can be used to identify characteristic intra- and interband transitions between the Rashba spin-split bands in all three bismuth tellurohalides. We further calculate the refractive indices and dielectric constants, which in turn are systematically compared to previous predictions and measurements. We expect that our quantitative analysis will contribute to the general assessment of bulk Rashba materials for their potential use in spintronics devices.
Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures
NASA Astrophysics Data System (ADS)
Debernardi, Alberto; Marchetti, Luigi
2016-06-01
Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.
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.
Accurate ab initio vibrational energies of methyl chloride
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2015-06-28
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup HL}, and CBS-37{sup HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup HL} and CBS-37{sup HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.
Ab initio liquid water from PBE0 hybrid functional simulations
NASA Astrophysics Data System (ADS)
Li, Zhaofeng; Wu, Xifan; Car, Roberto
2010-03-01
For reasons of computational efficiency, so far most ab initio molecular dynamics simulations of liquid water have been based on semi-local density functional approximations, such as PBE and BLYP. These approaches yield a liquid structure that, albeit qualitatively correct, is overstructured compared to experiment, even after nuclear quantum effects have been taken into account.footnotetextJ. A. Morrone and R. Car, Phys. Rev. Lett. 101, 017801(2008) A major cause of this inaccuracy is the delocalization error associated to semi-local density functional approximations, which, as a consequence, overestimate slightly the hydrogen bond strength in the liquid. In this work we adopt the PBE0 hybrid functional approximation, which, by mixing a fraction of exact (Hartree-Fock) exchange, reduces significantly the delocalization error of semi-local functionals. Our approach is based on a numerically efficient order-N implementation of exact exchange.footnotetextX. Wu, A. Selloni, and R. Car, Phys. Rev. B 79, 085102(2009) We find that PBE0 systematically improves the agreement of the simulated liquid with experiment. Our conclusion is substantiated by the calculated radial distribution functions, H-bond statistics, and molecular dipole distribution.
Ab initio predictions of the symmetry energy and recent constraints
NASA Astrophysics Data System (ADS)
Sammarruca, Francesca
2017-01-01
The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.
An efficient approach to ab initio Monte Carlo simulation.
Leiding, Jeff; Coe, Joshua D
2014-01-21
We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β(0)), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where-depending on the quality of the reference system potential-acceptance probabilities were enhanced by factors of 1.2-28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.
Ab initio studies of phosphorene island single electron transistor
NASA Astrophysics Data System (ADS)
Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.
2016-05-01
Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.
Ab-Initio Molecular Dynamics Simulation of Graphene Sheet
NASA Astrophysics Data System (ADS)
Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.
2017-01-01
The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.
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.
Perovskite transparent conducting oxides: an ab initio study.
Dabaghmanesh, S; Saniz, R; Amini, M N; Lamoen, D; Partoens, B
2013-10-16
We present an ab initio study of the electronic structure and of the formation energies of various point defects in BaSnO3 and SrGeO3. We show that La and Y impurities substituting Ba or Sr are shallow donors with a preferred 1 + charge state. These defects have a low formation energy within all the suitable equilibrium growth conditions considered. Oxygen vacancies behave as shallow donors as well, preferring the 2 + charge state. Their formation energies, however, are higher in most growth conditions, indicating a limited contribution to conductivity. The calculated electron effective mass in BaSnO3, with a value of 0.21 m(e), and the very high mobility reported recently in La-doped BaSnO3 single-crystals, suggest that remarkably low scattering rates can be achieved in the latter. In the case of SrGeO3, our results point to carrier density and mobility values in the low range for typical polycrystalline TCOs, in line with experiment.
Ab initio calculations of nuclear reactions important for astrophysics
NASA Astrophysics Data System (ADS)
Navratil, Petr; Dohet-Eraly, Jeremy; Calci, Angelo; Horiuchi, Wataru; Hupin, Guillaume; Quaglioni, Sofia
2016-09-01
In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. One of the newly developed approaches is the No-Core Shell Model with Continuum (NCSMC), capable of describing both bound and scattering states in light nuclei simultaneously. We will present NCSMC results for reactions important for astrophysics that are difficult to measure at relevant low energies, such as 3He(α,γ)7Be and 3H(α,γ)7Li and 11C(p,γ)12N radiative capture, as well as the 3H(d,n)4He fusion. We will also address prospects of calculating the 2H(α,γ)6Li capture reaction within the NCSMC formalism. Prepared in part by LLNL under Contract DE-AC52-07NA27344. Supported by the U.S. DOE, OS, NP, under Work Proposal No. SCW1158, and by the NSERC Grant No. SAPIN-2016-00033. TRIUMF receives funding from the NRC Canada.
Ab Initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
An Ab Initio Based Potential Energy Surface for Water
NASA Technical Reports Server (NTRS)
Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)
1996-01-01
We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.
Ab initio modeling of decomposition in iron based alloys
NASA Astrophysics Data System (ADS)
Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.
2016-12-01
This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.
Ab initio calculation of infrared intensities for hydrogen peroxide
NASA Technical Reports Server (NTRS)
Rogers, J. D.; Hillman, J. J.
1982-01-01
Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.
Ab initio calculations of correlated electron dynamics in ultrashort pulses
NASA Astrophysics Data System (ADS)
Feist, Johannes
2010-03-01
The availability of ultrashort and intense light pulses on the femtosecond and attosecond timescale promises to allow to directly probe and control electron dynamics on their natural timescale. A crucial ingredient to understanding the dynamics in many-electron systems is the influence of electron correlation, induced by the interelectronic repulsion. In order to study electron correlation in ultrafast processes, we have implemented an ab initio simulation of the two-electron dynamics in helium atoms. We solve the time-dependent Schr"odinger equation in its full dimensionality, with one temporal and five spatial degrees of freedom in linearly polarized laser fields. In our computational approach, the wave function is represented through a combination of time-dependent close coupling with the finite element discrete variable representation, while time propagation is performed using an Arnoldi-Lanczos approximation with adaptive step size. This approach is optimized to allow for efficient parallelization of the program and has been shown to scale linearly using up to 1800 processor cores for typical problem sizes. This has allowed us to perform highly accurate and well- converged computations for the interaction of ultrashort laser pulses with He. I will present some recent results on using attosecond and femtosecond pulses to probe and control the temporal structure of the ionization process. This work was performed in collaboration with Stefan Nagele, Renate Pazourek, Andreas Kaltenb"ack, Emil Persson, Barry I. Schneider, Lee A. Collins, and Joachim Burgd"orfer.
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
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 Calculations of the Interaction between CO _{2} and the Acetate Ion
Steckel, Janice A.
2012-11-29
A series of ab initio calculations designed to investigate the interaction of CO{sub 2} with acetate are presented. The lowest energy structure, AC–CO{sub 2}-η{sup 2}, is predicted by CCSD(T)/aVTZ to be bound by -10.6 kcal/mol. Six of the bound complexes have binding energies on the order of -8 kcal/mol, but analysis shows that the η{sup 1}-CT complex is fundamentally different from the others. The η{sup 1}-CT complex is characterized by geometric distortion, large polarization and induction effects and charge transfer whereas the other five complexes have little geometric distortion and negligible charge transfer. The amount of charge that is transferred from the anion to the CO{sub 2} in the η{sup 1}-CT complex is estimated to be about half an electron by NPA, DMA, CHELPG, and Mulliken analyses, whereas the EDA-ALMO-CTA (B3LYP) approach predicts a charge transfer of 75 me{sup –}. However, the transfer of this small amount of charge leads to an energy lowering of -56 kcal/mol, without which the complex would not be bound. The RI-MP2 geometries closely approximate those resulting from the CCSD optimizations, and the optimized second-order opposite spin (O2) method performs well for all the complexes except for the η{sup 1}-CT complex. DFT methods do not reproduce all the ab initio geometries, binding energies and/or energy ordering of these complexes although the range-separated hybrid meta-GGA (M11) and nonlocal (VV10 and vdwDF10) functionals are shown to yield results significantly better than other functionals considered for this system. The fact that there is such variation among DFT methods has implications for DFT-based ab initio molecular dynamics simulations and for the parametrization of classical force fields based on DFT calculations.
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
NASA Astrophysics Data System (ADS)
Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär
2017-02-01
The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.
Superconductivity in an expanded phase of ZnO: an ab initio study
NASA Astrophysics Data System (ADS)
Hapiuk, D.; Marques, M. A. L.; Mélinon, P.; Botti, S.; Masenelli, B.; Flores-Livas, J. A.
2015-04-01
It is known that covalent semiconductors become superconducting if conveniently doped with large concentration of impurities. In this article we investigate, using ab initio methods, if the same situation is possible for an ionic, large-band gap semiconductor such as ZnO. We concentrate on the cage-like sodalite phase, with very similar electronic and phononic properties as wurtzite ZnO, but allow for endohedral doping of the cages. We find that sodalite ZnO becomes superconducting for a variety of dopants, reaching a maximum critical temperature of 7 K. This value is comparable to the transition temperatures of doped silicon clathrates, cubic silicon, and diamond.
Structure and dynamics of the Lu2Si2O7 lattice: Ab initio calculation
NASA Astrophysics Data System (ADS)
Nazipov, D. V.; Nikiforov, A. E.
2017-01-01
The ab initio calculations have been carried out for the crystal structure and Raman spectrum of a single crystal of lutetium pyrosilicate Lu2Si2O7. The types of fundamental vibrations and their frequencies and intensities in the Raman spectrum for two polarizations of the crystal have been determined. The calculations have been performed within the framework of the density functional theory (DFT) using the hybrid functionals. The ions involved in the vibrations have been identified using the method of isotopic substitution. The results of the calculations are in good agreement with the experiment.
NASA Astrophysics Data System (ADS)
Persico, Maurizio; Cacelli, Ivo; Ferretti, Alessandro
1991-04-01
We have determined ab initio potential energy surfaces of the S0 and S1 states of dimethylnitrosamine, with particular care for the N-N bond dissociation pathway. The electronic correlation has been taken into account by a multireference perturbation method, CIPSI. Classical trajectories in the S1 surface have been run with statistically determined initial conditions. Computed lifetimes and orientation parameters for the recoil velocity and the NO fragment angular momentum are in agreement with experimental data. Large amplitude internal motions are of primary importance in determining such quantities.
Flexible Ab initio boundary conditions: simulating isolated dislocations in bcc Mo and Ta.
Woodward, C; Rao, S I
2002-05-27
We report the first ab initio density-functional study of the strain field and Peierls stress of isolated <111> screw dislocations in bcc Mo and Ta. The local dislocation strain field is self-consistently coupled to the long-range elastic field using a flexible boundary condition method. This reduces the mesoscopic atomistic calculation to one involving only degrees of freedom near the dislocation core. The predicted equilibrium core for Mo is significantly different from previous atomistic results and the Peierls stress shows significant non-Schmid behavior as expected for the bcc metals.
Ab initio no core calculations of light nuclei and preludes to Hamiltonian quantum field theory
Vary, J. P.; Maris, P.; Honkanen, H.; Li, J.; Shirokov, A. M.; Brodsky, S. J.; Harindranath, A.
2009-12-17
Recent advances in ab initio quantum many-body methods and growth in computer power now enable highly precise calculations of nuclear structure. The precision has attained a level sufficient to make clear statements on the nature of 3-body forces in nuclear physics. Total binding energies, spin-dependent structure effects, and electroweak properties of light nuclei play major roles in pinpointing properties of the underlying strong interaction. Eventually, we anticipate a theory bridge with immense predictive power from QCD through nuclear forces to nuclear structure and nuclear reactions. Light front Hamiltonian quantum field theory offers an attractive pathway and we outline key elements.
Ab initio no core calculations of light nuclei and preludes to Hamiltonian quantum field theory
Vary, J.P.; Maris, P.; Shirokov, A.M.; Honkanen, H.; li, J.; Brodsky, S.J.; Harindranath, A.; Teramond, G.F.de; /Costa Rica U.
2009-08-03
Recent advances in ab initio quantum many-body methods and growth in computer power now enable highly precise calculations of nuclear structure. The precision has attained a level sufficient to make clear statements on the nature of 3-body forces in nuclear physics. Total binding energies, spin-dependent structure effects, and electroweak properties of light nuclei play major roles in pinpointing properties of the underlying strong interaction. Eventually,we anticipate a theory bridge with immense predictive power from QCD through nuclear forces to nuclear structure and nuclear reactions. Light front Hamiltonian quantum field theory offers an attractive pathway and we outline key elements.
Ab initio calculation of the deuterium quadrupole coupling in liquid water
NASA Astrophysics Data System (ADS)
Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc
1992-10-01
The quadrupole coupling constant and asymmetry parameter for the deuteron in liquid heavy water was determined using purely theoretical methods. Molecular-dynamics simulations with the ab initio potential-energy surface of Lie and Clementi were used to generate snapshots of the liquid. The electric-field gradient at the deuteron was then calculated for these configurations and averaged to obtain the liquid quadrupole coupling constant. At 300 K a quadrupole coupling constant of 256±5 kHz and an asymmetry parameter of 0.164±0.003 were obtained. The temperature dependence of the quadrupole coupling constant was investigated.
Communication: Multiple-timestep ab initio molecular dynamics with electron correlation.
Steele, Ryan P
2013-07-07
A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Moøller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.
Communication: Multiple-timestep ab initio molecular dynamics with electron correlation
NASA Astrophysics Data System (ADS)
Steele, Ryan P.
2013-07-01
A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Møller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.
Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides
NASA Astrophysics Data System (ADS)
Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki
2012-09-01
Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Aβ and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Aβ and inhibit the Aβ aggregation.
Accurate calculation of the p Ka of trifluoroacetic acid using high-level ab initio calculations
NASA Astrophysics Data System (ADS)
Namazian, Mansoor; Zakery, Maryam; Noorbala, Mohammad R.; Coote, Michelle L.
2008-01-01
The p Ka value of trifluoroacetic acid has been successfully calculated using high-level ab initio methods such as G3 and CBS-QB3. Solvation energies have been calculated using CPCM continuum model of solvation at the HF and B3-LYP levels of theory with various basis sets. Excellent agreement with experiment (to within 0.4 p Ka units) was obtained using CPCM solvation energies at the B3-LYP/6-31+G(d) level (or larger) in conjunction with CBS-QB3 or G3 gas-phase energies of trifluoroacetic acid and its anion.
NASA Astrophysics Data System (ADS)
Nechaev, I. A.; Krasovskii, E. E.
2016-11-01
We present a method to microscopically derive a small-size k .p Hamiltonian in a Hilbert space spanned by physically chosen ab initio spinor wave functions. Without imposing any complementary symmetry constraints, our formalism equally treats three- and two-dimensional systems and simultaneously yields the Hamiltonian parameters and the true Z2 topological invariant. We consider bulk crystals and thin films of Bi2Se3 , Bi2Te3 , and Sb2Te3 . It turns out that the effective continuous k .p models with open boundary conditions often incorrectly predict the topological character of thin films.
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.
Ab initio calculations of elastic properties of Ru1-xNixAl superalloys
NASA Astrophysics Data System (ADS)
Bleskov, I. D.; Smirnova, E. A.; Vekilov, Yu. Kh.; Korzhavyi, P. A.; Johansson, B.; Katsnelson, M.; Vitos, L.; Abrikosov, I. A.; Isaev, E. I.
2009-04-01
Ab initio total energy calculations based on the exact muffin-tin orbitals method, combined with the coherent potential approximation, have been used to study the thermodynamical and elastic properties of substitutional refractory Ru1-xNixAl alloys. We have found that the elastic constants C' and C11 exhibit pronounced peculiarities near the concentration of about 40 at. % Ni, which we ascribe to electronic topological transitions. Our suggestion is supported by the Fermi surface calculations in the whole concentration range. Results of our calculations show that one can design Ru-Ni-Al alloys substituting Ru by Ni (up to 40 at. %) with almost invariable elastic constants and reduced density.
Ab initio synthesis of linearly compensated zoom lenses by evolutionary programming.
Pal, Sourav; Hazra, Lakshminarayan
2011-04-01
An approach for ab initio synthesis of the thin lens structure of linearly compensated zoom lenses is reported. This method uses evolutionary programming that explores the available configuration space formed by powers of the individual components, the intercomponent separations, and the relative movement parameters of the moving components. Useful thin lens structures of optically and linearly compensated zoom lens systems are obtained by suitable formulation of the merit function of optimization. This paper reports our investigations on three-component zoom lens structures. Illustrative numerical results are presented.
Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.
2013-12-12
Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.
NASA Astrophysics Data System (ADS)
Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei
2014-06-01
New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).
Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides
NASA Astrophysics Data System (ADS)
Sharma, Vinit; Krogel, Jaron T.; Kent, P. R. C.; Reboredo, Fernando A.
One of the critical scientific challenges of contemporary research is to obtain an accurate theoretical description of the electronic properties of strongly correlated systems such as transition metal oxides and rare-earth compounds, since state-of-art ab-initio methods based on approximate density functionals are not always sufficiently accurate. Quantum Monte Carlo (QMC) methods, which use statistical sampling to evaluate many-body wave functions, have the potential to answer this challenge. Owing to the few fundamental approximations made and the direct treatment of electron correlation, QMC methods are among the most accurate electronic structure methods available to date. We assess the accuracy of the diffusion Monte Carlo method in the case of rocksalt manganese oxide (MnO). We study the electronic properties of this strongly-correlated oxide, which has been identified as a suitable candidate for many applications ranging from catalysts to electronic devices. ``This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.'' Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides.
Liu, Lihong; Wang, Yating; Fang, Qiu
2017-02-14
Ethylene-bridged azobenzene (br-AB) has aroused broad interests due to its unique photoswitching properties. Numerous dynamical simulations have been performed for the br-AB photoisomerization, which focused mainly on the conformational effect and the funnel role of minimum-energy conical intersection (MECI) on the mechanism. In the present work, we use the "full quantum" ab initio multiple spawning method to simulate the br-AB photoisomerization, which provides new insights into the mechanism. Upon irradiation of br-AB to the first excited singlet state (S1), most of the excess energies are trapped in the azo-moiety. Since the intramolecular vibrational energy redistribution is slower than the S1 relaxation processes, the nonadiabatic transition from S1 to the ground state (S0) occurs in the vicinity of high-energy crossing seam and even the largest probabilities of the S1 → S0 transition are not distributed in the MECI regions. Once decaying to the S0 state through the high-energy region, the subsequent isomerization and re-formation of the initial isomer are ultrafast processes in the S0 state. It is the nonergodic behavior of the S1 and S0 dynamics that is mainly responsible for the unique photoswitching properties of the ethylene-bridged azobenzene, which will be discussed in detail.
NASA Astrophysics Data System (ADS)
Liu, Lihong; Wang, Yating; Fang, Qiu
2017-02-01
Ethylene-bridged azobenzene (br-AB) has aroused broad interests due to its unique photoswitching properties. Numerous dynamical simulations have been performed for the br-AB photoisomerization, which focused mainly on the conformational effect and the funnel role of minimum-energy conical intersection (MECI) on the mechanism. In the present work, we use the "full quantum" ab initio multiple spawning method to simulate the br-AB photoisomerization, which provides new insights into the mechanism. Upon irradiation of br-AB to the first excited singlet state (S1), most of the excess energies are trapped in the azo-moiety. Since the intramolecular vibrational energy redistribution is slower than the S1 relaxation processes, the nonadiabatic transition from S1 to the ground state (S0) occurs in the vicinity of high-energy crossing seam and even the largest probabilities of the S1 → S0 transition are not distributed in the MECI regions. Once decaying to the S0 state through the high-energy region, the subsequent isomerization and re-formation of the initial isomer are ultrafast processes in the S0 state. It is the nonergodic behavior of the S1 and S0 dynamics that is mainly responsible for the unique photoswitching properties of the ethylene-bridged azobenzene, which will be discussed in detail.
Velaga, Srinath C; Anderson, Brian J
2014-01-16
Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations.
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
Zhang, Yang
2014-02-01
We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems.
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
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.
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 molecular dynamics of liquid hydrogen chloride
NASA Astrophysics Data System (ADS)
Dubois, Vincent; Pasquarello, Alfredo
2005-03-01
We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (ℓ-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)2 dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in ℓ-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.
Ab initio 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.
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 a ^{4}He+n+n description of ^{6}He 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 (^{4}He) polarization effects.
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.
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.
4He+n+n continuum within an ab initio framework
Romero-Redondo, Carolina; Quaglioni, Sofia; Navratil, Petr; ...
2014-07-16
In this study, the low-lying continuum spectrum of the 6He nucleus is investigated for the first time within an ab initio framework that encompasses the 4He+n+n three-cluster dynamics characterizing its lowest decay channel. This is achieved through an extension of the no-core shell model combined with the resonating-group method, in which energy-independent nonlocal interactions among three nuclear fragments can be calculated microscopically, starting from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with three-body scattering boundary conditions by means of the hyperspherical-harmonics method on a Lagrange mesh. Using amore » soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we find the known Jπ = 2+ resonance as well as a result consistent with a new low-lying second 2+ resonance recently observed at GANIL at ~2.6 MeV above the He6 ground state. We also find resonances in the 2–, 1+, and 0– channels, while no low-lying resonances are present in the 0+ and 1– channels.« less
Ab initio study of the SeS local oscillator in zinc sulfide
NASA Astrophysics Data System (ADS)
Petzke, K.
1999-11-01
A method is presented to calculate the energy and symmetry of local vibrational modes (LVM's) at point defects in semiconductors from first principles. The force constants for the disturbed and undisturbed systems are calculated using a variant of the direct approach. The ab initio results are used as input parameters for a cluster simulation with up to 489 vibrating atoms, which accounts for hybridization effects between the LVM and the host lattice modes. The method is applied to the LVM of ZnS:SeS, which shows a pronounced fine structure due to both host and ligand induced isotope effects. The energy of the main peak, which represents the most abundant Selen isotope 80Se, is calculated as 229.6 cm-1. This agrees very well with the result of 229.2 cm-1 from Fourier transform infrared experiments found in the literature. It is shown that the ab initio result improves the understanding of the LVM, when compared to the previously used ad hoc model, especially in the low-energy region.
Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.
2004-03-01
Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the “Wannier gauge.” An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches.
Multiple-Time Step Ab Initio Molecular Dynamics Based on Two-Electron Integral Screening.
Fatehi, Shervin; Steele, Ryan P
2015-03-10
A multiple-timestep ab initio molecular dynamics scheme based on varying the two-electron integral screening method used in Hartree-Fock or density functional theory calculations is presented. Although screening is motivated by numerical considerations, it is also related to separations in the length- and timescales characterizing forces in a molecular system: Loose thresholds are sufficient to describe fast motions over short distances, while tight thresholds may be employed for larger length scales and longer times, leading to a practical acceleration of ab initio molecular dynamics simulations. Standard screening approaches can lead, however, to significant discontinuities in (and inconsistencies between) the energy and gradient when the screening threshold is loose, making them inappropriate for use in dynamics. To remedy this problem, a consistent window-screening method that smooths these discontinuities is devised. Further algorithmic improvements reuse electronic-structure information within the dynamics step and enhance efficiency relative to a naı̈ve multiple-timestepping protocol. The resulting scheme is shown to realize meaningful reductions in the cost of Hartree-Fock and B3LYP simulations of a moderately large system, the protonated sarcosine/glycine dipeptide embedded in a 19-water cluster.
Deviational simulation of phonon transport in graphene ribbons with ab initio scattering
Landon, Colin D.; Hadjiconstantinou, Nicolas G.
2014-10-28
We present a deviational Monte Carlo method for solving the Boltzmann-Peierls equation with ab initio 3-phonon scattering, for temporally and spatially dependent thermal transport problems in arbitrary geometries. Phonon dispersion relations and transition rates for graphene are obtained from density functional theory calculations. The ab initio scattering operator is simulated by an energy-conserving stochastic algorithm embedded within a deviational, low-variance Monte Carlo formulation. The deviational formulation ensures that simulations are computationally feasible for arbitrarily small temperature differences, while the stochastic treatment of the scattering operator is both efficient and exhibits no timestep error. The proposed method, in which geometry and phonon-boundary scattering are explicitly treated, is extensively validated by comparison to analytical results, previous numerical solutions and experiments. It is subsequently used to generate solutions for heat transport in graphene ribbons of various geometries and evaluate the validity of some common approximations found in the literature. Our results show that modeling transport in long ribbons of finite width using the homogeneous Boltzmann equation and approximating phonon-boundary scattering using an additional homogeneous scattering rate introduces an error on the order of 10% at room temperature, with the maximum deviation reaching 30% in the middle of the transition regime.
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.
Ab initio study of structural and magnetic properties of Si-doped Fe2P
NASA Astrophysics Data System (ADS)
Delczeg-Czirjak, E. K.; Delczeg, L.; Punkkinen, M. P. J.; Johansson, B.; Eriksson, O.; Vitos, L.
2010-08-01
Ab initio electronic-structure methods are used to study the properties of Fe2P1-xSix in ferromagnetic and paramagnetic states. The site preference and lattice relaxation are calculated with the projector augmented wave method as implemented in the Vienna ab initio simulation package. The paramagnetic state is modeled by the disordered local magnetic moment scheme, and the chemical and magnetic disorder is treated using the coherent potential approximation in combination with the exact muffin-tin orbital formalism. The calculated lattice parameters, atomic positions, and magnetic properties are in good agreement with the experimental and other theoretical results. In contrast to the observation, for the ferromagnetic state the body centered orthorhombic structure (bco, space group Imm2&barbelow; ) is predicted to have lower energy than the hexagonal structure (hex, space group P6¯2m ). The zero-point spin fluctuation energy difference is found to be large enough to stabilize the hex phase. For the paramagnetic state, the hex structure is calculated to be the stable phase and the computed total energy versus composition indicates a hex to bco crystallographic phase transition with increasing Si content. The phonon vibrational free energy, estimated from the theoretical equation of state, turns out to stabilize the hexagonal phase, whereas the electronic and magnetic entropies favor the low symmetry orthorhombic structure.
2014-08-01
Technical Paper 3. DATES COVERED (From - To) December 2013- August 2014 4. TITLE AND SUBTITLE Ab initio Kinetics of Methylamine Radical Thermal...phase kinetics of H-abstraction reactions from CH3NHNH2 by H atoms was further investigated by ab initio second-order multireference perturbation...distribution unlimited Ab initio Kinetics of Methylamine Radical Thermal Decomposition and H-abstraction from Monomethylhydrazine by H Atom
Operator evolution for ab initio electric dipole transitions of 4He
Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; ...
2015-07-24
A goal of nuclear theory is to make quantitative predictions of low-energy nuclear observables starting from accurate microscopic internucleon forces. A major element of such an effort is applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence of ab initio calculations as a function of the model space size. The consistent simultaneous transformation of external operators, however, has been overlooked in applications of the theory, particularly for nonscalar transitions. We study the evolution of the electric dipole operator in the framework of the similarity renormalization group method and apply the renormalized matrix elements to the calculationmore » of the 4He total photoabsorption cross section and electric dipole polarizability. All observables are calculated within the ab initio no-core shell model. Furthermore, we find that, although seemingly small, the effects of evolved operators on the photoabsorption cross section are comparable in magnitude to the correction produced by including the chiral three-nucleon force and cannot be neglected.« less
Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores
Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; ...
2015-01-31
In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimentalmore » observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less
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.
Ab initio simulation of elastic and mechanical properties of Zn- and Mg-doped hydroxyapatite (HAP).
Aryal, Sitaram; Matsunaga, Katsuyuki; Ching, Wai-Yim
2015-07-01
Hydroxyapatite (HAP) is an important bioceramic which constitutes the mineral components of bones and hard tissues in mammals. It is bioactive and used as bioceramic coatings for metallic implants and bone fillers. HAP readily absorbs a large amount of impurities. Knowledge on the elastic and mechanical properties of impurity-doped HAP is a subject of great importance to its potential for biomedical applications. Zn and Mg are the most common divalent cations HAP absorbs. Using density function theory based ab initio methods, we have carried out a large number of ab initio calculations to obtain the bulk elastic and mechanical properties of HAP with Zn or Mg doped in different concentration at the Ca1 and Ca2 sites using large 352-atom supercells. Detailed information on their dependece on the concetraion of the substitued impurity is obtained. Our results show that Mg enhances overall elastic and bulk mechanical properties whereas Zn tends to degrade except at low concentrations. At a higher concentration, the mechanical properties of Zn and Mg doped HAP also depend significantly on impurity distribution between the Ca1 and Ca2 sites. There is a strong evidence that Zn prefers Ca2 site for substituion whereas Mg has no such preference. These results imply that proper control of dopant concentration and their site preference must carefully considered in using doped HAP for specific biomedical applications.
Renison, C Alicia; Fernandes, Kyle D; Naidoo, Kevin J
2015-07-05
This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc.
Ab initio results for intermediate-mass, open-shell nuclei
NASA Astrophysics Data System (ADS)
Baker, Robert B.; Dytrych, Tomas; Launey, Kristina D.; Draayer, Jerry P.
2017-01-01
A theoretical understanding of nuclei in the intermediate-mass region is vital to astrophysical models, especially for nucleosynthesis. Here, we employ the ab initio symmetry-adapted no-core shell model (SA-NCSM) in an effort to push first-principle calculations across the sd-shell region. The ab initio SA-NCSM's advantages come from its ability to control the growth of model spaces by including only physically relevant subspaces, which allows us to explore ultra-large model spaces beyond the reach of other methods. We report on calculations for 19Ne and 20Ne up through 13 harmonic oscillator shells using realistic interactions and discuss the underlying structure as well as implications for various astrophysical reactions. This work was supported by the U.S. NSF (OCI-0904874 and ACI -1516338) and the U.S. DOE (DE-SC0005248), and also benefitted from the Blue Waters sustained-petascale computing project and high performance computing resources provided by LSU.
Full-dimensional (15-dimensional) ab initio analytical potential energy surface for the H7+ cluster
NASA Astrophysics Data System (ADS)
Barragán, Patricia; Prosmiti, Rita; Wang, Yimin; Bowman, Joel M.
2012-06-01
Full-dimensional ab initio potential energy surface is constructed for the H_7^+ cluster. The surface is a fit to roughly 160 000 interaction energies obtained with second-order MöllerPlesset perturbation theory and the cc-pVQZ basis set, using the invariant polynomial method [B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577 (2009), 10.1080/01442350903234923]. We employ permutationally invariant basis functions in Morse-type variables for all the internuclear distances to incorporate permutational symmetry with respect to interchange of H atoms into the representation of the surface. We describe how different configurations are selected in order to create the database of the interaction energies for the linear least squares fitting procedure. The root-mean-square error of the fit is 170 cm-1 for the entire data set. The surface dissociates correctly to the H_5^+ + H2 fragments. A detailed analysis of its topology, as well as comparison with additional ab initio calculations, including harmonic frequencies, verify the quality and accuracy of the parameterized potential. This is the first attempt to present an analytical representation of the 15-dimensional surface of the H_7^+ cluster for carrying out dynamics studies.
Emergent properties of nuclei from ab initio coupled-cluster calculations
Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.
2016-05-17
Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO${}_{{\\rm{sat}}}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the ${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$ states in ${}^{\\mathrm{17,23,25}}$O, and—contrary to naive shell-model expectations—the level ordering of the ${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$ states in ${}^{\\mathrm{53,55,61}}$Ca.
Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping.
Cheng, Xiaolu; Herr, Jonathan D; Steele, Ryan P
2016-04-12
This work investigates the use of multiple-timestep schemes in imaginary time for computationally efficient ab initio equilibrium path integral simulations of quantum molecular motion. In the simplest formulation, only every n(th) path integral replica is computed at the target level of electronic structure theory, whereas the remaining low-level replicas still account for nuclear motion quantum effects with a more computationally economical theory. Motivated by recent developments for multiple-timestep techniques in real-time classical molecular dynamics, both 1-electron (atomic-orbital basis set) and 2-electron (electron correlation) truncations are shown to be effective. Structural distributions and thermodynamic averages are tested for representative analytic potentials and ab initio molecular examples. Target quantum chemistry methods include density functional theory and second-order Møller-Plesset perturbation theory, although any level of theory is formally amenable to this framework. For a standard two-level splitting, computational speedups of 1.6-4.0x are observed when using a 4-fold reduction in time slices; an 8-fold reduction is feasible in some cases. Multitiered options further reduce computational requirements and suggest that quantum mechanical motion could potentially be obtained at a cost not significantly different from the cost of classical simulations.
Emergent properties of nuclei from ab initio coupled-cluster calculations
NASA Astrophysics Data System (ADS)
Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.
2016-06-01
Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO{}{{sat}} is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon-nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. The coupling to the continuum impacts the energies of the {J}π =1/{2}-,3/{2}-,7/{2}-,3/{2}+ states in {}{17,23,25}O, and—contrary to naive shell-model expectations—the level ordering of the {J}π =3/{2}+,5/{2}+,9/{2}+ states in {}{53,55,61}Ca. ).
Thürmer, Stephan; Seidel, Robert; Winter, Bernd; Ončák, Milan; Slavíček, Petr
2011-06-16
The effect of hydration on the electronic structure of H(2)O(2) is investigated by liquid-jet photoelectron spectroscopy measurements and ab initio calculations. Experimental valence electron binding energies of the H(2)O(2) orbitals in water are, on average, 1.9 eV red-shifted with respect to the gas-phase molecule. A smaller width of the first peak was observed in the photoelectron spectrum from the solution. Our experiment is complemented by simulated photoelectron spectra, calculated at the ab initio level of theory (with EOM-IP-CCSD and DFT methods), and using path-integral sampling of the ground-state density. The observed shift in ionization energy upon solvation is attributed to a combination of nonspecific electrostatic effects (long-range polarization) and of the specific interactions between H(2)O(2) and H(2)O molecules in the first solvation shell. Changes in peak widths are found to result from merging of the two lowest ionized states of H(2)O(2) in water due to conformational changes upon solvation. Hydration effects on H(2)O(2) are stronger than on the H(2)O molecule. In addition to valence spectra, we report oxygen 1s core-level photoelectron spectra from H(2)O(2)(aq), and observed energies and spectral intensities are discussed qualitatively.
Ab initio 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%).
NASA Astrophysics Data System (ADS)
Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D.
2013-11-01
We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform.
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.
Ab initio many-body calculations of nucleon-nucleus scattering
NASA Astrophysics Data System (ADS)
Quaglioni, Sofia; Navrátil, Petr
2009-04-01
We develop a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach preserves translational symmetry and the Pauli principle. We outline technical details and present phase-shift results for neutron scattering on H3, He4, and Be10 and proton scattering on He3,4, using realistic nucleon-nucleon (NN) potentials. Our A=4 scattering results are compared to earlier ab initio calculations. We find that the CD-Bonn NN potential in particular provides an excellent description of nucleon-He4S-wave phase shifts. In contrast, the experimental nucleon-He4P-wave phase shifts are not well reproduced by any NN potential we use. We demonstrate that a proper treatment of the coupling to the n-Be10 continuum is successful in explaining the parity-inverted ground state in Be11.
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
Lindenmaier, Rodica; Tipton, Nicole; Sams, Robert L.; Brauer, Carolyn S.; Blake, Thomas A.; Williams, Stephen D.; Johnson, Timothy J.
2016-08-04
Hydroxyacetone (acetol) is a simple organic molecule of interest in both the astrophysical and atmospheric communities, having recently been observed in biomass burning events, as well as a known degradation product of isoprene oxidation. However, its vibrational assignment has never been fully completed, and few quantitative data are available for its detection via infrared spectroscopy. Our recent acquisition of both the pressure-broadened gas-phase data and the far-IR spectra now allow for unambiguous assignment of several (new) bands. In particular, the observed C-type bands of several fundamentals (particularly in the far-infrared) and a few combination bands demonstrate that the monomer is in a planar (Cs) conformation, at least a majority of the time. As suggested by other researchers, the monomer is a cis-cis conformer stabilized by an intramolecular O—H···O=C hydrogen bond forming a five-membered planar ring structure. Band assignments in the Cs point group are justified (at least for a good fraction of the molecules in the ensemble) by the presence of the C-type bands. The results and band assignments are well confirmed by both ab initio MP2-ccpvtz calculations as well as GAMESS (B3LYP) theoretical calculations. In addition, using vetted methods for quantitative measurements, we report the first IR absorption band strengths of acetol (also in electronic format) that can be used for atmospheric monitoring and other applications.
Prabakaran, A; Muthu, S
2012-12-01
The FT-IR and FT-Raman spectra of (2S)-2-amino-3-(3,4-dihydroxyphenyl)-2-methylpropanoic acid (2ADMA) were recorded in the region 4000-400 cm(-1) and 4000-100 cm(-1), respectively. The geometrical structure, harmonic vibrational frequency, infrared intensity, Raman activities and bonding features of this compound was carried out by ab initio HF and DFT methods with 6-31G (d,p) basis set. The complete vibrational frequency assignments were made by normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMF). The electric dipole moment (μ) and the first-order hyperpolarizability (β(0)) values have been the computed quantum mechanically. The calculated HOMO and LUMO energies show that, the charge transfer occurs within the molecule. The charge delocalizations of these molecules have been analyzed using NBO analysis. The solvent effects have been calculated using TD-DFT in combination with the polarized continuum model (PCM), and the results are in good agreement with experimental measurements. The other molecular properties like Mulliken population analysis, electrostatic potential (ESP) and thermodynamic properties of the title compound at the different temperatures have been calculated. Finally, the calculation results were applied to simulate infrared and Raman spectra of the title compound which shows good agreement with observed spectra.
Quantifying statistical uncertainties in ab initio nuclear physics using Lagrange multipliers
NASA Astrophysics Data System (ADS)
Carlsson, B. D.
2017-03-01
Theoretical predictions need quantified uncertainties for a meaningful comparison to experimental results. This is an idea which presently permeates the field of theoretical nuclear physics. In light of the recent progress in estimating theoretical uncertainties in ab initio nuclear physics, I here present and compare methods for evaluating the statistical part of the uncertainties. A special focus is put on the (for the field) novel method of Lagrange multipliers (LM). Uncertainties from the fit of the nuclear interaction to experimental data are propagated to a few observables in light-mass nuclei to highlight any differences between the presented methods. The main conclusion is that the LM method is more robust, while covariance-based methods are less demanding in their evaluation.
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
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.
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.
Verevkin, Sergey P; Emel'yanenko, Vladimir N; Kozlova, Svetlana A
2008-10-23
This work has been undertaken in order to obtain data on thermodynamic properties of organic carbonates and to revise the group-additivity values necessary for predicting their standard enthalpies of formation and enthalpies of vaporization. The standard molar enthalpies of formation of dibenzyl carbonate, tert-butyl phenyl carbonate, and diphenyl carbonate were measured using combustion calorimetry. Molar enthalpies of vaporization of these compounds were obtained from the temperature dependence of the vapor pressure measured by the transpiration method. Molar enthalpy of sublimation of diphenyl carbonate was measured in the same way. Ab initio calculations of molar enthalpies of formation of organic carbonates have been performed using the G3MP2 method, and results are in excellent agreement with the available experiment. Then the group-contribution method has been developed to predict values of the enthalpies of formation and enthalpies of vaporization of organic carbonates.
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.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics
Nakamura, Makoto Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki
2014-05-14
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics
NASA Astrophysics Data System (ADS)
Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki
2014-05-01
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics.
Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki
2014-05-14
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
NASA Astrophysics Data System (ADS)
Yamaguchi, Yukio; Schaefer, Henry F., III
1997-12-01
Four electronically lowest-lying ( X˜ 3B 1, ã 1A 1, b˜ 1B 1, and c˜ 1A 1) states of CH 2 have been investigated systematically using ab initio electronic structure theory. Complete active space (CAS) self-consistent-field (SCF) second-order configuration interaction (SOCI) and state-averaged (SA) CASSCF-SOCI levels of theory have been employed. The CASSCF reference wave function was constructed by minimizing the total energy of a specified state, while the SACASSCF reference wave function was obtained by minimizing the equally weighted total energy of the four ( X˜ 3B 1, ã 1A 1, b˜ 1B 1, and c˜ 1A 1) states. The third excited state ( c˜ 1A 1 or 2 1A 1) is of particular theoretical interest because it is represented by the second root of CASSCF and SOCI Hamiltonian matrices. Theoretical treatments of states not the lowest of their symmetry require special attention due to their tendency of variational collapse to the lower-lying state(s). For these four lowest-lying states total energies and physical properties including dipole moments, harmonic vibrational frequencies, and associated infrared (IR) intensities were determined and compared with the results from the configuration interaction with single and double excitations (CISD) method and available experimental values. The CASSCF-SOCI method should provide the most reliable energetics and physical properties in the present study owing to its fully variational nature in the molecular orbital (MO) and CI spaces for a given state. It is demonstrated that the SACASSCF-SOCI wave functions produce results which are quite consistent with those from the CASSCF-SOCI method. Thus significantly increased application of the SACASSCF-SOCI method to the excited states of a wide variety of molecular systems is expected.
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.
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.
Ab initio study on SN2 reaction of methyl p-nitrobenzenesulfonate and chloride anion in [mmim][PF6].
Hayaki, Seigo; Kido, Kentaro; Sato, Hirofumi; Sakaki, Shigeyoshi
2010-02-28
A S(N)2 reaction of methyl p-nitrobenzenesulfonate (p-NBS) and chloride anion in ionic liquid ([mmim][PF(6)]) was studied using RISM-SCF-SEDD method coupled with a highly sophisticated ab initio electronic structure theory (CCSD). The solvation structure as well as the energy profile along the reaction were discussed through comparison with an ordinary solvent system, dichloromethane.
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 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.
Bâldea, Ioan
2017-03-23
Recent advances in nano/molecular electronics and electrochemistry made it possible to continuously tune the fractional charge q of single molecules and to use vibrational spectroscopic methods to monitor such changes. Approaches to compute vibrational frequencies ω(q) of fractionally charged species based on the density functional theory (DFT) are faced with an important issue: the basic quantity used in these calculations, the total energy, should exhibit piecewise linearity with respect to the fractional charge, but approximate, commonly utilized exchange correlation functionals do not obey this condition. In this paper, with the aid of a simple and representative example, we benchmark results for ω(q) obtained within the DFT against ab initio methods, namely, coupled cluster singles and doubles and also second- and third-order Møller-Plesset perturbation) expansions. These results indicate that, in spite of missing the aforementioned piecewise linearity, DFT-based values ω(q) can reasonably be trusted.
NASA Astrophysics Data System (ADS)
Dadsetani, Mehrdad; Nejatipour, Hajar; Ebrahimian, Ali
2015-05-01
Using the ab initio methods for solving the Bethe-Salpeter equation on the basis of the FPLAPW method, optical properties of crystalline phenanthrene were calculated, in a comparison to its isomer, anthracene. It was found that despite the similarity of the structural, electronic, and the overall optical properties in a 40 eV energy range, phenanthrene and anthracene show significant differences in their optical spectra in the energy range below band gaps. Phenanthrene has two spin singlet excitonic features whereas anthracene shows one. The singlet and the lowest triplet binding energies of phenanthrene were found to be larger than anthracene. In this study, in addition, a comparison has been made between the optical spectra in RPA and the existing experimental data.
Lister, C.J.; McCutchan, E.A.
2014-06-15
A new generation of ab-initio calculations, based on realistic two- and three-body forces, is having a profound impact on our view of how nuclei work. To improve the numerical methods, and the parameterization of 3-body forces, new precise data are needed. Electromagnetic transitions are very sensitive to the dynamics which drive mixing between configurations. We have made a series of precise (< 3%) measurements of electromagnetic transitions in the A=10 nuclei {sup 10}C and {sup 10}Be by using the Doppler Shift Attenuation method carefully. Many interesting features can be reproduced including the strong α clustering. New measurements on {sup 8}Be and {sup 12}Be highlight the interplay between the alpha clusters and their valence neutrons.
Magnetic properties of vanadium doped CdTe: Ab initio calculations
NASA Astrophysics Data System (ADS)
Goumrhar, F.; Bahmad, L.; Mounkachi, O.; Benyoussef, A.
2017-04-01
In this paper, we are applying the ab initio calculations to study the magnetic properties of vanadium doped CdTe. This study is based on the Korringa-Kohn-Rostoker method (KKR) combined with the coherent potential approximation (CPA), within the local density approximation (LDA). This method is called KKR-CPA-LDA. We have calculated and plotted the density of states (DOS) in the energy diagram for different concentrations of dopants. We have also investigated the magnetic and half-metallic properties of this compound and shown the mechanism of exchange interaction. Moreover, we have estimated the Curie temperature Tc for different concentrations. Finally, we have shown how the crystal field and the exchange splittings vary as a function of the concentrations.
Curchod, Basile F. E.; Rauer, Clemens; Marquetand, Philipp; ...
2016-03-11
Full Multiple Spawning is a formally exact method to describe the excited-state dynamics of molecular systems beyond the Born-Oppenheimer approximation. However, it has been limited until now to the description of radiationless transitions taking place between electronic states with the same spin multiplicity. This Communication presents a generalization of the full and ab initio Multiple Spawning methods to both internal conversion (mediated by nonadiabatic coupling terms) and intersystem crossing events (triggered by spin-orbit coupling matrix elements) based on a spin-diabatic representation. Lastly, the results of two numerical applications, a model system and the deactivation of thioformaldehyde, validate the presented formalismmore » and its implementation.« less
Harris, Travis V.; Morokuma, Keiji; Kurashige, Yuki; Yanai, Takeshi
2014-02-07
The applicability of ab initio multireference wavefunction-based methods to the study of magnetic complexes has been restricted by the quickly rising active-space requirements of oligonuclear systems and dinuclear complexes with S > 1 spin centers. Ab initio density matrix renormalization group (DMRG) methods built upon an efficient parameterization of the correlation network enable the use of much larger active spaces, and therefore may offer a way forward. Here, we apply DMRG-CASSCF to the dinuclear complexes [Fe{sub 2}OCl{sub 6}]{sup 2−} and [Cr{sub 2}O(NH{sub 3}){sub 10}]{sup 4+}. After developing the methodology through systematic basis set and DMRG M testing, we explore the effects of extended active spaces that are beyond the limit of conventional methods. We find that DMRG-CASSCF with active spaces including the metal d orbitals, occupied bridging-ligand orbitals, and their virtual double shells already capture a major portion of the dynamic correlation effects, accurately reproducing the experimental magnetic coupling constant (J) of [Fe{sub 2}OCl{sub 6}]{sup 2−} with (16e,26o), and considerably improving the smaller active space results for [Cr{sub 2}O(NH{sub 3}){sub 10}]{sup 4+} with (12e,32o). For comparison, we perform conventional MRCI+Q calculations and find the J values to be consistent with those from DMRG-CASSCF. In contrast to previous studies, the higher spin states of the two systems show similar deviations from the Heisenberg spectrum, regardless of the computational method.
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Dytrych, T.; Maris, Pieter; Launey, K. D.; Draayer, J. P.; Vary, James; Langr, D.; Saule, E.; Caprio, M. A.; Catalyurek, U.; Sosonkina, M.
2016-06-09
We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for ^{6}Li and ^{12}C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.
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
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ceriotti, Michele; More, Joshua; Manolopoulos, David E.
2014-03-01
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic
Ab initio study of perovskite type oxide materials for solid oxide fuel cells
NASA Astrophysics Data System (ADS)
Lee, Yueh-Lin
2011-12-01
Perovskite type oxides form a family of materials of significant interest for cathodes and electrolytes of solid oxide fuel cells (SOFCs). These perovskites not only are active catalysts for surface oxygen reduction (OR) reactions but also allow incorporating the spilt oxygen monomers into their bulk, an unusual and poorly understood catalytic mechanism that couples surface and bulk properties. The OR mechanisms can be influenced strongly by defects in perovskite oxides, composition, and surface defect structures. This thesis work initiates a first step in developing a general strategy based on first-principles calculations for detailed control of oxygen vacancy content, transport rates of surface and bulk oxygen species, and surface/interfacial reaction kinetics. Ab initio density functional theory methods are used to model properties relevant for the OR reactions on SOFC cathodes. Three main research thrusts, which focus on bulk defect chemistry, surface defect structures and surface energetics, and surface catalytic properties, are carried to investigate different level of material chemistry for improved understanding of key physics/factors that govern SOFC cathode OR activity. In the study of bulk defect chemistry, an ab initio based defect model is developed for modeling defect chemistry of LaMnO 3 under SOFC conditions. The model suggests an important role for defect interactions, which are typically excluded in previous defect models. In the study of surface defect structures and surface energetics, it is shown that defect energies change dramatically (1˜2 eV lower) from bulk values near surfaces. Based on the existing bulk defect model with the calculated ab initio surface defect energetics, we predict the (001) MnO 2 surface oxygen vacancy concentration of (La0.9Sr0.1 )MnO3 is about 5˜6 order magnitude higher than that of the bulk under typical SOFC conditions. Finally, for surface catalytic properties, we show that area specific resistance, oxygen
Le, Hung M; Raff, Lionel M
2010-01-14
The classical reaction dynamics of a four-body, bimolecular reaction on a neural network (NN) potential-energy surface (PES) fitted to a database obtained solely from ab initio MP2/6-311G(d,p) calculations are reported. The present work represents the first reported application of ab initio NN methods to a four-body, bimolecular, gas-phase reaction where bond extensions reach 8.1 A for the BeH + H(2) --> BeH(2) + H reaction. A modified, iterative novelty sampling method is used to select data points based on classical trajectories computed on temporary NN surfaces. After seven iterations, the sampling process is found to converge after selecting 9604 configurations. Incorporation of symmetry increases this to 19 208 BeH(3) configurations. The analytic PES for the system is obtained from the ensemble average of a five-member (6-60-1) NN committee. The mean absolute error (MAE) for the committee is 0.0046 eV (0.44 kJ mol(-1)). The total energy range of the BeH(3) database is 147.0 kJ mol(-1). Therefore, this MAE represents a percent energy error of 0.30%. Since it is the gradient of the PES that constitutes the most important quantity in molecular dynamics simulations, the paper also reports mean absolute error for the gradient. This result is 0.026 eV A(-1) (2.51 kJ mol(-1) A(-1)). Since the gradient magnitudes span a range of 15.32 eV A(-1) over the configuration space tested, this mean absolute gradient error represents a percent error of 0.17%. The mean percent absolute relative gradient error is 4.67%. The classically computed reaction cross sections generally increase with total energy. They vary from 0.007 to 0.030 A(2) when H(2) is at ground state, and from 0.05 to 0.10 A(2) when H(2) is in the first excited state. Trajectory integration is very fast using the five-member NN PES. The average trajectory integration time is 1.07 s on a CPU with a clock speed of 2.4 GHz. Zero angular momentum collisions are also investigated and compared with previously reported
Makhov, Dmitry V.; Saita, Kenichiro; Martinez, Todd J.; ...
2014-12-11
In this study, we report a detailed computational simulation of the photodissociation of pyrrole using the ab initio Multiple Cloning (AIMC) method implemented within MOLPRO. The efficiency of the AIMC implementation, employing train basis sets, linear approximation for matrix elements, and Ehrenfest configuration cloning, allows us to accumulate significant statistics. We calculate and analyze the total kinetic energy release (TKER) spectrum and Velocity Map Imaging (VMI) of pyrrole and compare the results directly with experimental measurements. Both the TKER spectrum and the structure of the velocity map image (VMI) are well reproduced. Previously, it has been assumed that the isotropicmore » component of the VMI arises from long time statistical dissociation. Instead, our simulations suggest that ultrafast dynamics contributes significantly to both low and high energy portions of the TKER spectrum.« less
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.
Comparison between phenomenological and ab-initio reaction and relaxation models in DSMC
NASA Astrophysics Data System (ADS)
Sebastião, Israel B.; Kulakhmetov, Marat; Alexeenko, Alina
2016-11-01
New state-specific vibrational-translational energy exchange and dissociation models, based on ab-initio data, are implemented in direct simulation Monte Carlo (DSMC) method and compared to the established Larsen-Borgnakke (LB) and total collision energy (TCE) phenomenological models. For consistency, both the LB and TCE models are calibrated with QCT-calculated O2+O data. The model comparison test cases include 0-D thermochemical relaxation under adiabatic conditions and 1-D normal shockwave calculations. The results show that both the ME-QCT-VT and LB models can reproduce vibrational relaxation accurately but the TCE model is unable to reproduce nonequilibrium rates even when it is calibrated to accurate equilibrium rates. The new reaction model does capture QCT-calculated nonequilibrium rates. For all investigated cases, we discuss the prediction differences based on the new model features.
Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study
Xiong, L H; Lou, H B; Wang, X D; Debela, T T; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z
2014-04-01
The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt-Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of < 0,4,4,0 >, < 0,3, 6,0 > and < 0,4,4,2 > with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy. (C) 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.
Ab-initio study of quasi one-dimensional Br adsorption on Pt(110)
NASA Astrophysics Data System (ADS)
Franchini, Cesare; Redinger, Josef; Podloucky, Raimund
2001-03-01
Halogen atoms interact strongly with metal surfaces. For this reason they play an important role in many technologically important processes. The Pt(110) surface is known to reconstruct into an (1x2) structure of "missing-row" type (MR). Its strong anisotropic character can be used as template to prepare single crystal surfaces of Pt-Br-Pt chains, which exhibit quasi one-dimensional (1D) behavior. We present ab-initio investigations based on the Full-potential Linearized Augmented Plane Wave method (FLAPW), as implemented in the FLEUR package, and the Tersoff-Hamann model for simulating STM images. Structural and electronic properties of the Br/Pt(110) surface at half coverage and of the clean Pt(110) surface and its (1x2) MR reconstruction are studied in detail. Results are compared to available LEED and STM data.
Ab initio calculation of vibrational properties of a-Si:H with inner voids
NASA Astrophysics Data System (ADS)
Nakhmanson, S. M.; Drabold, D. A.
1998-05-01
We have performed an ab initio calculation of vibrational properties of hydrogenated amorphous silicon (a-Si:H) using a molecular dynamics method. A Wooten, Winer, Weaire (WWW) 216 atom model for pure amorphous silicon (a-Si) updated by Djordjevic, Thorpe and Wooten has been employed as a ``base'' for our a-Si:H models with voids that were made by removing a cluster of silicon atoms out of the bulk and terminating the resulting dangling bonds with hydrogens. Our calculation shows that the presence of voids leads to localized low energy (30-50 cm-1) states in vibrational spectrum of the system. The nature and localization properies of these states are carefully analysed by various visualization techniques. Web resources: http://www.phy.ohiou.edu/ ĩnakhmans/Professional/Bubbles/bubpr.htm
Ab initio and density functional studies of hydrocarbon adsorption in zeolites.
Curtiss, L. A.
1998-08-21
The adsorption energies of methane and ethane in zeolites are investigated with ab initio molecular orbital theory and density functional theory. In this work we have used zeolite cluster models containing two, three, and five tetrahedral (Si, Al) atoms and have found equilibrium structures for complexes of methane, ethane, and propane with an acid site. If a large enough cluster is used and correlation effects are included via perturbation theory, the calculated adsorption energy for ethane is about 5 kcal/mol compared with the experimental value of 7.5 kcal/mol. The B3LYP density functional method gives a much smaller binding of {approximately}1 kcal/mol for ethane. The reason for the failure of density fictional theory is unclear.
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.
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 atomic recombination reaction energetics on model heat shield surfaces
NASA Technical Reports Server (NTRS)
Senese, Fredrick; Ake, Robert
1992-01-01
Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.
NASA Astrophysics Data System (ADS)
Nomura, Yusuke; Arita, Ryotaro
2015-12-01
We formulate an ab initio downfolding scheme for electron-phonon-coupled systems. In this scheme, we calculate partially renormalized phonon frequencies and electron-phonon coupling, which include the screening effects of high-energy electrons, to construct a realistic Hamiltonian consisting of low-energy electron and phonon degrees of freedom. We show that our scheme can be implemented by slightly modifying the density functional-perturbation theory (DFPT), which is one of the standard methods for calculating phonon properties from first principles. Our scheme, which we call the constrained DFPT, can be applied to various phonon-related problems, such as superconductivity, electron and thermal transport, thermoelectricity, piezoelectricity, dielectricity, and multiferroicity. We believe that the constrained DFPT provides a firm basis for the understanding of the role of phonons in strongly correlated materials. Here, we apply the scheme to fullerene superconductors and discuss how the realistic low-energy Hamiltonian is constructed.
Optimized Structures and Proton Affinities of Fluorinated Dimethyl Ethers: An Ab Initio Study
NASA Technical Reports Server (NTRS)
Orgel, Victoria B.; Ball, David W.; Zehe, Michael J.
1996-01-01
Ab initio methods have been used to investigate the proton affinity and the geometry changes upon protonation for the molecules (CH3)2O, (CH2F)2O, (CHF2)2O, and (CF3)2O. Geometry optimizations were performed at the MP2/3-2 I G level, and the resulting geometries were used for single-point energy MP2/6-31G calculations. The proton affinity calculated for (CH3)2O was 7 Kjoule/mole from the experimental value, within the desired variance of +/- 8Kjoule/mole for G2 theory, suggesting that the methodology used in this study is adequate for energy difference considerations. For (CF3)20, the calculated proton affinity of 602 Kjoule/mole suggests that perfluorinated ether molecules do not act as Lewis bases under normal circumstances; e.g. degradation of commercial lubricants in tribological applications.
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 NH_{3} to those of ab initio molecular dynamics (AIMD). Furthermore, we find that there are regions of state space for which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.
Muchová, Eva; Slavícek, Petr; Sobolewski, Andrzej L; Hobza, Pavel
2007-06-21
The goal of this study is to explore the photochemical processes following optical excitation of the glycine molecule into its two low-lying excited states. We employed electronic structure methods at various levels to map the PES of the ground state and the two low-lying excited states of glycine. It follows from our calculations that the photochemistry of glycine can be regarded as a combination of photochemical behavior of amines and carboxylic acid. The first channel (connected to the presence of amino group) results in ultrafast decay, while the channels characteristic for the carboxylic group occur on a longer time scale. Dynamical calculations provided the branching ratio for these channels. We also addressed the question whether conformationally dependent photochemistry can be observed for glycine. While electronic structure calculations favor this possibility, the ab initio multiple spawning (AIMS) calculations showed only minor relevance of the reaction path resulting in conformationally dependent dynamics.
Equation of state and phase diagram of ammonia at high pressures from ab initio simulations.
Bethkenhagen, Mandy; French, Martin; Redmer, Ronald
2013-06-21
We present an equation of state as well as a phase diagram of ammonia at high pressures and high temperatures derived from ab initio molecular dynamics simulations. The predicted phases of ammonia are characterized by analyzing diffusion coefficients and structural properties. Both the phase diagram and the subsequently computed Hugoniot curves are compared to experimental results. Furthermore, we discuss two methods that allow us to take into account nuclear quantum effects, which are of considerable importance in molecular fluids. Our data cover pressures up to 330 GPa and a temperature range from 500 K to 10,000 K. This regime is of great interest for interior models of the giant planets Uranus and Neptune, which contain, besides water and methane, significant amounts of ammonia.
Ab initio electronic structure, magnetism, and magnetocrystalline anisotropy of UGa2
NASA Astrophysics Data System (ADS)
Diviš, Martin; Richter, Manuel; Eschrig, Helmut; Steinbeck, Lutz
1996-04-01
Ab initio electronic structure calculations for the intermetallic compound UGa2 were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5f states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5f states, which have been treated by self-interaction corrected local-density theory. This approach with 5f2 occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant.
Ab initio based polarizable force field generation and application to liquid silica and magnesia
NASA Astrophysics Data System (ADS)
Beck, Philipp; Brommer, Peter; Roth, Johannes; Trebin, Hans-Rainer
2011-12-01
We extend the program potfit, which generates effective atomic interaction potentials from ab initio data, to electrostatic interactions and induced dipoles. The potential parametrization algorithm uses the Wolf direct, pairwise summation method with spherical truncation. The polarizability of oxygen atoms is modeled with the Tangney-Scandolo interatomic force field approach. Due to the Wolf summation, the computational effort in simulation scales linearly in the number of particles, despite the presence of electrostatic interactions. Thus, this model allows to perform large-scale molecular dynamics simulations of metal oxides with realistic potentials. Details of the implementation are given, and the generation of potentials for SiO2 and MgO is demonstrated. The approach is validated by simulations of microstructural, thermodynamic, and vibrational properties of liquid silica and magnesia.
High-pressure elastic properties of cubic Ir2P from ab initio calculations
NASA Astrophysics Data System (ADS)
Sun, Xiao-Wei; Bioud, Nadhira; Fu, Zhi-Jian; Wei, Xiao-Ping; Song, Ting; Li, Zheng-Wei
2016-10-01
A study of the high-pressure elastic properties of new synthetic Ir2P in the anti-fluorite structure is conducted using ab initio calculations based on density functional theory. The elastic constants C11, C12 and C44 for the cubic Ir2P are obtained by the stress-strain method and the elastic stability calculations under pressure indicate that it is stable at least 100 GPa. Additionally, the electronic density of states, the aggregate elastic moduli, that is bulk modulus, shear modulus, and Young's modulus along with the Debye temperature, Poisson's ratio, and elastic anisotropy factor are all successfully obtained. Moreover, the pressure dependence of the longitudinal and shear wave velocities in three different directions [100], [110], and [111] for Ir2P are also predicted for the first time.
Experimental and ab initio study of the photofragmentation of DNA and RNA sugars
Ha, D. T.; Huels, M. A.; Huttula, M.; Urpelainen, S.; Kukk, E.
2011-09-15
The photoelectron-photoion-photoion coincidence method is used to measure the photodissociation of doubly charged D-ribose (C{sub 5}H{sub 10}O{sub 5}), the RNA sugar molecules, and 2-deoxy-D-ribose (C{sub 5}H{sub 10}O{sub 4}), the DNA sugar molecules, following normal Auger decay after initial C 1s and O 1s core ionizations. The fragment identification is facilitated by measuring isotopically labeled D-ribose, such as D-ribose deuterated at C(1), and with {sup 13}C at the C(5) position. Ab initio quantum chemistry calculations are used to gain further insight into the abundant appearance of the CHO{sup +} fragment.
Chaban, Vitaly V; Prezhdo, Oleg V
2016-07-07
The Haber-Bosch process is the main industrial method for producing ammonia from diatomic nitrogen and hydrogen. We use a combination of ab initio thermochemical analysis and reactive molecular dynamics to demonstrate that a significant increase in the ammonia production yield can be achieved using hydroxylated graphene and related species. Exploiting the polarity difference between N2/H2 and NH3, as well as the universal proton acceptor behavior of NH3, we demonstrate a strong shift of the equilibrium of the Haber-Bosch process toward ammonia (ca. 50 kJ mol(-1) enthalpy gain and ca. 60-70 kJ mol(-1) free energy gain). The modified process is of significant importance to the chemical industry.
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.
Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; ...
2015-02-09
In this study, the response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser,more » electron and ion irradiations.« less
Density functional and ab initio investigation of S2N2 and (SN)2
NASA Astrophysics Data System (ADS)
Moon, Jiwon; Chae, Myoungju; Kim, Joonghan
2017-03-01
Quantum chemical calculations were performed to calculate the molecular properties of the 1Ag state of disulfur dinitride, S2N2, and the 1A1 state of the SN dimer, (SN)2, using density functional theory (DFT) and ab initio methods. The molecular structure of (SN)2 is a trapezoid instead of a rectangle. Because the multireference character of (SN)2 is considerable, most hybrid DFTs poorly describe its molecular properties. In contrast, old generalized gradient approximations give qualitatively correct descriptions of the molecular properties of (SN)2. Multi-state second-order multiconfigurational perturbation theory gives results that are close to those from multireference configuration interaction with the Davidson correction. The multireference character should be considered when calculating the molecular properties of poly sulfur nitride systems.
Pressure-induced semimetallic behavior of calcium from ab initio calculations
NASA Astrophysics Data System (ADS)
Magnitskaya, M. V.; Matsko, N. L.; Baturin, V. S.; Uspenskii, Yu A.
2014-05-01
A loss of metallic properties in fcc calcium under high pressure is studied ab initio using the density functional theory (DFT) and GW approximation. It is found that a more correct description of many-electron effects given by GW method does not provide significant changes in the behavior of electronic spectrum in comparison with DFT approach. We note that the obtained width of (pseudo)gap is highly sensitive to the k-point sampling used for density of states calculation. The analysis of fcc calcium's band structure at p ~ 20 GPa shows that the crossing of bands at the Fermi level is removed if the spin-orbit coupling is taken into account.
Ab initio oscillator strengths and transition probabilities in aluminum-like calcium, Ca VIII
Karpuskiene, R. Bogdanovich, P.
2009-07-15
An ab initio study of aluminum-like calcium is presented. The calculations are performed within the configuration interaction method in the basis of transformed radial orbitals with a variable parameter. Relativistic effects are accounted for within the Breit-Pauli approximation. Energy spectra, transition characteristics and lifetimes of excited levels of configurations 3s{sup 2}3p, 3s3p{sup 2}, 3s{sup 2}3d, 3p{sup 3}, 3s3p3d, 3p{sup 2}3d, 3s{sup 2}4s, 3s{sup 2}4p, 3s{sup 2}4d, 3s{sup 2}4f, 3s3p4s, and 3s3p4p are obtained. The results are compared with available experimental and theoretical 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.
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.
AB INITIO Modeling of Thermomechanical Properties of Mo-Based Alloys for Fossil Energy Conversion
Ching, Wai-Yim
2013-12-31
In this final scientific/technical report covering the period of 3.5 years started on July 1, 2011, we report the accomplishments on the study of thermo-mechanical properties of Mo-based intermetallic compounds under NETL support. These include computational method development, physical properties investigation of Mo-based compounds and alloys. The main focus is on the mechanical and thermo mechanical properties at high temperature since these are the most crucial properties for their potential applications. In particular, recent development of applying ab initio molecular dynamic (AIMD) simulations to the T1 (Mo{sub 5}Si{sub 3}) and T2 (Mo{sub 5}SiB{sub 2}) phases are highlighted for alloy design in further improving their properties.
Ab initio study of pressure induced structural and electronic properties in TmPo
Makode, Chandrabhan Pataiya, Jagdish; Sanyal, Sankar P.; Panwar, Y. S.; Aynyas, Mahendra
2015-06-24
We report an ab initio calculation of pressure induced structural phase transition and electronic properties of Thulium Polonide (TmPo).The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). It is found that TmPo is stable in NaCl-type (B{sub 1}-phase) structure to CsCl-type (B{sub 2}-phase) structure of this compound in the pressure range of 7.0 GPa. We also calculate the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure and density of states. From energy diagram it is observed that TmPo exhibit metallic behavior. The calculated values of equilibrium lattice parameter and bulk modulus are in general good agreement.
Ab-initio calculations of electronic, transport, and structural properties of boron phosphide
Ejembi, J. I.; Nwigboji, I. H.; Franklin, L.; Malozovsky, Y.; Zhao, G. L.; Bagayoko, D.
2014-09-14
We present results from ab-initio, self-consistent density functional theory calculations of electronic and related properties of zinc blende boron phosphide (zb-BP). We employed a local density approximation potential and implemented the linear combination of atomic orbitals formalism. This technique follows the Bagayoko, Zhao, and Williams method, as enhanced by the work of Ekuma and Franklin. The results include electronic energy bands, densities of states, and effective masses. The calculated band gap of 2.02 eV, for the room temperature lattice constant of a=4.5383 Å, is in excellent agreement with the experimental value of 2.02±0.05 eV. Our result for the bulk modulus, 155.7 GPa, agrees with experiment (152–155 GPa). Our predictions for the equilibrium lattice constant and the corresponding band gap, for very low temperatures, are 4.5269 Å and 2.01 eV, respectively.
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)-,
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.
The keto-enol equilibrium in substituted acetaldehydes: focal-point analysis and ab initio limit
NASA Astrophysics Data System (ADS)
Balabin, Roman M.
2011-10-01
High-level ab initio electronic structure calculations up to the CCSD(T) theory level, including extrapolations to the complete basis set (CBS) limit, resulted in high precision energetics of the tautomeric equilibrium in 2-substituted acetaldehydes (XH2C-CHO). The CCSD(T)/CBS relative energies of the tautomers were estimated using CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z calculations with MP2/aug-cc-pVTZ geometries. The relative enol (XHC = CHOH) stabilities (ΔE e,CCSD(T)/CBS) were found to be 5.98 ± 0.17, -1.67 ± 0.82, 7.64 ± 0.21, 8.39 ± 0.31, 2.82 ± 0.52, 10.27 ± 0.39, 9.12 ± 0.18, 5.47 ± 0.53, 7.50 ± 0.43, 10.12 ± 0.51, 8.49 ± 0.33, and 6.19 ± 0.18 kcal mol-1 for X = BeH, BH2, CH3, Cl, CN, F, H, NC, NH2, OCH3, OH, and SH, respectively. Inconsistencies between the results of complex/composite energy computations methods Gn/CBS (G2, G3, CBS-4M, and CBS-QB3) and high-level ab initio methods (CCSD(T)/CBS and MP2/CBS) were found. DFT/aug-cc-pVTZ results with B3LYP, PBE0 (PBE1PBE), TPSS, and BMK density functionals were close to the CCSD(T)/CBS levels (MAD = 1.04 kcal mol-1).
Ab-initio simulations of materials using VASP: Density-functional theory and beyond.
Hafner, Jürgen
2008-10-01
During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science-promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces
Yu, Ling; Yang, Zhong-Zhi
2010-05-07
Structures, binding energies, and vibrational frequencies of (NH(3))(n) (n=2-5) isomers and dynamical properties of liquid ammonia have been explored using a transferable intermolecular potential eight point model including fluctuating charges and flexible body based on a combination of the atom-bond electronegativity equalization and molecular (ABEEM) mechanics (ABEEM ammonia-8P) in this paper. The important feature of this model is to divide the charge sites of one ammonia molecule into eight points region containing four atoms, three sigma bonds, and a lone pair, and allows the charges in system to fluctuate responding to the ambient environment. Due to the explicit descriptions of charges and special treatment of hydrogen bonds, the results of equilibrium geometries, dipole moments, cluster interaction energies, vibrational frequencies for the gas phase of small ammonia clusters, and radial distribution function for liquid ammonia calculated with the ABEEM ammonia-8P potential model are in good agreement with those measured by available experiments and those obtained from high level ab initio calculations. The properties of ammonia dimer are studied in detail involving the structure and one-dimensional, two-dimensional potential energy surface. As for interaction energies, the root mean square deviation is 0.27 kcal/mol, and the linear correlation coefficient reaches 0.994.
Maschio, Lorenzo; Kirtman, Bernard; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto
2013-10-28
We present a fully analytical formulation for calculating Raman intensities of crystalline periodic systems using a local basis set. Numerical differentiation with respect to atomic coordinates and with respect to wavevectors is entirely avoided as is the determination of crystal orbital coefficient derivatives with respect to nuclear displacements. Instead, our method utilizes the orbital energy-weighted density matrix and is based on the self-consistent solution of first- and second-order Coupled Perturbed Hartree-Fock/Kohn-Sham equations for the electronic response to external electric fields at the equilibrium geometry. This method has also been implemented in the Crystal program, which uses a Gaussian type basis set.
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 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.
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.
Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R
2016-07-07
Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.
Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)
NASA Astrophysics Data System (ADS)
Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang
2001-01-01
Semiempirical PM3, ab initio HF/3-21g ∗, and DFT B3LYP/6-31g ∗ calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.
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.
NASA Astrophysics Data System (ADS)
Jameson, Cynthia J.; de Dios, Angel C.
1992-07-01
The chemical shifts observed in nuclear magnetic resonance experiments are the differences in shielding of the nuclear spin in different electronic environments. These are known to depend on intermolecular interactions as evidenced by density-dependent chemical shifts in the gas phase, gas-to-liquid shifts, and adsorption shifts on surfaces. We present the results of the first ab initio intermolecular chemical shielding function calculated for a pair of interacting atoms for a wide range of internuclear separations. We used the localized orbital local origin (LORG) approach of Hansen and Bouman and also investigated the second-order electron correlation contributions using second-order LORG (SOLO). The 39Ar shielding in Ar2 passes through zero at some very short distance, going through a minimum, and asymptotically approaches zero at larger separations. The 21Ne shielding function in Ne2 has a similar shape. The Drude model suggests a method of scaling that portion of the shielding function that is weighted most heavily by exp[-V(R)/kT]. The scaling factors, which have been verified in the comparison of 21Ne in Ne2 against 39Ar in Ar2 ab initio results, allows us to project out from the same 39Ar in Ar2 ab initio values the appropriate 129Xe shielding functions in the Xe-Ar, Xe-Kr, and Xe-Xe interacting pairs. These functions lead to temperature-dependent second virial coefficients of chemical shielding which agree with experiments in the gas phase. Ab initio calculations of 39Ar shielding in clusters of argon are used to model the observed 129Xe chemical shifts of Xe, Xe2,...,Xe8 trapped in the cages of zeolite NaA.
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
Barker, John R; Nguyen, Thanh Lam; Stanton, John F
2012-06-21
Calculations were carried out for 25 isotopologues of the title reaction for various combinations of (35)Cl, (37)Cl, (12)C, (13)C, (14)C, H, and D. The computed rate constants are based on harmonic vibrational frequencies calculated at the CCSD(T)/aug-cc-pVTZ level of theory and X(ij) vibrational anharmonicity coefficients calculated at the CCSD(T) /aug-cc-pVDZ level of theory. For some reactions, anharmonicity coefficients were also computed at the CCSD(T)/aug-cc-pVTZ level of theory. The classical reaction barrier was taken from Eskola et al. [J. Phys. Chem. A 2008, 112, 7391-7401], who extrapolated CCSD(T) calculations to the complete basis set limit. Rate constants were calculated for temperatures from ∼100 to ∼2000 K. The computed ab initio rate constant for the normal isotopologue is in good agreement with experiments over the entire temperature range (∼10% lower than the recommended experimental value at 298 K). The ab initio H/D kinetic isotope effects (KIEs) for CH(3)D, CH(2)D(2), CHD(3), and CD(4) are in very good agreement with literature experimental data. The ab initio (12)C/(13)C KIE is in error by ∼2% at 298 K for calculations using X(ij) coefficients computed with the aug-cc-pVDZ basis set, but the error is reduced to ∼1% when X(ij) coefficients computed with the larger aug-cc-pVTZ basis set are used. Systematic improvements appear to be possible. The present SCTST results are found to be more accurate than those from other theoretical calculations. Overall, this is a very promising method for computing ab initio kinetic isotope effects.
NASA Astrophysics Data System (ADS)
Sivaranjani, T.; Periandy, S.; Xavier, S.
2016-03-01
The FT-IR and FT-Raman spectra of 3-pyridinemethanol (3PYRM) have been recorded in the regions 4000-400 and 4000-100 cm-1 respectively. The vibrational analysis of 3PYRM was carried out using wavenumbers computed by HF and DFT (B3LYP) methods with 6-311++G (d, p) basis set, along with experimental values. The conformational analyses were performed and the energies of the different possible conformers were determined. The total electron density and MESP surfaces of the molecules were constructed using B3LYP/6-311++G (d, p) method to display nucleophilic and electrophilic region globally. The HOMO and LUMO energies were measured and different reactivity descriptors are discussed the active sites of the molecule. Natural Bond Orbital Analysis is discussed and possible transition are correlated with the electronic transitions. Milliken's net charges and the atomic natural charges are also predicted. The 13C and 1H NMR chemical shifts were computed at the B3LYP/6-311++G (2d, p) level by applying GIAO theory and compared with the experimental spectra recorded using the high resolution of 100 MHz and 400 MHz NMR spectrometer with electromagnetic field strength 9.1T, respectively. The temperature dependence of the thermodynamic properties; heat capacity, entropy and enthalpy for the title compounds were also determined by B3LYP/6-311++G (d, p) method.
Tachikawa, Hiroto
2006-01-12
Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.
Dane Morgan
2010-06-10
The project began March 13, 2006, allocated for three years, and received a one year extension from March 13, 2009 to March 12, 2010. It has now completed 48 of 48 total months. The project was focused on using ab initio methods to gain insights into radiation induced segregation (RIS) in Ni-Fe-Cr alloys. The project had the following key accomplishments • Development of a large database of ab initio energetics that can be used by many researchers in the future for increased understanding of this system. For example, we have the first calculations showing a dramatic stabilization effect of Cr-Cr interstitial dumbbells in Ni. • Prediction of both vacancy and interstitial diffusion constants for Ni-Cr and Ni-Fe for dilute Cr and Fe. This work included generalization of widely used multifrequency models to make use of ab initio derived energetics and thermodynamics. • Prediction of qualitative trends of RIS from vacancy and interstitial mechanisms, suggesting the two types of defect fluxes drive Cr RIS in opposite directions. • Detailed kinetic Monte Carlo modeling of diffusion by vacancy mechanism in Ni-Cr as a function of Cr concentration. The results demonstrate that Cr content can have a significant effect on RIS. • Development of a quantitative RIS transport model, including models for thermodynamic factors and boundary conditions.
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.
Emergent properties of nuclei from ab initio coupled-cluster calculations
Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; ...
2016-05-17
Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLOmore » $${}_{{\\rm{sat}}}$$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the $${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$$ states in $${}^{\\mathrm{17,23,25}}$$O, and—contrary to naive shell-model expectations—the level ordering of the $${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$$ states in $${}^{\\mathrm{53,55,61}}$$Ca.« less
Ab initio virial equation of state for argon using a new nonadditive three-body potential.
Jäger, Benjamin; Hellmann, Robert; Bich, Eckard; Vogel, Eckhard
2011-08-28
An ab initio nonadditive three-body potential for argon has been developed using quantum-chemical calculations at the CCSD(T) and CCSDT levels of theory. Applying this potential together with a recent ab initio pair potential from the literature, the third and fourth to seventh pressure virial coefficients of argon were computed by standard numerical integration and the Mayer-sampling Monte Carlo method, respectively, for a wide temperature range. All calculated virial coefficients were fitted separately as polynomials in temperature. The results for the third virial coefficient agree with values evaluated directly from experimental data and with those computed for other nonadditive three-body potentials. We also redetermined the second and third virial coefficients from the best experimental pρT data utilizing the computed higher virial coefficients as constraints. Thus, a significantly closer agreement of the calculated third virial coefficients with the experimental data was achieved. For different orders of the virial expansion, pρT data have been calculated and compared with results from high quality measurements in the gaseous and supercritical region. The theoretically predicted pressures are within the very small experimental errors of ±0.02% for p ≤ 12 MPa in the supercritical region near room temperature, whereas for subcritical temperatures the deviations increase up to +0.3%. The computed pressure at the critical density and temperature is about 1.3% below the experimental value. At pressures between 200 MPa and 1000 MPa and at 373 K, the calculated values deviate by 1% to 9% from the experimental results.
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
NASA Astrophysics Data System (ADS)
Dalbouha, S.; Senent, M. L.; Komiha, N.; Domínguez-Gómez, R.
2016-09-01
Various astrophysical relevant molecules obeying the empirical formula C2H3NO are characterized using explicitly correlated coupled cluster methods (CCSD(T)-F12). Rotational and rovibrational parameters are provided for four isomers: methyl isocyanate (CH3NCO), methyl cyanate (CH3OCN), methyl fulminate (CH3ONC), and acetonitrile N-oxide (CH3CNO). A CH3CON transition state is inspected. A variational procedure is employed to explore the far infrared region because some species present non-rigidity. Second order perturbation theory is used for the determination of anharmonic frequencies, rovibrational constants, and to predict Fermi resonances. Three species, methyl cyanate, methyl fulminate, and CH3CON, show a unique methyl torsion hindered by energy barriers. In methyl isocyanate, the methyl group barrier is so low that the internal top can be considered a free rotor. On the other hand, acetonitrile N-oxide presents a linear skeleton, C3v symmetry, and free internal rotation. Its equilibrium geometry depends strongly on electron correlation. The remaining isomers present a bend skeleton. Divergences between theoretical rotational constants and previous parameters fitted from observed lines for methyl isocyanate are discussed on the basis of the relevant rovibrational interaction and the quasi-linearity of the molecular skeleton.
Dalbouha, S; Senent, M L; Komiha, N; Domínguez-Gómez, R
2016-09-28
Various astrophysical relevant molecules obeying the empirical formula C2H3NO are characterized using explicitly correlated coupled cluster methods (CCSD(T)-F12). Rotational and rovibrational parameters are provided for four isomers: methyl isocyanate (CH3NCO), methyl cyanate (CH3OCN), methyl fulminate (CH3ONC), and acetonitrile N-oxide (CH3CNO). A CH3CON transition state is inspected. A variational procedure is employed to explore the far infrared region because some species present non-rigidity. Second order perturbation theory is used for the determination of anharmonic frequencies, rovibrational constants, and to predict Fermi resonances. Three species, methyl cyanate, methyl fulminate, and CH3CON, show a unique methyl torsion hindered by energy barriers. In methyl isocyanate, the methyl group barrier is so low that the internal top can be considered a free rotor. On the other hand, acetonitrile N-oxide presents a linear skeleton, C3v symmetry, and free internal rotation. Its equilibrium geometry depends strongly on electron correlation. The remaining isomers present a bend skeleton. Divergences between theoretical rotational constants and previous parameters fitted from observed lines for methyl isocyanate are discussed on the basis of the relevant rovibrational interaction and the quasi-linearity of the molecular skeleton.
NASA Astrophysics Data System (ADS)
Dixit, Anant; Alouani, M.
2016-10-01
X-ray absorption and X-ray magnetic circular dichroism (XMCD) are very powerful tools for probing the orbital and spin moments of each atomic species orbital of magnetic materials. In this work, we present the implementation of a module for computing the X-ray absorption and XMCD spectra into the VASP code. We provide a derivation of the absorption cross-section in the electric dipole approximation. The matrix elements, which make up the X-ray absorption cross-section for a given polarization of light, are then computed using either the momentum operator p or the position operator r, within the projector augmented wave method. The core electrons are described using the relativistic basis-set whereas for the valence electrons, the spin-orbit coupling is added perturbatively to the semi-relativistic Hamiltonian. We show that both the p and the r implementations lead to the same results. The results for the K-edge and L23-edges of bcc-iron are then computed and compared to experiment.
Martonak; Molteni; Parrinello
2000-01-24
We present a new constant-pressure ab initio molecular dynamics method suitable for studying, e.g., pressure-induced structural transformations in finite nonperiodic systems such as clusters. We immerse an ab initio treated cluster into a model classical liquid, described by a soft-sphere potential, which acts as a pressure reservoir. The pressure is varied by tuning the parameter of the liquid potential. We apply the method to a Si35H36 cluster, which undergoes a pressure-induced amorphization at approximately 35 GPa, and remains in a disordered state even upon pressure release.
Assary, Rajeev S.; Kim, Taijin; Low, John; Greeley, Jeffrey P.; Curtiss, Larry A.
2012-12-28
Molecular level understanding of acid-catalysed conversion of sugar molecules to platform chemicals such as hydroxy-methyl furfural (HMF), furfuryl alcohol (FAL), and levulinic acid (LA) is essential for efficient biomass conversion. In this paper, the high-level G4MP2 method along with the SMD solvation model is employed to understand detailed reaction energetics of the acid-catalysed decomposition of glucose and fructose to HMF. Based on protonation free energies of various hydroxyl groups of the sugar molecule, the relative reactivity of gluco-pyranose, fructo-pyranose and fructo-furanose are predicted. Calculations suggest that, in addition to the protonated intermediates, a solvent assisted dehydration of one of the fructo-furanosyl intermediates is a competing mechanism, indicating the possibility of multiple reaction pathways for fructose to HMF conversion in aqueous acidic medium. Two reaction pathways were explored to understand the thermodynamics of glucose to HMF; the first one is initiated by the protonation of a C2–OH group and the second one through an enolate intermediate involving acyclic intermediates. Additionally, a pathway is proposed for the formation of furfuryl alcohol from glucose initiated by the protonation of a C2–OH position, which includes a C–C bond cleavage, and the formation of formic acid. The detailed free energy landscapes predicted in this study can be used as benchmarks for further exploring the sugar decomposition reactions, prediction of possible intermediates, and finally designing improved catalysts for biomass conversion chemistry in the future.
Native Defect Properties in Beta-SiC: Ab Initio and Empirical Potential Calculations
Gao, Fei; Bylaska, Eric J.; Weber, William J.; Corrales, Louis R.
2001-06-25
There is considerable ambiguity about the formation of native defects and their clusters in SiC, since different empirical potential gives different results, particular related to the stability of interstitial configurations. Ab intio pseudopotential methods are used to study the formation and properties of native defects in beta-SiC. The results are compared with those calculated by molecular dynamics (MD) using a Tersoff potential, where the various cut-off distances found in the literature are employed. The formation energy of vacancies and antisite defects obtained by ab initio calculations are in good agreement with those given by the Tersoff potential, regardless of the cut-off distances, but there is a disparity for interstitials between the two methods, depending on the cut-off distances used in the Tersoff potential. The present results, however, provide guidelines for evaluating the quality and fit of empirical potentials for large-scale simulations of irradiation damage (displacement cascades) and point defect migration (recombination or annealing) in SiC.
NASA Astrophysics Data System (ADS)
Das, Koyeli; Bomzan, Pranish; Das, Rajesh Kumar; Rajbanshi, Biplab; Roy, Mahendra Nath
2017-03-01
Solvation nature of Lithium iodide (LiI) for both polar and nonpolar organic solvents viz., acetonitrile and benzonitrile have been explored by effect of geometry, spectroscopic, conductometric, ab initio methods . Results of vibrational spectroscopic data were compared with experimental values. Centre of attraction is iodide anion on significant vibrational bands of benzonitrile. Fluorescence spectra provide a supporting to the mentioned facts. Ab initio calculations used for shaping the optimum location of Li+ and I- ions in ion-solvent interactions containing varying nitriles as solvent sphere. Emission band positions, intensity, shape of solvent-sensitive molecules in organic solvents of varying polarities are studied.
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
Ab initio calculation of bowl, cage, and ring isomers of C20 and C20-.
An, Wei; Gao, Yi; Bulusu, Satya; Zeng, X C
2005-05-22
High-level ab initio calculations have been carried out to reexamine relative stability of bowl, cage, and ring isomers of C(20) and C(20)(-). The total electronic energies of the three isomers show different energy orderings, strongly depending on the hybrid functionals selected. It is found that among three popular hybrid density-functional (DF) methods B3LYP, B3PW91, PBE1PBE, and a new hybrid-meta-DF method TPSSKCIS, only the PBE1PBE method (with cc-pVTZ basis set) gives qualitatively correct energy ordering as that predicted from ab initio CCSD(T)/cc-pVDZ [CCSD(T)-coupled-cluster method including singles, doubles, and noniterative perturbative triples; cc-pVDZ-correlation consistent polarized valence double zeta] as well as from MP4(SDQ)/cc-pVTZ [MP4-fourth-order Moller-Plesset; cc-pVTZ-correlation consistent polarized valence triple zeta] calculations. Both CCSD(T) and MP4 calculations indicate that the bowl is most likely the global minimum of neutral C(20) isomers, followed by the fullerene cage and ring. For the anionic counterparts, the PBE1PBE calculation also agrees with MP4/cc-pVTZ calculation, both predicting that the bowl is still the lowest-energy structure of C(20)(-) at T=0 K, followed by the ring and the cage. In contrast, both B3LYP/cc-pVTZ and B3PW91/cc-pVTZ calculations predict that the ring is the lowest-energy structure of C(20)(-). Apparently, this good reliability in predicting the energy ordering renders the hybrid PBE method a leading choice for predicting relative stability among large-sized carbon clusters and other carbon nanostructures (e.g., finite-size carbon nanotubes, nano-onions, or nanohorns). The relative stabilities derived from total energy with Gibbs free-energy corrections demonstrate a changing ordering in which ring becomes more favorable for both C(20) and C(20)(-) at high temperatures. Finally, photoelectron spectra (PES) for the anionic C(20)(-) isomers have been computed. With binding energies up to 7 eV, the
Molecular tailoring approach: a route for ab initio treatment of large clusters.
Sahu, Nityananda; Gadre, Shridhar R
2014-09-16
Conspectus Chemistry on the scale of molecular clusters may be dramatically different from that in the macroscopic bulk. Greater understanding of chemistry in this size regime could greatly influence fields such as materials science and atmospheric and environmental chemistry. Recent advances in experimental techniques and computational resources have led to accurate investigations of the energies and spectral properties of weakly bonded molecular clusters. These have enabled researchers to learn how the physicochemical properties evolve from individual molecules to bulk materials and to understand the growth patterns of clusters. Experimental techniques such as infrared, microwave, and photoelectron spectroscopy are the most popular and powerful tools for probing molecular clusters. In general, these experimental techniques do not directly reveal the atomistic details of the clusters but provide data from which the structural details need to be unearthed. Furthermore, the resolution of the spectral properties of energetically close cluster conformers can be prohibitively difficult. Thus, these investigations of molecular aggregates require a combination of experiments and theory. On the theoretical front, researchers have been actively engaged in quantum chemical ab initio calculations as well as simulation-based studies for the last few decades. To obtain reliable results, there is a need to use correlated methods such as Møller-Plesset second order method, coupled cluster theory, or dispersion corrected density functional theory. However, due to nonlinear scaling of these methods, optimizing the geometry of large clusters still remains a formidable quantum chemistry challenge. Fragment-based methods, such as divide-and-conquer, molecular tailoring approach (MTA), fragment molecular orbitals, and generalized energy-based fragmentation approach, provide alternatives for overcoming the scaling problem for spatially extended molecular systems. Within MTA, a large
Communication: Towards ab initio self-energy embedding theory in quantum chemistry
Lan, Tran Nguyen; Kananenka, Alexei A.; Zgid, Dominika
2015-12-28
The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green’s function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.
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.
B28: the smallest all-boron cage from an ab initio global search
NASA Astrophysics Data System (ADS)
Zhao, Jijun; Huang, Xiaoming; Shi, Ruili; Liu, Hongsheng; Su, Yan; King, R. Bruce
2015-09-01
Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures.Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures. Electronic supplementary information (ESI) available: Planar isomer structures of B28 and spatial distributions of front molecular orbitals. See DOI: 10.1039/c5nr04034e
Ab initio electron mobility and polar phonon scattering in GaAs
NASA Astrophysics Data System (ADS)
Zhou, Jin-Jian; Bernardi, Marco
2016-11-01
In polar semiconductors and oxides, the long-range nature of the electron-phonon (e -ph ) interaction is a bottleneck to compute charge transport from first principles. Here, we develop an efficient ab initio scheme to compute and converge the e -ph relaxation times (RTs) and electron mobility in polar materials. We apply our approach to GaAs, where by using the Boltzmann equation with state-dependent RTs, we compute mobilities in excellent agreement with experiment at 250 -500 K . The e -ph RTs and the phonon contributions to intravalley and intervalley e -ph scattering are also analyzed. Our work enables efficient ab initio computations of transport and carrier dynamics in polar materials.
Properties of metals during the heating by intense laser irradiation using ab initio simulations
NASA Astrophysics Data System (ADS)
Holst, Bastian; Recoules, Vanina; Torrent, Marc; Mazevet, Stephane
2011-10-01
Ultrashort laser pulses irradiating a target heat the electrons to very high temperatures. In contrast, the ionic lattice is unaffected on the time scale of the laser pulse since the heat capacity of electrons is much smaller than that of the lattice. This non-equilibrium system can be described as a composition of two subsystems: one consisting of hot electrons and the other of an ionic lattice at low temperature. We studied the effect of this intense electronic excitations on the optical properties of gold using ab initio simulations. We additionally use ab initio linear response to compute the phonon spectrum and the electron-phonon coupling constant within Density Functional Theory for several electronic temperatures of few eV. LULI, Ecole Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau, France.
Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.
Yang, Jianjun; Tse, John S
2011-11-17
The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.
Ab initio simulation of atomic-scale imaging in noncontact atomic force microscopy.
Caciuc, V; Hölscher, H
2009-07-01
In this paper, we summarize some results of our ab initio simulations aimed at investigating the mechanism of the NC-AFM image contrast on semiconductor and metallic surfaces. We start with an introduction into the basic ideas behind the ab initio simulation process of the NC-AFM experimental results. Our simulations reveal that the interaction of a clean silicon tip with a semiconductor surface like InAs(110) might lead to bond-formation and bond-breaking processes during the approach and retraction of the tip. This imaging mechanism is very similar to that observed on a metallic surface like Ag(110). Interestingly, a clean silicon tip can become contaminated with Ag surface atoms. On both types of surface we observe a significant energy dissipation which is caused by a hysteresis in the tip-sample force curves calculated on the approach and retraction path.
[Photoelectron Spectra of CCl2-: Ab Initio Calculation and Franck-Condon Analysis].
Wu, Jun
2015-12-01
Geometry optimization and harmonic vibrational frequency calculations were performed on the X¹A₁ state of CCl₂ and X²B₁ state of CCl₂⁻ at the B3LYP, MP2, CCSD levels. Franck-Condon analysis and spectral simulations were carried out on the photoelectron band of CCl₂⁻ including Duschinsky effects. The simulated spectra obtained are in excellent agreement with the experiment. Note that Duschinsky effect between bending vibration and the symmetric stretch modes should be considered in the CCl₂ (X¹A₁)-CCl₂⁻ (X²B₁) photodetachment process. By combining ab initio calculations with Franck-Condon analyses, the assignment of spectrum observed is firmly established to the X¹A₁-X²B₁ photodetachment process of the CCl₂⁻ radical, and the recommended geometric parameters of which in the literature are confirmed again base on ab initio theory and IFCA process.
Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation
NASA Astrophysics Data System (ADS)
Correa, J. D.; Cisternas, E.
2016-09-01
By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.
Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2014-04-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and lead (l-Pb). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2015-05-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2016-05-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.
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.
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.
Alonso, J L; Andrade, X; Echenique, P; Falceto, F; Prada-Gracia, D; Rubio, A
2008-08-29
A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schrödinger-like equation, where the orbital time derivative is multiplied by a parameter. This parameter controls the time scale of the fictitious electronic motion and speeds up the calculations with respect to standard Ehrenfest dynamics. In contrast with other methods, wave function orthogonality needs not be imposed as it is automatically preserved, which is of paramount relevance for large-scale AIMD simulations.
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.
Steady-state ab initio laser theory for N-level lasers.
Cerjan, Alexander; Chong, Yidong; Ge, Li; Stone, A Douglas
2012-01-02
We show that Steady-state Ab initio Laser Theory (SALT) can be applied to find the stationary multimode lasing properties of an N-level laser. This is achieved by mapping the N-level rate equations to an effective two-level model of the type solved by the SALT algorithm. This mapping yields excellent agreement with more computationally demanding N-level time domain solutions for the steady state.
NASA Astrophysics Data System (ADS)
Yurchenko, Sergei N.; Carvajal, Miguel; Thiel, Walter; Jensen, Per
2006-09-01
We report a six-dimensional CCSD(T)/aug-cc-pVTZ dipole moment surface for the electronic ground state of PH 3 computed ab initio on a large grid of 10 080 molecular geometries. Parameterized, analytical functions are fitted through the ab initio data, and the resulting dipole moment functions are used, together with a potential energy function determined by refining an existing ab initio surface in fittings to experimental wavenumber data, for simulating absorption spectra of the first three polyads of PH 3, i.e., ( ν2, ν4), ( ν1, ν3, 2 ν2, 2 ν4, ν2 + ν4), and ( ν1 + ν2, ν3 + ν2, ν1 + ν4, ν3 + ν4, 2 ν2 + ν4, ν2 + 2 ν4, 3 ν2, 3 ν4). The resulting theoretical transition moments show excellent agreement with experiment. A line-by-line comparison of the simulated intensities of the ν2/ ν4 band system with 955 experimental intensity values reported by Brown et al. [L.R. Brown, R.L. Sams, I. Kleiner, C. Cottaz, L. Sagui, J. Mol. Spectrosc. 215 (2002) 178-203] gives an average absolute percentage deviation of 8.7% (and a root-mean-square deviation of 0.94 cm -1 for the transition wavenumbers). This is very remarkable since the calculations rely entirely on ab initio dipole moment surfaces and do not involve any adjustment of these surfaces to reproduce the experimental intensities. Finally, we predict the line strengths for transitions between so-called cluster levels (near-degenerate levels formed at high rotational excitation) for J up to 60.
First fully ab initio potential energy surface of methane with a spectroscopic accuracy
NASA Astrophysics Data System (ADS)
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2016-09-01
Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.
Ab initio equation of state of hydrogen for inertial fusion applications
NASA Astrophysics Data System (ADS)
Benedict, Lorin X.; Morales, Miguel A.; Schwegler, Eric; Tamblyn, Isaac; Bonev, Stanimir A.; Correa, Alfredo A.; Clark, Daniel S.; Haan, Steven W.; LLNL Collaboration
2011-06-01
We describe ab initio electronic structure calculations (DFT molecular dynamics and quantum Monte Carlo) of the equation of state of hydrogen in a regime relevant for ICF applications. We find the computed EOS to be quite close to that of the most recent SESAME table (constructed by G. Kerley, 2004). A simple density-dependent correction brings the recent SESAME EOS into nearly perfect agreement with ours in the chosen region. Simulations of ICF applications with this corrected SESAME table are discussed.
Ab initio molecular dynamics study of liquid sodium and cesium up to critical point
Yuryev, Anatoly A.; Gelchinski, Boris R.
2015-08-17
Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.
Ab initio molecular dynamics study of liquid sodium and cesium up to critical point
NASA Astrophysics Data System (ADS)
Yuryev, Anatoly A.; Gelchinski, Boris R.
2015-08-01
Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.
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.
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.
NASA Astrophysics Data System (ADS)
Tachikawa, Masanori; Shiga, Motoyuki
2004-09-01
We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.
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.
Yamaji, Youhei
2015-12-31
Recently, condensed-matter ab initio approaches to strongly correlated electrons confined in crystalline solids have been developed and applied to transition-metal oxides and molecular conductors. In this paper, an ab initio scheme based on constrained random phase approximations and localized Wannier orbitals is applied to a spin liquid candidate Na{sub 2}IrO{sub 3} and is shown to reproduce experimentally observed specific heat.
NASA Astrophysics Data System (ADS)
Dézerald, Lucile; Ventelon, Lisa; Willaime, François; Clouet, Emmanuel; Rodney, David
2014-06-01
Ab initio methods, based on the Density Functional Theory (DFT), have been extensively used to study point defects and defect clusters in materials. Present HPC resources and DFT codes now allow similar investigations to be performed on dislocations. The study of these extended defects requires not only larger simulation cells but also a higher accuracy because the energy differences, which are involved, are rather small, typically 50-to-100 meV for supercells containing 50-to-500 atoms. The topology of the Peierls potential of screw dislocations with 1/2 <111>Burgers vector, i.e. the 2D energy landscape seen by these dislocations, is being completely revisited by DFT calculations. From results obtained in all body-centered cubic (bcc) transition metals, except Cr (V, Nb, Ta, Mo, W and Fe), using the PWSCF code, which is part of the Quantum-Espresso package, we concluded that the 2D Peierls potentials have two common features: the single-hump shape of the barrier between two minima of the potential, and the presence of a maximum - and not a minimum as predicted by most empirical potentials - around the split core. In iron, the topology of the Peierls potential is reversed compared to the classical sinusoidal picture: the location of the saddle point and the maximum are indeed inverted with unexpected flat regions. The first results obtained within the framework of the PRACE project, DIMAIM (DIslocations in Metals using Ab Initio Methods), started at the beginning of 2013, will also be presented. In particular, in order to address the twinning-antitwinning asymmetry often observed in bcc metals and regarded as the major contribution to the breakdown of Schmid's law, we have determined the crystal orientation dependence of the Peierls stress, i.e. the critical stress required for dislocation motion. These computationally most expensive simulations were performed on the PRACE Tier-0 system at Barcelona Supercomputing Center (Marenostrum III). The scalability results
Shrestha, Rojan; Simoncini, David; Zhang, Kam Y J
2012-11-01
Recent advancements in computational methods for protein-structure prediction have made it possible to generate the high-quality de novo models required for ab initio phasing of crystallographic diffraction data using molecular replacement. Despite those encouraging achievements in ab initio phasing using de novo models, its success is limited only to those targets for which high-quality de novo models can be generated. In order to increase the scope of targets to which ab initio phasing with de novo models can be successfully applied, it is necessary to reduce the errors in the de novo models that are used as templates for molecular replacement. Here, an approach is introduced that can identify and rebuild the residues with larger errors, which subsequently reduces the overall C(α) root-mean-square deviation (CA-RMSD) from the native protein structure. The error in a predicted model is estimated from the average pairwise geometric distance per residue computed among selected lowest energy coarse-grained models. This score is subsequently employed to guide a rebuilding process that focuses on more error-prone residues in the coarse-grained models. This rebuilding methodology has been tested on ten protein targets that were unsuccessful using previous methods. The average CA-RMSD of the coarse-grained models was improved from 4.93 to 4.06 Å. For those models with CA-RMSD less than 3.0 Å, the average CA-RMSD was improved from 3.38 to 2.60 Å. These rebuilt coarse-grained models were then converted into all-atom models and refined to produce improved de novo models for molecular replacement. Seven diffraction data sets were successfully phased using rebuilt de novo models, indicating the improved quality of these rebuilt de novo models and the effectiveness of the rebuilding process. Software implementing this method, called MORPHEUS, can be downloaded from http://www.riken.jp/zhangiru/software.html.
High-level ab initio computations of the absorption spectra of organic iridium complexes.
Plasser, Felix; Dreuw, Andreas
2015-02-12
The excited states of fac-tris(phenylpyridinato)iridium [Ir(ppy)3] and the smaller model complex Ir(C3H4N)3 are computed using a number of high-level ab initio methods, including the recently implemented algebraic diagrammatic construction method to third-order ADC(3). A detailed description of the states is provided through advanced analysis methods, which allow a quantification of different charge transfer and orbital relaxation effects and give extended insight into the many-body wave functions. Compared to the ADC(3) benchmark an unexpected striking difference of ADC(2) is found for Ir(C3H4N)3, which derives from an overstabilization of charge transfer effects. Time-dependent density functional theory (TDDFT) using the B3LYP functional shows an analogous but less severe error for charge transfer states, whereas the ωB97 results are in good agreement with ADC(3). Multireference configuration interaction computations, which are in reasonable agreement with ADC(3), reveal that static correlation does not play a significant role. In the case of the larger Ir(ppy)3 complex, results at the TDDFT/B3LYP and TDDFT/ωB97 levels of theory are presented. Strong discrepancies between the two functionals, which are found with respect to the energies, characters, as well as the density of the low lying states, are discussed in detail and compared to experiment.
Ab initio transport calculations of molecular wires with electron-phonon couplings
NASA Astrophysics Data System (ADS)
Hirose, Kenji; Kobayashi, Nobuhiko
2009-03-01
Understanding of electron transport through nanostructures becomes important with the advancement of fabrication process to construct atomic-scale devices. Due to the drastic change of transport properties by contact conditions to electrodes in local electric fields, first-principles calculation approaches are indispensable to understand and characterize the transport properties of nanometer-scale molecular devices. Here we study the transport properties of molecular wires between metallic electrodes, especially focusing on the effects of contacts to electrodes and of the electron-phonon interactions. We use an ab initio calculation method based on the scattering waves, which are obtained by the recursion-transfer-matrix (RTM) method, combined with non-equilibrium Green's function (NEGF) method including the electron-phonon scatterings. We find that conductance shows exponential behaviors as a function of the length of molecular wires due to tunneling process determined by the HOMO-LUMO energy gap. From the voltage drop behaviors inside the molecular wires, we show that the contact resistances are dominant source for the bias drop and thus are related to local heating. We will present the electron-phonon coupling effects at contact on the inelastic scattering and discuss on the local heating and local temperature, comparing them with those of metallic atomic wires.
Ab initio study for the hydrogen abstraction reactions on toluene and tetralin.
Beste, Ariana; Harrison, Robert J; Britt, Phillip F; Buchanan III, A C
2006-01-01
Hydrogen abstraction reactions play a key role in many thermal and catalytic processes involved in the production of fuels and chemicals. In this paper, the hydrogen abstraction reactions on toluene and tetralin by the benzyl radical are investigated by ab initio methods. These reactions are representatives of similar reactions occurring in the thermolysis of lignin model compounds containing the phenethyl phenyl ether (PPE) structural moiety. The title reactions serve to calibrate the theoretical methods to be used in the study of PPE pyrolysis through comparison of the reaction barriers with reliable experimental values. We used two different hybrid density functionals (BHandHLYP, B3LYP) and second-order perturbation theory to obtain equilibrium and transition state geometries. We recomputed selected energy barriers at the B3LYP geometries with the coupled cluster singles and doubles (CCSD) method. Multiple transition states were found for both reactions. BHandHLYP underestimates and second-order perturbation theory overestimates the reaction barriers; B3LYP energy barriers agree well with experiment and the corresponding CCSD energy barriers. The flat potential energy surface around the saddle points causes numerical inaccuracies. We observe the break down of the harmonic approximation in the calculation of low frequencies.
Ab initio study of hydrogen migration across n-alkyl radicals.
Davis, Alexander C; Francisco, Joseph S
2011-04-14
A thorough ab initio investigation is conducted on all possible hydrogen migration pathways for the 1-ethyl, 1-propyl, 1-butyl, 1-pentyl, 1-hexyl, 1-heptyl, and 1-octyl radicals in order to determine underlying trends in reaction enthalpies, activation energies, Arrhenius A-factors, tunneling, and rate coefficients. The G4, G2, and CBS-Q composite methods are used to determine the enthalpy of reaction and activation energy barrier for each reaction. Each method shows excellent agreement with eight experimental enthalpy of reaction values, with root mean squared values of 0.8, 0.9, and 0.6 kcal mol(-1) for CBS-Q, G2, and G4, respectively. Differences in barrier heights, A-factors, tunneling, and rate coefficients are observed for axial and equatorial arrangements as well as between secondary hydrogen migration sites, depending on the location of the secondary site relative to the terminal carbon. The validity of using cycloalkane model systems to estimate rate parameters is also assessed. The failure of two key assumptions inherent to the cycloalkane models, resulting in a breakdown in the accuracy of these methods for larger transition states, is discussed. This study has significant ramifications for future theoretical, experimental, and modeling studies involving the decomposition of n-alkanes.
Enthalpy of the gas-phase CO2 + Mg reaction from ab initio total energies.
Lesar, Antonija; Prebil, Sasa; Hodoscek, Milan
2002-01-01
Various highly accurate ab initio composite methods of Gaussian-n (G1, G2, G3), their variations (G2(MP2), G3(MP2), G3//B3LYP, G3(MP2)//B3LYP), and complete basis set (CBS-Q, CBS-Q//B3LYP) series of models were applied to compute reaction enthalpies of the ground-state reaction of CO2 with Mg. All model chemistries predict highly endothermic reactions, with DeltaH(298) = 63.6-69.7 kcal x mol(-1). The difference between the calculated reaction enthalpies and the experimental value, evaluated with recommended experimental standard enthalpies of formation for products and reactants, is more than 20 kcal x mol(-1) for all methods. This difference originates in the incorrect experimental enthalpy of formation of gaseous MgO given in thermochemical databases. When the theoretical formation enthalpy for MgO calculated by a particular method is used, the deviation is reduced to 1.3 kcal x mol(-1). The performance of the methodologies used to calculate the heat of this particular reaction and the enthalpy of formation of MgO are discussed.
Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds
NASA Astrophysics Data System (ADS)
Yexin, Feng; Ji, Chen; Xin-Zheng, Li; Enge, Wang
2016-01-01
The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).
Ab initio investigation of high-entropy alloys of 3d elements
NASA Astrophysics Data System (ADS)
Tian, Fuyang; Varga, Lajos Karoly; Chen, Nanxian; Delczeg, Lorand; Vitos, Levente
2013-02-01
Single-phase high-entropy alloys are investigated using the exact muffin-tin orbitals (EMTO) method in combination with the coherent potential approximation (CPA). Choosing the paramagnetic face-centered-cubic NiCoFeCr alloy as an example, we compare the CPA results with those obtained using the supercell (SC) method. For the equilibrium Wigner-Seitz radius and elastic properties, the single-site mean-field approximation turns out to yield consistent results with the SC approach. Next, we employ the EMTO-CPA method to study the bulk properties of CuNiCoFeCrTix (x=0.0-0.5,1.0) and NiCoFeCrTi high-entropy alloys. A detailed comparison between the theoretical results and the available experimental data demonstrates that ab initio theory can properly describe the fundamental properties of this important class of engineering alloys. Theory predicts NiCoFeCr and CuNiCoFeCr to be more isotropic and less ductile than the Ti-containing single-phase alloys (CuNiCoFeCrTix with x≳0.4 and NiCoFeCrTi).
Ab-initio Calculations of Electronic Properties of InP and GaP
NASA Astrophysics Data System (ADS)
Malozovsky, Yuriy; Franklin, Lashounda; Ekuma, Chinedu; Zhao, Guang-Lin; Bagayoko, Diola
2013-03-01
We present results from ab-initio, self consistent local density approximation (LDA) calculations of electronic and related properties of zinc blende indium and gallium phosphides (InP & GaP) We employed a local density approximation (LDA) potential and implemented the linear combination of atomic orbitals (LCAO) formalism. This implementation followed the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). This method searches for the optimal basis set that yields the minima of the occupied energies. This search entails methodically increasing the size of the basis set, up to the optimal one, and the accompanying enrichment of angular symmetry and of radial orbitals. Our calculated, direct band gap of 1.398 eV (1.40 eV) for InP, at the Γ point, is in excellent agreement with experimental values. We discuss our preliminary results for the indirect band gap, from Γ to X, of GaP. We also report calculated electron and hole effective masses for both InP and GaP and the total (DOS) and partial (pDOS) densities of states. This work was funded in part by the National Science Foundation and the Louisiana Board of Regents, through LASiGMA and LS-LAMP, [EPS-1003897, No. NSF (2010-15)-RII-SUBR, and HRD-1002541] and by the Louisiana Optical Network Initiative (LONI) at SUBR.
Ab initio molecular treatment for charge transfer by P{sup 3+} ions on hydrogen and helium
Moussa, A.; Zaidi, A.; Lahmar, S.; Bacchus-Montabonel, M.-C.
2010-02-15
A theoretical treatment of charge-transfer processes induced by collision of phosphorus P{sup 3+}(3s{sup 2}){sup 1}S ions on atomic hydrogen and helium has been carried out using ab initio potential-energy curves and couplings at the multireference configuration interaction level of theory. The cross sections calculated by means of semiclassical collision methods show the existence of a significant charge transfer in the 0.1-700-keV laboratory energy range. Radial and rotational coupling interactions were analyzed for both collision systems.
Ab initio study of the role of lysine 16 for the molecular switching mechanism of Ras protein p21.
Futatsugi, N; Hata, M; Hoshino, T; Tsuda, M
1999-01-01
Quantum chemical computations using the ab initio molecular orbital (MO) method have been performed to investigate the molecular switching mechanism of Ras protein p21, which has an important role in intracellular signal cascades. Lys(16) was demonstrated to be crucial to the function of Ras p21, and the hydrolysis of GTP to GDP was found to be an one-step reaction. The potential energy barrier of this hydrolysis reaction from GTP to (GDP + P) was calculated to be approximately 42 kcal/mol. The role of GAP (GTPase-activating protein) was also discussed in terms of the delivery of the water molecules required for the hydrolysis. PMID:10585950
Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...
2016-06-30
We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.
Timoshenko, Janis; Shivhare, Atal; Scott, Robert W J; Lu, Deyu; Frenkel, Anatoly I
2016-07-20
We adopted ab initio X-ray absorption near edge structure (XANES) modeling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modeling, where the candidate structures are known, and the inverse modeling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by revealing the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.
Koput, Jacek
2015-06-30
The accurate ground-state potential energy function of imidogen, NH, has been determined from ab initio calculations using the multireference averaged coupled-pair functional (MR-ACPF) method in conjunction with the correlation-consistent core-valence basis sets up to octuple-zeta quality. The importance of several effects, including electron correlation beyond the MR-ACPF level of approximation, the scalar relativistic, adiabatic, and nonadiabatic corrections were discussed. Along with the large one-particle basis set, all of these effects were found to be crucial to attain "spectroscopic" accuracy of the theoretical predictions of vibration-rotation energy levels of NH.
AB Initio Study of the Structure and Spectroscopic Properties of Halogenated Thioperoxy Radicals
NASA Technical Reports Server (NTRS)
Munoz, Luis A.; Binning, R. C., Jr.; Weiner, Brad R.; Ishikawa, Yasuyuki
1997-01-01
Thioperoxy (XSO or XOS) radicals exist in a variety of chemical environments, and they have as a consequence drawn some interest. HSO, an important species in the chemistry of the troposphere, has been examined both experimentally. The halogenated (X = F, Cl or Br) peroxy species and isovalent thioperoxy species have been studied less, but they too are potentially interesting because oxidized sulfur species and halogen sources are present in the atmosphere. Learning the fate of XSO and XOS radicals is important to understanding the atmospheric oxidation chemistry of sulfur compounds. Of these, FSO and ClSO are particularly interesting because they have been directly detected spectroscopically. Recent studies in our laboratory on the photochemistry of thionyl halides (X2SO; where X = F or Cl) have suggested new ways to generate XSO species. The laser-induced photodissociation of thionyl fluoride, F2SO, at 193 nm and thionyl chloride, ClSO, at 248 nm is characterized by a radical mechanism, X2SO -> XSO + X. The structure of FSO has been characterized experimentally by Endo et cd. employing microwave spectroscopy. Using the unrestricted Hartree-Fock (UHF) self-consistent field (SCF) method, Sakai and Morokuma computed the electronic structure of the ground (sup 2)A" and the first excited (sup 2)A' states of FSO. Electron correlation was not taken into account in their study. In a laser photodissociation experiment, Huber et al. identified ClSO mass spectromctrically. ClSO has also been detected in low temperature matrices by EPR and in the gas phase by far IR laser magnetic resonance. Although the structure of FSO is known in detail, the only study, experimental or theoretical, of CISO has been an ab initio HFSCF study by Hinchliffe. Electron correlation corrections were also excluded from this study. In order to better understand the isomerization and dissociation dynamics of the radical species, we have performed ab initio correlated studies of the potential energy
Ab initio study of structural, electronic, and thermal properties of Pt1-xPdx alloys
NASA Astrophysics Data System (ADS)
Ahmed, Shabbir; Zafar, Muhammad; Shakil, M.; Choudhary, M. A.; Hashmi, Muhammad Raza-Ur-Rehman
2017-01-01
We report a systematic theoretical study of Pt1-xPdx alloys using ab initio density functional theory (DFT) by pseudo potential method. We have used super cell approach to investigate structural, electronic and thermal properties of Platinum (Pt), Palladium (Pd) and their alloys Pt1-xPdx(x = 0.00, 0.25, 0.50, 0.75, 1.00). The calculated lattice constants and bulk moduli are in good agreement with available literature data. The results of electronic properties revealed that the alloys are metallic in nature. The thermal properties were investigated through density functional perturbation theory (DFPT) and quasi-harmonic approximation. The contribution to the free energy from the lattice vibration was calculated using the phonon densities of states (DOS) derived by means of the linear-response theory. The DFPT with quasi-harmonic approximation methods was applied to determine the phonon DOS and thermal quantities i.e., the Debye temperatures, vibration energy, entropy and constant-volume specific heat.
Interatomic Coulombic decay in a He dimer: Ab initio potential-energy curves and decay widths
Kolorenc, Premysl; Kryzhevoi, Nikolai V.; Sisourat, Nicolas; Cederbaum, Lorenz S.
2010-07-15
The energy gained by either of the two helium atoms in a helium dimer through simultaneous ionization and excitation can be efficiently transferred to the other helium atom, which then ionizes. The respective relaxation process called interatomic Coulombic decay (ICD) is the subject of the present paper. Specifically, we are interested in ICD of the lowest of the ionized excited states, namely, the He{sup +}(n=2)He states, for which we calculated the relevant potential-energy curves and the interatomic decay widths. The full-configuration interaction method was used to obtain the potential-energy curves. The decay widths were computed by utilizing the Fano ansatz, Green's-function methods, and the Stieltjes imaging technique. The behavior of the decay widths with the interatomic distance is examined and is elucidated, whereby special emphasis is given to the asymptotically large interatomic separations. Our calculations show that the electronic ICD processes dominate over the radiative decay mechanisms over a wide range of interatomic distances. The ICD in the helium dimer has recently been measured by Havermeier et al. [Phys. Rev. Lett. 104, 133401 (2010)]. The impact of nuclear dynamics on the ICD process is extremely important and is discussed by Sisourat et al. [Nat. Phys. 6, 508 (2010)] based on the ab initio data computed in the present paper.
Systematic improvements of ab-initio in-medium similarity renormalization group calculations
NASA Astrophysics Data System (ADS)
Morris, Titus Dan
The In-Medium Similarity Renormalization Group (IM-SRG) is an ab initio many-body method that has enjoyed increasing prominence in nuclear theory, due to its soft polynomial scaling with system size, and the flexibility to target ground and excited states of both closed- and open-shell systems. Despite many successful applications of the IM-SRG to microscopic calculations of medium-mass nuclei in recent years, the conventional formulation of the method suffers a number of limitations. Key amongst these are i) large memory demands that limit calculations in heavier systems and render the calculation of observables besides energy spectra extremely difficult, and ii) the lack of a computationally feasible sequence of improved approximations that converge to the exact solution in the appropriate limit, thereby verifying that the IM-SRG is systematically improvable. In this thesis, I present a novel formulation of the IM-SRG based on the Magnus expansion. I will show that this improved formulation, guided by intuition gleaned from a diagrammatic analysis of the perturbative content of different truncations and parallels with coupled-cluster theory, allows one to bypass the computational limitations of traditional implementations, and provides computationally viable approximations that go beyond the truncations used to date. The effectiveness of the new Magnus formulation is illustrated for several many-nucleon and many-electron systems.
Progress in low-resolution ab initio phasing with CrowdPhase
Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.
2016-01-01
Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data. PMID:26960132
Progress in low-resolution ab initio phasing with CrowdPhase.
Jorda, Julien; Sawaya, Michael R; Yeates, Todd O
2016-03-01
Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented. Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.
Aqueous solutions: state of the art in ab initio molecular dynamics.
Hassanali, Ali A; Cuny, Jérôme; Verdolino, Vincenzo; Parrinello, Michele
2014-03-13
The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born-Oppenheimer and Car-Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.
High-level ab initio studies of hydrogen abstraction from prototype hydrocarbon systems.
Temelso, Berhane; Sherrill, C David; Merkle, Ralph C; Freitas, Robert A
2006-09-28
Symmetric and nonsymmetric hydrogen abstraction reactions are studied using state-of-the-art ab initio electronic structure methods. Second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] methods with large correlation consistent basis sets (cc-pVXZ, where X = D,T,Q) are used in determining the transition-state geometries, activation barriers, and thermodynamic properties of several representative hydrogen abstraction reactions. The importance of basis set, electron correlation, and choice of zeroth-order reference wave function in the accurate prediction of activation barriers and reaction enthalpies are also investigated. The ethynyl radical (*CCH), which has a very high affinity for hydrogen atoms, is studied as a prototype hydrogen abstraction agent. Our high-level quantum mechanical computations indicate that hydrogen abstraction using the ethynyl radical has an activation energy of less than 3 kcal mol(-1) for hydrogens bonded to an sp(2) or sp(3) carbon. These low activation barriers further corroborate previous studies suggesting that ethynyl-type radicals would make good tooltips for abstracting hydrogens from diamondoid surfaces during mechanosynthesis. Modeling the diamond C(111) surface with isobutane and treating the ethynyl radical as a tooltip, hydrogen abstraction in this reaction is predicted to be barrierless.
Progress in low-resolution ab initio phasing with CrowdPhase
Jorda, Julien; Sawaya, Michael R.; Yeates, Todd O.
2016-03-01
Ab initio phasing by direct computational methods in low-resolution X-ray crystallography is a long-standing challenge. A common approach is to consider it as two subproblems: sampling of phase space and identification of the correct solution. While the former is amenable to a myriad of search algorithms, devising a reliable target function for the latter problem remains an open question. Here, recent developments in CrowdPhase, a collaborative online game powered by a genetic algorithm that evolves an initial population of individuals with random genetic make-up (i.e. random phases) each expressing a phenotype in the form of an electron-density map, are presented.more » Success relies on the ability of human players to visually evaluate the quality of these maps and, following a Darwinian survival-of-the-fittest concept, direct the search towards optimal solutions. While an initial study demonstrated the feasibility of the approach, some important crystallographic issues were overlooked for the sake of simplicity. To address these, the new CrowdPhase includes consideration of space-group symmetry, a method for handling missing amplitudes, the use of a map correlation coefficient as a quality metric and a solvent-flattening step. Lastly, performances of this installment are discussed for two low-resolution test cases based on bona fide diffraction data.« less
Three-dimensional ab initio potential energy surface for H-CO(X̃(2)A').
Song, Lei; van der Avoird, Ad; Groenenboom, Gerrit C
2013-08-15
We present an ab initio potential for the H-CO(X̃(2)A') complex in which the CO bond length is varied and the long-range interactions between H and CO are accurately represented. It was computed using the spin-unrestricted open-shell single and double excitation coupled cluster method with perturbative triples [RHF-UCCSD(T)]. Three doubly augmented correlation-consistent basis sets were utilized to extrapolate the correlation energy to the complete basis set limit. More than 4400 data points were calculated and used for an analytic fit of the potential: long-range terms with inverse power dependence on the H-CO distance R were fit to the data points for large R, the reproducing kernel Hilbert space (RKHS) method was applied to the data at smaller distances. Our potential was compared with previous calculations and with some data extracted from spectroscopy. Furthermore, it was used in three-dimensional discrete variable representation (DVR) calculations of the vibrational frequencies and rotational constants of HCO, which agree very well with the most recently measured data. Also the dissociation energy D0 = 0.623 eV of HCO into H + CO obtained from these calculations agrees well with experimental values. Finally, we made preliminary two-dimensional (2D) calculations of the cross sections for rotationally inelastic H-CO collisions with the CO bond length fixed and obtained good agreement with recently published 2D results.
Ab Initio ONIOM-Molecular Dynamics (MD) Study on the Deamination Reaction by Cytidine Deaminase
Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako
2007-08-23
We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket of the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determing step is the release of the NH3 molecule. TM and MA were supported in part by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan. MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.
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.
An ab initio molecular dynamics analysis of lignin as a potential antioxidant for hydrocarbons.
Pan, Tongyan; Cheng, Cheng
2015-11-01
Lignins are complex phenolic polymers with limited industrial uses. To identify new applications of lignins, this study aims to evaluate the conifer alcohol lignin as a potential antioxidant for hydrocarbons, using the petroleum asphalt as an example. Using the ab initio molecular dynamics (AIMD) method, the evaluation is accomplished by tracking the generation of critical species in a lignin-asphalt mixture under a simulated oxidative condition. The generation of new species was detected using nuclear magnetic resonance and four analytical methods including density of states analysis, highest occupied molecular orbital and lowest unoccupied molecular orbital analyses, bonding and energy level analysis, and electrostatic potential energy analysis. Results of the analyses show that the chemical radicals of carbon, nitrogen and sulfur generated in the oxidation process could enhance the agglomeration and/or decomposition tendency of asphalt. The effectiveness of lignins as an antioxidant depends on their chemical compositions. Lignins with a HOMO-LUMO gap larger than the HOMO-LUMO gap of the hydrocarbon system to be protected, such as the conifer alcohol lignin to protect petroleum asphalt as was studied in this work, do not demonstrate beneficial anti-oxidation capacity. Lignins, however, may be effective oxidants for hydrocarbon systems with a larger HOMO-LUMO gap. In addition, lignins may contain more polar sites than the hydrocarbons to be protected; thus the lignins' hydrophobicity and compatibility with the host hydrocarbons need to be well evaluated. The developed AIMD model provides a useful tool for developing antioxidants for generic hydrocarbons.
NASA Astrophysics Data System (ADS)
Hafner, Jürgen
2010-09-01
During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.
Ab-initio Calculation of Optoelectronic and Structural Properties of Cubic Lithium Oxide (Li2O)
NASA Astrophysics Data System (ADS)
Ziegler, Joshua; Polin, Daniel; Malozovsky, Yuriy; Bagayoko, Diola
Using the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF), we performed ab-initio, density functional theory (DFT) calculations of optoelectronic, transport, and bulk properties of Li2S. In so doing, we avoid ``band gap'' and problems plaguing many DET calculations [AIP Advances 4, 127104 (2014)]. We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). With the BZW-EF method, our results possess the full, physical content of DFT and agree with available, corresponding experimental ones. In particular, we found a room temperature indirect band gap of 6.659 eV that compares favorably with experimental values ranging from 5 to 7.99 eV. We also calculated total and partial density of states (DOS and PDOS), effective masses of charge carriers, the equilibrium lattice constant, and the bulk modulus. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award Nos. DE-NA0001861 and DE- NA0002630), LaSPACE, and LONI-SUBR.
Ab initio studies on the structure of and atomic interactions in cellulose III(I) crystals.
Ishikawa, Tetsuya; Hayakawa, Daichi; Miyamoto, Hitomi; Ozawa, Motoyasu; Ozawa, Tomonaga; Ueda, Kazuyoshi
2015-11-19
The crystal structure of cellulose III(I)was analyzed using first-principles density functional theory (DFT). The geometry was optimized using variable-cell relaxation, as implemented in Quantum ESPRESSO. The Perdew-Burke-Ernzerhof (PBE) functional with a correction term for long-range van der Waals interactions (PBE-D) reproduced the experimental structure well. By using the optimized crystal structure, the interactions existed among the cellulose chains in the crystal were precisely investigated using the NBO analysis. The results showed that the weak bonding nature of CH/O and the hydrogen bonding occur among glucose molecules in the optimized crystal structure. To investigate the strength of interaction, dimeric and trimeric glucose units were extracted from the crystal, and analyzed using MP2 ab initio counterpoise methods with BSSE correction. The results estimated the strength of the interactions. That is, the packed chains along with a-axis interacts with weak bonding nature of CH/O and dispersion interactions by -7.50 kcal/mol, and two hydrogen bonds of O2HO2…O6 and O6HO6…O2 connect the neighboring packed chains with -11.9 kcal/mol. Moreover, FMO4 calculation was also applied to the optimized crystal structure to estimate the strength of the interactions. These methods can well estimate the interactions existed in the crystal structure of cellulose III(I).
Marrying ab initio calculations and Halo-EFT: 7Li and 7Be radiative nucleon captures
NASA Astrophysics Data System (ADS)
Zhang, Xilin; Nollett, Kenneth; Phillips, Daniel
2013-10-01
We combine ab initio quantum-Monte-Carlo (QMC) calculations with the Halo-Effective-Field-Theory (Halo-EFT) framework, in order to study low-energy radiative nucleon capture to a weakly bound (halo) nucleus. Here we focus on the reactions 7Li(n, γ)8Li and 7Be(p, γ)8B, which are subjects of long-standing interest for astrophysics. In the low-energy region we can approximate 8Li (8B) as composed of a 7Li (7Be) core (and also its excitation), and a neutron (proton) with an anomalously extended wave function. The scattering and bound states can be studied in Halo-EFT, in which both core and the nucleon are treated as fundamental degrees of freedom. In our leading order calculation, we use asymptotic normalization coefficients from QMC calculations to fix the parameters in the Lagrangian, which we then apply to study radiative captures. This obviates computing the captures by directly using numerically intensive QMC methods, while still incorporating the nuclear dynamics that these methods provide. In addition, the model-independent EFT framework provides novel insights into the manner in which these two nucleon-capture processes are related to one another. This work is supported by US Department of Energy under grant DE-FG02-93ER-40756.