An effective scheme for selecting basis sets for ab initio calculations
Institute of Scientific and Technical Information of China (English)
张瑞勤; 黄建华; 步宇翔; 韩克利; 李述汤; 何国钟
2000-01-01
An effective scheme for selecting economical basis sets for ab initio calculations has been proposed for wide-range systems based on the analysis of different functions in the currently used basis sets. Accordingly, the selection of the basis sets should be made according to the different properties and real chemical surrounding of the atoms in the systems. For normal systems, the size and level of the basis sets used for the descriptions of the constituent atoms should be increased from left to right according to the position of the atom in the periodic table. Moreover, the more the atom is negatively charged, the more the basis functions and suitable polarization functions and diffuse functions should be utilized. whereas, for the positively charged atoms, the size of basis set may be reduced. it is not necessary to use the polarization and diffuse functions for the covalently saturated atoms with normal valence states. However, for the system involving hy-drogen-bonding, weak interactions, functional
An effective scheme for selecting basis sets for ab initio calculations
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
An effective scheme for selecting economical basis sets for ab initio calculations has been proposed for wide-range systems based on the analysis of different functions in the currently used basis sets. Accordingly, the selection of the basis sets should be made according to the different properties and real chemical surrounding of the atoms in the systems. For normal systems, the size and level of the basis sets used for the descriptions of the constituent atoms should be increased from left to right according to the position of the atom in the periodic table. Moreover, the more the atom is negatively charged, the more the basis functions and suitable polarization functions and diffuse functions should be utilized. Whereas, for the positively charged atoms, the size of basis set may be reduced. It is not necessary to use the polarization and diffuse functions for the covalently saturated atoms with normal valence states. However, for the system involving hydrogen-bonding, weak interactions, functional groups, metallic bonding with zero valence or low positive valence, and other sensitive interactions, the polarization and diffuse functions must be used. With this scheme, reliable calculation results may be obtained with suitable basis sets and smaller computational capability. By detailed analysis of a series of systems, it has been demonstrated that this scheme is very practical and effective. This scheme may be used in Hartree-Fock, M?ller-Plesset and density functional theoretical calculations. It is expected that the scheme would find important applications in the extensive calculations of large systems in chemistry, materials science, and life and biological sciences.
Plascencia, Cesar; Wang, Jiaqi; Wilson, Angela K.
2017-10-01
The impact of basis set choice has been considered for a series of transition metal (TM) species. The need for higher level correlation consistent basis sets on both the metal and ligand has been investigated, and permutations in the pairings of basis set used for TM's and basis set used for ligands can lead to effective routes to complete basis set (CBS) limit extrapolations of thermochemical energetics with little change in thermochemical predictions as compared to those resulting from the use of traditional basis set pairings, while enabling computational cost savings. Basis set superposition errors (BSSE) that can arise have also been considered.
The Raman Spectrum of the Squarate (C4O4-2 Anion: An Ab Initio Basis Set Dependence Study
Directory of Open Access Journals (Sweden)
Miranda Sandro G. de
2002-01-01
Full Text Available The Raman excitation profile of the squarate anion, C4O4-2 , was calculated using ab initio methods at the Hartree-Fock using Linear Response Theory (LRT for six excitation frequencies: 632.5, 514.5, 488.0, 457.9, 363.8 and 337.1 nm. Five basis set functions (6-31G*, 6-31+G*, cc-pVDZ, aug-cc-pVDZ and Sadlej's polarizability basis set were investigated aiming to evaluate the performance of the 6-31G* set for numerical convergence and computational cost in relation to the larger basis sets. All basis sets reproduce the main spectroscopic features of the Raman spectrum of this anion for the excitation interval investigated. The 6-31G* basis set presented, on average, the same accuracy of numerical results as the larger sets but at a fraction of the computational cost showing that it is suitable for the theoretical investigation of the squarate dianion and its complexes and derivatives.
Energy Technology Data Exchange (ETDEWEB)
Caravaca, M A [Facultad de Ingenieria, Universidad Nacional del Nordeste, Avenida Las Heras 727, 3500-Resistencia (Argentina); Casali, R A [Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad, 5600-Corrientes (Argentina)
2005-09-21
The SIESTA approach based on pseudopotentials and a localized basis set is used to calculate the electronic, elastic and equilibrium properties of P 2{sub 1}/c, Pbca, Pnma, Fm3m, P4{sub 2}nmc and Pa3 phases of HfO{sub 2}. Using separable Troullier-Martins norm-conserving pseudopotentials which include partial core corrections for Hf, we tested important physical properties as a function of the basis set size, grid size and cut-off ratio of the pseudo-atomic orbitals (PAOs). We found that calculations in this oxide with the LDA approach and using a minimal basis set (simple zeta, SZ) improve calculated phase transition pressures with respect to the double-zeta basis set and LDA (DZ-LDA), and show similar accuracy to that determined with the PPPW and GGA approach. Still, the equilibrium volumes and structural properties calculated with SZ-LDA compare better with experiments than the GGA approach. The bandgaps and elastic and structural properties calculated with DZ-LDA are accurate in agreement with previous state of the art ab initio calculations and experimental evidence and cannot be improved with a polarized basis set. These calculated properties show low sensitivity to the PAO localization parameter range between 40 and 100 meV. However, this is not true for the relative energy, which improves upon decrease of the mentioned parameter. We found a non-linear behaviour in the lattice parameters with pressure in the P 2{sub 1}/c phase, showing a discontinuity of the derivative of the a lattice parameter with respect to external pressure, as found in experiments. The common enthalpy values calculated with the minimal basis set give pressure transitions of 3.3 and 10.8?GPa for P2{sub 1}/c {yields} Pbca and Pbca {yields} Pnma, respectively, in accordance with different high pressure experimental values.
Lee, Hee-Seung; Tuckerman, Mark E.
2007-04-01
Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.
Energy Technology Data Exchange (ETDEWEB)
Alam, T.M.
1998-09-01
The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.
Berski, Slawomir; Latajka, Zdzislaw; Gordon, Agnieszka J
2010-11-15
The article focus on the isomerization of nitrous acid HONO to hydrogen nitryl HNO(2). Density functional (B3LYP) and MP2 methods, and a wide variety of basis sets, have been chosen to investigate the mechanism of this reaction. The results clearly show that there are two possible paths: 1) Uncatalysed isomerisation, trans-HONO --> HNO(2), involving 1,2-hydrogen shift and characterized by a large energetic barrier 49.7 divided by 58.9 kcal/mol, 2) Catalysed double hydrogen transfer process, trans-HONO + cis-HONO --> HNO(2) + cis-HONO, which displays a significantly lower energetic barrier in a range of 11.6 divided by 18.9 kcal/mol. Topological analysis of the Electron Localization Function (ELF) shows that the hydrogen transfer for both studied reactions takes place through the formation of a 'dressed' proton along the reaction path. Use of a wide variety of basis sets demonstrates a clear basis set dependence on the ELF topology of HNO(2). Less saturated basis sets yield two lone pair basins, V(1)(N), V(2)(N), whereas more saturated ones (for example aug-cc-pVTZ and aug-cc-pVQZ) do not indicate a lone pair on the nitrogen atom. Topological analysis of the Electron Localizability Indication (ELI-D) at the CASSCF (12,10) confirms these findings, showing the existence of the lone pair basins but with decreasing populations as the basis set becomes more saturated (0.35e for the cc-pVDZ basis set to 0.06e for the aug-cc-pVTZ). This confirms that the choice of basis set not only can influence the value of the electron population at the particular atom, but can also lead to different ELF topology. 2010 Wiley Periodicals, Inc.
DEFF Research Database (Denmark)
Avery, John Scales; Rettrup, Sten; Avery, James Emil
In theoretical physics, theoretical chemistry and engineering, one often wishes to solve partial differential equations subject to a set of boundary conditions. This gives rise to eigenvalue problems of which some solutions may be very difficult to find. For example, the problem of finding...... eigenfunctions and eigenvalues for the Hamiltonian of a many-particle system is usually so difficult that it requires approximate methods, the most common of which is expansion of the eigenfunctions in terms of basis functions that obey the boundary conditions of the problem. The computational effort needed...
Spackman, Peter R.; Karton, Amir
2015-05-01
Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/Lα two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol-1. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol-1.
Energy Technology Data Exchange (ETDEWEB)
Spackman, Peter R.; Karton, Amir, E-mail: amir.karton@uwa.edu.au [School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA 6009 (Australia)
2015-05-15
Coupled cluster calculations with all single and double excitations (CCSD) converge exceedingly slowly with the size of the one-particle basis set. We assess the performance of a number of approaches for obtaining CCSD correlation energies close to the complete basis-set limit in conjunction with relatively small DZ and TZ basis sets. These include global and system-dependent extrapolations based on the A + B/L{sup α} two-point extrapolation formula, and the well-known additivity approach that uses an MP2-based basis-set-correction term. We show that the basis set convergence rate can change dramatically between different systems(e.g.it is slower for molecules with polar bonds and/or second-row elements). The system-dependent basis-set extrapolation scheme, in which unique basis-set extrapolation exponents for each system are obtained from lower-cost MP2 calculations, significantly accelerates the basis-set convergence relative to the global extrapolations. Nevertheless, we find that the simple MP2-based basis-set additivity scheme outperforms the extrapolation approaches. For example, the following root-mean-squared deviations are obtained for the 140 basis-set limit CCSD atomization energies in the W4-11 database: 9.1 (global extrapolation), 3.7 (system-dependent extrapolation), and 2.4 (additivity scheme) kJ mol{sup –1}. The CCSD energy in these approximations is obtained from basis sets of up to TZ quality and the latter two approaches require additional MP2 calculations with basis sets of up to QZ quality. We also assess the performance of the basis-set extrapolations and additivity schemes for a set of 20 basis-set limit CCSD atomization energies of larger molecules including amino acids, DNA/RNA bases, aromatic compounds, and platonic hydrocarbon cages. We obtain the following RMSDs for the above methods: 10.2 (global extrapolation), 5.7 (system-dependent extrapolation), and 2.9 (additivity scheme) kJ mol{sup –1}.
Energy Technology Data Exchange (ETDEWEB)
Rossi, Tuomas P., E-mail: tuomas.rossi@alumni.aalto.fi; Sakko, Arto; Puska, Martti J. [COMP Centre of Excellence, Department of Applied Physics, Aalto University School of Science, P.O. Box 11100, FI-00076 Aalto (Finland); Lehtola, Susi, E-mail: susi.lehtola@alumni.helsinki.fi [COMP Centre of Excellence, Department of Applied Physics, Aalto University School of Science, P.O. Box 11100, FI-00076 Aalto (Finland); Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Nieminen, Risto M. [COMP Centre of Excellence, Department of Applied Physics, Aalto University School of Science, P.O. Box 11100, FI-00076 Aalto (Finland); Dean’s Office, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto (Finland)
2015-03-07
We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers. We obtain basis sets of improving accuracy up to the complete basis set limit and demonstrate that the performance of the basis sets transfers to simulations of larger nanoparticles and nanoalloys as well as to calculations with various exchange-correlation functionals. This work promotes the use of the local basis set approach of controllable accuracy in first-principles nanoplasmonics simulations and beyond.
Conductance calculations with a wavelet basis set
DEFF Research Database (Denmark)
Thygesen, Kristian Sommer; Bollinger, Mikkel; Jacobsen, Karsten Wedel
2003-01-01
. The linear-response conductance is calculated from the Green's function which is represented in terms of a system-independent basis set containing wavelets with compact support. This allows us to rigorously separate the central region from the contacts and to test for convergence in a systematic way...
Accurate basis set truncation for wavefunction embedding
Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.
2013-07-01
Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.
Hill, J Grant
2011-07-28
Auxiliary basis sets specifically matched to the correlation consistent cc-pVnZ-PP, cc-pwCVnZ-PP, aug-cc-pVnZ-PP, and aug-cc-pwCVnZ-PP orbital basis sets (used in conjunction with pseudopotentials) for the 5d transition metal elements Hf-Pt have been optimized for use in density fitting second-order Møller-Plesset perturbation theory and other correlated ab initio methods. Calculations of the second-order Møller-Plesset perturbation theory correlation energy, for a test set of small to medium sized molecules, indicate that the density fitting error when utilizing these sets is negligible at three to four orders of magnitude smaller than the orbital basis set incompleteness error.
Basis set independent calculation of molecular polarizabilities
Talman, James D.
2012-08-01
It is shown that e-F, where F is the Hartree-Fock (HF) operator, can be inverted, for molecular systems, in numerical Cartesian coordinates. The method was originally applied to finding corrections to approximate Hartree-Fock orbitals [J. D. Talman, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.82.052518 82, 052518 (2010)]. The approach is applied to determine basis set independent dipole polarizabilities for the water molecule using the Sternheimer method within the uncoupled HF and coupled perturbed HF approximations.
A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data
Eckl, Bernhard; Hasse, Hans
2009-01-01
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e. vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl...
Denis, Pablo A
2005-09-01
We have investigated the SX (X = first- or second-row atom), SO2, and SO3 molecules employing the correlation-consistent (cc), the recently developed polarization-consistent (pc), and three Pople-type basis sets, in conjunction with the B3LYP functional. The results confirmed that the aug-pc basis sets represent a great contribution in terms of cost-benefits. In the case of the B3LYP functional, when employing the aug-pc-3 and aug-pc-4 basis sets, it is possible to obtain results that are of aug-cc-pV(5+d)Z and aug-cc-pV(6+d)Z quality, respectively, at a much lower cost. The estimations obtained employing smaller members of the family are of nearly double-ζ quality and do not provide reliable results. There is no basis set of quadruple-ζ quality among the polarized-consistent basis sets, although in terms of composition, the aug-pc-3 basis set is a QZ basis set. A precise estimation of the Kohn-Sham complete basis set (CBS) limit with the aug-pc-X basis sets is too difficult for the B3LYP functional because the ∞(aug-pc-4, aug-pc-3, aug-pc-2) extrapolation gives the same results as those of the aug-pc-4 basis set. This is in contrast with the results observed for ab initio methodologies for which the largest basis sets provided the best estimation of the CBS limit. In our opinion, the closest results to the B3LYP/CBS limit are expected to be those obtained with a two-point extrapolation employing the aug-cc-pV(X+d)Z (X = 5, 6) basis sets. The results obtained with this extrapolation are very close to those predicted by the ∞(aug-pc-3, aug-pc-2, aug-pc-1) extrapolation, and that provides a cheaper but more inaccurate alternative to estimate the CBS limit. Minor problems were found for the aug-pc-X basis sets and the B3LYP functional for molecules in which sulfur is bound to a very electronegative element, such as SO, SF, SO2, and SO3. For these molecules, the cc basis sets were demonstrated to be more useful. The importance of tight d functions was observed
The Role of the Basis Set: Assessing Density Functional Theory
Boese, A D; Handy, N C; Martin, Jan M. L.; Handy, Nicholas C.
2003-01-01
When developing and assessing density functional theory methods, a finite basis set is usually employed. In most cases, however, the issue of basis set dependency is neglected. Here, we assess several basis sets and functionals. In addition, the dependency of the semiempirical fits to a given basis set for a generalised gradient approximation and a hybrid functional is investigated. The resulting functionals are then tested for other basis sets, evaluating their errors and transferability.
Tests for Wavelets as a Basis Set
Baker, Thomas; Evenbly, Glen; White, Steven
A wavelet transformation is a special type of filter usually reserved for image processing and other applications. We develop metrics to evaluate wavelets for general problems on test one-dimensional systems. The goal is to eventually use a wavelet basis in electronic structure calculations. We compare a variety of orthogonal wavelets such as coiflets, symlets, and daubechies wavelets. We also evaluate a new type of orthogonal wavelet with dilation factor three which is both symmetric and compact in real space. This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award #DE-SC008696.
ORBITAL CONNECTIONS FOR PERTURBATION-DEPENDENT BASIS-SETS
DEFF Research Database (Denmark)
Olsen, Jeppe; Bak, Keld L.; Ruud, K.
1995-01-01
The use of perturbation-dependent basis sets is analysed with emphasis on the connection between the basis sets at different values of the perturbation strength. A particular connection, the natural connection, that minimizes the change of the basis set orbitals is devised and the second quantiza......The use of perturbation-dependent basis sets is analysed with emphasis on the connection between the basis sets at different values of the perturbation strength. A particular connection, the natural connection, that minimizes the change of the basis set orbitals is devised and the second...... quantization realization of this connection is introduced. It is shown that the natural connection is important for the efficient evaluation of molecular properties and for the physical interpretation of the terms entering the calculated properties. For example, in molecular Hessian calculations the natural...
Basis Set Exchange: A Community Database for Computational Sciences
Energy Technology Data Exchange (ETDEWEB)
Schuchardt, Karen L.; Didier, Brett T.; Elsethagen, Todd O.; Sun, Lisong; Gurumoorthi, Vidhya; Chase, Jared M.; Li, Jun; Windus, Theresa L.
2007-05-01
Basis sets are one of the most important input data for computational models in the chemistry, materials, biology and other science domains that utilize computational quantum mechanics methods. Providing a shared, web accessible environment where researchers can not only download basis sets in their required format, but browse the data, contribute new basis sets, and ultimately curate and manage the data as a community will facilitate growth of this resource and encourage sharing both data and knowledge. We describe the Basis Set Exchange (BSE), a web portal that provides advanced browsing and download capabilities, facilities for contributing basis set data, and an environment that incorporates tools to foster development and interaction of communities. The BSE leverages and enables continued development of the basis set library originally assembled at the Environmental Molecular Sciences Laboratory.
Basis set exchange: a community database for computational sciences.
Schuchardt, Karen L; Didier, Brett T; Elsethagen, Todd; Sun, Lisong; Gurumoorthi, Vidhya; Chase, Jared; Li, Jun; Windus, Theresa L
2007-01-01
Basis sets are some of the most important input data for computational models in the chemistry, materials, biology, and other science domains that utilize computational quantum mechanics methods. Providing a shared, Web-accessible environment where researchers can not only download basis sets in their required format but browse the data, contribute new basis sets, and ultimately curate and manage the data as a community will facilitate growth of this resource and encourage sharing both data and knowledge. We describe the Basis Set Exchange (BSE), a Web portal that provides advanced browsing and download capabilities, facilities for contributing basis set data, and an environment that incorporates tools to foster development and interaction of communities. The BSE leverages and enables continued development of the basis set library originally assembled at the Environmental Molecular Sciences Laboratory.
Groebner basis, resultants and the generalized Mandelbrot set
Energy Technology Data Exchange (ETDEWEB)
Geum, Young Hee [Centre of Research for Computational Sciences and Informatics in Biology, Bioindustry, Environment, Agriculture and Healthcare, University of Malaya, 50603 Kuala Lumpur (Malaysia)], E-mail: conpana@empal.com; Hare, Kevin G. [Department of Pure Mathematics, University of Waterloo, Waterloo, Ont., N2L 3G1 (Canada)], E-mail: kghare@math.uwaterloo.ca
2009-10-30
This paper demonstrates how the Groebner basis algorithm can be used for finding the bifurcation points in the generalized Mandelbrot set. It also shows how resultants can be used to find components of the generalized Mandelbrot set.
KINETIC BALANCE IN CONTRACTED BASIS-SETS FOR RELATIVISTIC CALCULATIONS
VISSCHER, L; AERTS, PJC; VISSER, O; NIEUWPOORT, WC
1991-01-01
A demonstration of kinetic balance failure in heavily contracted basis sets is given. Other possible methods of constructing small component basis sets for 4-component relativistic calculations are discussed. The position of the additional negative energy levels in extended balance calculations in s
Anharmonic Vibrational Frequency Calculations Are Not Worthwhile for Small Basis Sets.
Jacobsen, Ruth L; Johnson, Russell D; Irikura, Karl K; Kacker, Raghu N
2013-02-12
Anharmonic calculations using vibrational perturbation theory are known to provide near-spectroscopic accuracy when combined with high-level ab initio potential energy functions. However, performance with economical, popular electronic structure methods is less well characterized. We compare the accuracy of harmonic and anharmonic predictions from Hartree-Fock, second-order perturbation, and density functional theories combined with 6-31G(d) and 6-31+G(d,p) basis sets. As expected, anharmonic frequencies are closer than harmonic frequencies to experimental fundamentals. However, common practice is to correct harmonic predictions using multiplicative scaling. The surprising conclusion is that scaled anharmonic calculations are no more accurate than scaled harmonic calculations for the basis sets we used. The data used are from the Computational Chemistry Comparison and Benchmark Database (CCCBDB), maintained by the National Institute of Standards and Technology, which includes more than 3939 independent vibrations for 358 molecules.
Spackman, Peter R; Jayatilaka, Dylan; Karton, Amir
2016-09-14
We examine the basis set convergence of the CCSD(T) method for obtaining the structures of the 108 neutral first- and second-row species in the W4-11 database (with up to five non-hydrogen atoms). This set includes a total of 181 unique bonds: 75 H-X, 49 X-Y, 43 X=Y, and 14 X≡Y bonds (where X and Y are first- and second-row atoms). As reference values, geometries optimized at the CCSD(T)/aug'-cc-pV(6+d)Z level of theory are used. We consider the basis set convergence of the CCSD(T) method with the correlation consistent basis sets cc-pV(n+d)Z and aug'-cc-pV(n+d)Z (n = D, T, Q, 5) and the Weigend-Ahlrichs def2-n ZVPP basis sets (n = T, Q). For each increase in the highest angular momentum present in the basis set, the root-mean-square deviation (RMSD) over the bond distances is decreased by a factor of ∼4. For example, the following RMSDs are obtained for the cc-pV(n+d)Z basis sets 0.0196 (D), 0.0050 (T), 0.0015 (Q), and 0.0004 (5) Å. Similar results are obtained for the aug'-cc-pV(n+d)Z and def2-n ZVPP basis sets. The double-zeta and triple-zeta quality basis sets systematically and significantly overestimate the bond distances. A simple and cost-effective way to improve the performance of these basis sets is to scale the bond distances by an empirical scaling factor of 0.9865 (cc-pV(D+d)Z) and 0.9969 (cc-pV(T+d)Z). This results in RMSDs of 0.0080 (scaled cc-pV(D+d)Z) and 0.0029 (scaled cc-pV(T+d)Z) Å. The basis set convergence of larger basis sets can be accelerated via standard basis-set extrapolations. In addition, the basis set convergence of explicitly correlated CCSD(T)-F12 calculations is investigated in conjunction with the cc-pVnZ-F12 basis sets (n = D, T). Typically, one "gains" two angular momenta in the explicitly correlated calculations. That is, the CCSD(T)-F12/cc-pVnZ-F12 level of theory shows similar performance to the CCSD(T)/cc-pV(n+2)Z level of theory. In particular, the following RMSDs are obtained for the cc-pVnZ-F12 basis sets 0.0019 (D
Spackman, Peter R.; Jayatilaka, Dylan; Karton, Amir
2016-09-01
We examine the basis set convergence of the CCSD(T) method for obtaining the structures of the 108 neutral first- and second-row species in the W4-11 database (with up to five non-hydrogen atoms). This set includes a total of 181 unique bonds: 75 H—X, 49 X—Y, 43 X=Y, and 14 X≡Y bonds (where X and Y are first- and second-row atoms). As reference values, geometries optimized at the CCSD(T)/aug'-cc-pV(6+d)Z level of theory are used. We consider the basis set convergence of the CCSD(T) method with the correlation consistent basis sets cc-pV(n+d)Z and aug'-cc-pV(n+d)Z (n = D, T, Q, 5) and the Weigend-Ahlrichs def2-n ZVPP basis sets (n = T, Q). For each increase in the highest angular momentum present in the basis set, the root-mean-square deviation (RMSD) over the bond distances is decreased by a factor of ˜4. For example, the following RMSDs are obtained for the cc-pV(n+d)Z basis sets 0.0196 (D), 0.0050 (T), 0.0015 (Q), and 0.0004 (5) Å. Similar results are obtained for the aug'-cc-pV(n+d)Z and def2-n ZVPP basis sets. The double-zeta and triple-zeta quality basis sets systematically and significantly overestimate the bond distances. A simple and cost-effective way to improve the performance of these basis sets is to scale the bond distances by an empirical scaling factor of 0.9865 (cc-pV(D+d)Z) and 0.9969 (cc-pV(T+d)Z). This results in RMSDs of 0.0080 (scaled cc-pV(D+d)Z) and 0.0029 (scaled cc-pV(T+d)Z) Å. The basis set convergence of larger basis sets can be accelerated via standard basis-set extrapolations. In addition, the basis set convergence of explicitly correlated CCSD(T)-F12 calculations is investigated in conjunction with the cc-pVnZ-F12 basis sets (n = D, T). Typically, one "gains" two angular momenta in the explicitly correlated calculations. That is, the CCSD(T)-F12/cc-pVnZ-F12 level of theory shows similar performance to the CCSD(T)/cc-pV(n+2)Z level of theory. In particular, the following RMSDs are obtained for the cc-pVnZ-F12 basis sets 0
Efficient Diffuse Basis Sets for Density Functional Theory.
Papajak, Ewa; Truhlar, Donald G
2010-03-09
Eliminating all but the s and p diffuse functions on the non-hydrogenic atoms and all diffuse functions on the hydrogen atoms from the aug-cc-pV(x+d)Z basis sets of Dunning and co-workers, where x = D, T, Q, ..., yields the previously proposed "minimally augmented" basis sets, called maug-cc-pV(x+d)Z. Here, we present extensive and systematic tests of these basis sets for density functional calculations of chemical reaction barrier heights, hydrogen bond energies, electron affinities, ionization potentials, and atomization energies. The tests show that the maug-cc-pV(x+d)Z basis sets are as accurate as the aug-cc-pV(x+d)Z ones for density functional calculations, but the computational cost savings are a factor of about two to seven.
Point Set Denoising Using Bootstrap-Based Radial Basis Function
Ramli, Ahmad; Abd. Majid, Ahmad
2016-01-01
This paper examines the application of a bootstrap test error estimation of radial basis functions, specifically thin-plate spline fitting, in surface smoothing. The presence of noisy data is a common issue of the point set model that is generated from 3D scanning devices, and hence, point set denoising is one of the main concerns in point set modelling. Bootstrap test error estimation, which is applied when searching for the smoothing parameters of radial basis functions, is revisited. The main contribution of this paper is a smoothing algorithm that relies on a bootstrap-based radial basis function. The proposed method incorporates a k-nearest neighbour search and then projects the point set to the approximated thin-plate spline surface. Therefore, the denoising process is achieved, and the features are well preserved. A comparison of the proposed method with other smoothing methods is also carried out in this study. PMID:27315105
Srivastava, Saurabh; Sathyamurthy, N
2012-12-01
The spin forbidden transition a(1)Δ → X(3)Σ(-) in CH(-) has been studied using the Breit-Pauli Hamiltonian for a large number of geometries. This transition acquires intensity through spin-orbit coupling with singlet and triplet Π states. The transition moment matrix including more than one singlet and triplet Π states was calculated at the multi-reference configuration interaction/aug-cc-pV6Z level of theory. The computed radiative lifetime of 5.63 s is in good agreement with the experimental (5.9 s) and other theoretical (6.14 s) results. Transition moment values of the spin allowed A(3)Π → X(3)Σ(-) transition have also been calculated at the same level of theory. Calculations show that the corresponding radiative lifetime is considerably low, 2.4 × 10(-7) s. Complete basis set extrapolated potential energy curves for the ground state of CH and the ground state and six low lying excited states (a(1)Δ, b(1)Σ(+), two (3)Π, and two (1)Π) of CH(-) are reported. These curves are then used to calculate the vibrational bound states for CH and CH(-). The computed electron affinity of CH supports the electron affinity bounds reported by Okumura et al. [J. Chem. Phys. 85, 1971 (1986)].
The study of basis sets for the calculation of the structure and dynamics of the benzene-Kr complex
Energy Technology Data Exchange (ETDEWEB)
Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl [Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań (Poland)
2015-05-28
An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowed us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.
The study of basis sets for the calculation of the structure and dynamics of the benzene-Kr complex.
Shirkov, Leonid; Makarewicz, Jan
2015-05-28
An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowed us to design an optimal basis set composed of a small Dunning's basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.
Coupled-cluster based basis sets for valence correlation calculations
Claudino, Daniel; Gargano, Ricardo; Bartlett, Rodney J.
2016-03-01
Novel basis sets are generated that target the description of valence correlation in atoms H through Ar. The new contraction coefficients are obtained according to the Atomic Natural Orbital (ANO) procedure from CCSD(T) (coupled-cluster singles and doubles with perturbative triples correction) density matrices starting from the primitive functions of Dunning et al. [J. Chem. Phys. 90, 1007 (1989); ibid. 98, 1358 (1993); ibid. 100, 2975 (1993)] (correlation consistent polarized valence X-tuple zeta, cc-pVXZ). The exponents of the primitive Gaussian functions are subject to uniform scaling in order to ensure satisfaction of the virial theorem for the corresponding atoms. These new sets, named ANO-VT-XZ (Atomic Natural Orbital Virial Theorem X-tuple Zeta), have the same number of contracted functions as their cc-pVXZ counterparts in each subshell. The performance of these basis sets is assessed by the evaluation of the contraction errors in four distinct computations: correlation energies in atoms, probing the density in different regions of space via (-3 ≤ n ≤ 3) in atoms, correlation energies in diatomic molecules, and the quality of fitting potential energy curves as measured by spectroscopic constants. All energy calculations with ANO-VT-QZ have contraction errors within "chemical accuracy" of 1 kcal/mol, which is not true for cc-pVQZ, suggesting some improvement compared to the correlation consistent series of Dunning and co-workers.
Gauge origin independence in finite basis sets and perturbation theory
Sørensen, Lasse Kragh; Lindh, Roland; Lundberg, Marcus
2017-09-01
We show that origin independence in finite basis sets for the oscillator strengths is possibly in any gauge contrary to what is stated in literature. This is proved from a discussion of the consequences in perturbation theory when the exact eigenfunctions and eigenvalues to the zeroth order Hamiltonian H0 cannot be found. We demonstrate that the erroneous conclusion for the lack of gauge origin independence in the length gauge stems from not transforming the magnetic terms in the multipole expansion leading to the use of a mixed gauge. Numerical examples of exact origin dependence are shown.
Quiney, H. M.; Glushkov, V. N.; Wilson, S.; Sabin,; Brandas, E
2001-01-01
A comparison is made of the accuracy achieved in finite difference and finite basis set approximations to the Dirac equation for the ground state of the hydrogen molecular ion. The finite basis set calculations are carried out using a distributed basis set of Gaussian functions the exponents and pos
Quiney, H. M.; Glushkov, V. N.; Wilson, S.; Sabin,; Brandas, E
2001-01-01
A comparison is made of the accuracy achieved in finite difference and finite basis set approximations to the Dirac equation for the ground state of the hydrogen molecular ion. The finite basis set calculations are carried out using a distributed basis set of Gaussian functions the exponents and
Wang, Nick X; Wilson, Angela K
2005-08-18
The HSO and HOS isomers have been revisited using the DFT functionals, B3LYP, B3PW91, and PBE, in combination with tight d-augmented correlation consistent basis sets, cc-pV(x+d)Z and aug-cc-pV(x+d)Z for second-row atoms. Structures, vibrationally averaged structures, relative energies, harmonic and anharmonic frequencies, enthalpies of formation of HSO and HOS, and the barrier for the HSO/HOS isomerization have been determined. These results were compared with results from previous DFT and ab initio studies in which the standard correlation consistent basis sets were used. The relative energies of the two isomers converge more rapidly and smoothly with respect to increasing basis set size for the tight d-augmented sets than for the standard basis sets. Our best calculations, B3PW91/aug-cc-pV(5+d)Z, for the relative energy of the isomers are in excellent agreement with previous CCSD(T) results given by Wilson and Dunning.
Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.
Bielecki, Jakub; Lipiec, Ewelina
2016-02-01
Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople's basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.
Finite-basis-set expansion methods for scattering problems
Energy Technology Data Exchange (ETDEWEB)
Ladanyi, K.; Levay, P.; Apagyi, B.
1988-10-01
A wide variety of finite-basis-set expansion methods is applied to electron--hydrogen-atom scattering in the static-exchange approximation. All these methods are based on the Lippmann-Schwinger formalism. A careful analysis of the numerical results is presented with the aim of selecting efficient approaches to the solution of realistic electron-atom (and electron-molecule) scattering problems. The results show that the efficiency of the expansion methods may depend sensitively on the characteristics of the interaction terms. Some difficulties of the simple method of moments are pointed out. A particular least-squares method is proposed to avoid the spurious singularities encountered in applications of the Schwinger variational method to singlet scattering processes.
Basis set expansion for inverse problems in plasma diagnostic analysis
Jones, B.; Ruiz, C. L.
2013-07-01
A basis set expansion method [V. Dribinski, A. Ossadtchi, V. A. Mandelshtam, and H. Reisler, Rev. Sci. Instrum. 73, 2634 (2002)], 10.1063/1.1482156 is applied to recover physical information about plasma radiation sources from instrument data, which has been forward transformed due to the nature of the measurement technique. This method provides a general approach for inverse problems, and we discuss two specific examples relevant to diagnosing fast z pinches on the 20-25 MA Z machine [M. E. Savage, L. F. Bennett, D. E. Bliss, W. T. Clark, R. S. Coats, J. M. Elizondo, K. R. LeChien, H. C. Harjes, J. M. Lehr, J. E. Maenchen, D. H. McDaniel, M. F. Pasik, T. D. Pointon, A. C. Owen, D. B. Seidel, D. L. Smith, B. S. Stoltzfus, K. W. Struve, W. A. Stygar, L. K. Warne, J. R. Woodworth, C. W. Mendel, K. R. Prestwich, R. W. Shoup, D. L. Johnson, J. P. Corley, K. C. Hodge, T. C. Wagoner, and P. E. Wakeland, in Proceedings of the Pulsed Power Plasma Sciences Conference (IEEE, 2007), p. 979]. First, Abel inversion of time-gated, self-emission x-ray images from a wire array implosion is studied. Second, we present an approach for unfolding neutron time-of-flight measurements from a deuterium gas puff z pinch to recover information about emission time history and energy distribution. Through these examples, we discuss how noise in the measured data limits the practical resolution of the inversion, and how the method handles discontinuities in the source function and artifacts in the projected image. We add to the method a propagation of errors calculation for estimating uncertainties in the inverted solution.
Basis set expansion for inverse problems in plasma diagnostic analysis
Energy Technology Data Exchange (ETDEWEB)
Jones, B.; Ruiz, C. L. [Sandia National Laboratories, PO Box 5800, Albuquerque, New Mexico 87185 (United States)
2013-07-15
A basis set expansion method [V. Dribinski, A. Ossadtchi, V. A. Mandelshtam, and H. Reisler, Rev. Sci. Instrum. 73, 2634 (2002)] is applied to recover physical information about plasma radiation sources from instrument data, which has been forward transformed due to the nature of the measurement technique. This method provides a general approach for inverse problems, and we discuss two specific examples relevant to diagnosing fast z pinches on the 20–25 MA Z machine [M. E. Savage, L. F. Bennett, D. E. Bliss, W. T. Clark, R. S. Coats, J. M. Elizondo, K. R. LeChien, H. C. Harjes, J. M. Lehr, J. E. Maenchen, D. H. McDaniel, M. F. Pasik, T. D. Pointon, A. C. Owen, D. B. Seidel, D. L. Smith, B. S. Stoltzfus, K. W. Struve, W. A. Stygar, L. K. Warne, J. R. Woodworth, C. W. Mendel, K. R. Prestwich, R. W. Shoup, D. L. Johnson, J. P. Corley, K. C. Hodge, T. C. Wagoner, and P. E. Wakeland, in Proceedings of the Pulsed Power Plasma Sciences Conference (IEEE, 2007), p. 979]. First, Abel inversion of time-gated, self-emission x-ray images from a wire array implosion is studied. Second, we present an approach for unfolding neutron time-of-flight measurements from a deuterium gas puff z pinch to recover information about emission time history and energy distribution. Through these examples, we discuss how noise in the measured data limits the practical resolution of the inversion, and how the method handles discontinuities in the source function and artifacts in the projected image. We add to the method a propagation of errors calculation for estimating uncertainties in the inverted solution.
Nikolaev, A. V.; Lamoen, D.; Partoens, B.
2016-07-01
In order to increase the accuracy of the linearized augmented plane wave (LAPW) method, we present a new approach where the plane wave basis function is augmented by two different atomic radial components constructed at two different linearization energies corresponding to two different electron bands (or energy windows). We demonstrate that this case can be reduced to the standard treatment within the LAPW paradigm where the usual basis set is enriched by the basis functions of the tight binding type, which go to zero with zero derivative at the sphere boundary. We show that the task is closely related with the problem of extended core states which is currently solved by applying the LAPW method with local orbitals (LAPW+LO). In comparison with LAPW+LO, the number of supplemented basis functions in our approach is doubled, which opens up a new channel for the extension of the LAPW and LAPW+LO basis sets. The appearance of new supplemented basis functions absent in the LAPW+LO treatment is closely related with the existence of the u ˙ l -component in the canonical LAPW method. We discuss properties of additional tight binding basis functions and apply the extended basis set for computation of electron energy bands of lanthanum (face and body centered structures) and hexagonal close packed lattice of cadmium. We demonstrate that the new treatment gives lower total energies in comparison with both canonical LAPW and LAPW+LO, with the energy difference more pronounced for intermediate and poor LAPW basis sets.
Network Decomposition and Maximum Independent Set Part Ⅰ: Theoretic Basis
Institute of Scientific and Technical Information of China (English)
朱松年; 朱嫱
2003-01-01
The structure and characteristics of a connected network are analyzed, and a special kind of sub-network, which can optimize the iteration processes, is discovered. Then, the sufficient and necessary conditions for obtaining the maximum independent set are deduced. It is found that the neighborhood of this sub-network possesses the similar characters, but both can never be allowed incorporated together. Particularly, it is identified that the network can be divided into two parts by a certain style, and then both of them can be transformed into a pair sets network, where the special sub-networks and their neighborhoods appear alternately distributed throughout the entire pair sets network. By use of this characteristic, the network decomposed enough without losing any solutions is obtained. All of these above will be able to make well ready for developing a much better algorithm with polynomial time bound for an odd network in the the application research part of this subject.
Localized atomic basis set in the projector augmented wave method
DEFF Research Database (Denmark)
Larsen, Ask Hjorth; Vanin, Marco; Mortensen, Jens Jørgen
2009-01-01
representation. The possibility to switch seamlessly between the two representations implies that simulations employing the local basis can be fine tuned at the end of the calculation by switching to the grid, thereby combining the strength of the two representations for optimal performance. The implementation...... is tested by calculating atomization energies and equilibrium bulk properties of a variety of molecules and solids, comparing to the grid results. Finally, it is demonstrated how a grid-quality structure optimization can be performed with significantly reduced computational effort by switching between...
Nuclear second analytical derivative calculations using auxiliary basis set expansions
Deglmann, Peter; May, Klaus; Furche, Filipp; Ahlrichs, Reinhart
2004-01-01
We present an efficient implementation of second order analytical derivatives (force constants) within density functional theory which applies to non-hybrid functionals. The dominant step in force constant treatments concerns the solution of the coupled perturbed Kohn-Sham equations (CPKS). We employ an auxiliary basis expansion, the RI- J technique (resolution of the identity for the interelectronic Couomb energy J), to accelerate the solution of the CPKS equations. This results in pronounced reductions of computational work and implies insignificant losses in accuracy as is shown by extensive tests. A force constant calculation of cyanocobalamin is reported as a demonstrative application.
Accurate adapted Gaussian basis sets for the atoms from H through Xe
Energy Technology Data Exchange (ETDEWEB)
Jorge, F.E.; Muniz, E.P. [Univ. Federal do Espirito Santo, Vitoria, Espirito Santo (Brazil). Dept. de Fisica-CCE
1999-02-05
The authors have applied the generator coordinate Hartree-Fock method to generate adapted Gaussian basis sets for the atoms from H through Xe. The Griffin-Hill-Wheeler-Hartree-Fock equations are integrated numerically generating accurate basis sets for these atoms. The atomic wave functions are an improvement over those of Clementi et al. using larger atom-optimized geometrical Gaussian basis sets and Jorge et al. using a universal Gaussian basis set. In all cases, the current wave functions predict total energy results within 6.13 {times} 10{sup {minus}4} hartree of the numerical Hartree-Fock limit.
Miliordos, Evangelos; Xantheas, Sotiris S.
2015-03-01
We report the variation of the binding energy of the Formic Acid Dimer with the size of the basis set at the Coupled Cluster with iterative Singles, Doubles and perturbatively connected Triple replacements [CCSD(T)] level of theory, estimate the Complete Basis Set (CBS) limit, and examine the validity of the Basis Set Superposition Error (BSSE)-correction for this quantity that was previously challenged by Kalescky, Kraka, and Cremer (KKC) [J. Chem. Phys. 140, 084315 (2014)]. Our results indicate that the BSSE correction, including terms that account for the substantial geometry change of the monomers due to the formation of two strong hydrogen bonds in the dimer, is indeed valid for obtaining accurate estimates for the binding energy of this system as it exhibits the expected decrease with increasing basis set size. We attribute the discrepancy between our current results and those of KKC to their use of a valence basis set in conjunction with the correlation of all electrons (i.e., including the 1s of C and O). We further show that the use of a core-valence set in conjunction with all electron correlation converges faster to the CBS limit as the BSSE correction is less than half than the valence electron/valence basis set case. The uncorrected and BSSE-corrected binding energies were found to produce the same (within 0.1 kcal/mol) CBS limits. We obtain CCSD(T)/CBS best estimates for De = - 16.1 ± 0.1 kcal/mol and for D0 = - 14.3 ± 0.1 kcal/mol, the later in excellent agreement with the experimental value of -14.22 ± 0.12 kcal/mol.
Benchmarking DFT methods with small basis sets for the calculation of halogen-bond strengths.
Siiskonen, Antti; Priimagi, Arri
2017-02-01
In recent years, halogen bonding has become an important design tool in crystal engineering, supramolecular chemistry and biosciences. The fundamentals of halogen bonding have been studied extensively with high-accuracy computational methods. Due to its non-covalency, the use of triple-zeta (or larger) basis sets is often recommended when studying halogen bonding. However, in the large systems often encountered in supramolecular chemistry and biosciences, large basis sets can make the calculations far too slow. Therefore, small basis sets, which would combine high computational speed and high accuracy, are in great demand. This study focuses on comparing how well density functional theory (DFT) methods employing small, double-zeta basis sets can estimate halogen-bond strengths. Several methods with triple-zeta basis sets are included for comparison. Altogether, 46 DFT methods were tested using two data sets of 18 and 33 halogen-bonded complexes for which the complexation energies have been previously calculated with the high-accuracy CCSD(T)/CBS method. The DGDZVP basis set performed far better than other double-zeta basis sets, and it even outperformed the triple-zeta basis sets. Due to its small size, it is well-suited to studying halogen bonding in large systems.
Generation of basis sets with high degree of fulfillment of the Hellmann-Feynman theorem.
Rico, J Fernández; López, R; Ema, I; Ramírez, G
2007-03-01
A direct relationship is established between the degree of fulfillment of the Hellman-Feynman (electrostatic) theorem, measured as the difference between energy derivatives and electrostatic forces, and the stability of the basis set, measured from the indices that characterize the distance of the space generated by the basis functions to the space of their derivatives with respect to the nuclear coordinates. On the basis of this relationship, a criterion for obtaining basis sets of moderate size with a high degree of fulfillment of the theorem is proposed. As an illustrative application, previously reported Slater basis sets are extended by using this criterion. The resulting augmented basis sets are tested on several molecules finding that the differences between energy gradient and electrostatic forces are reduced by at least one order of magnitude.
LANL2DZ basis sets recontracted in the framework of density functional theory.
Chiodo, S; Russo, N; Sicilia, E
2006-09-14
In this paper we report recontracted LANL2DZ basis sets for first-row transition metals. The valence-electron shell basis functions were recontracted using the PWP86 generalized gradient approximation functional and the hybrid B3LYP one. Starting from the original LANL2DZ basis sets a cyclic method was used in order to optimize variationally the contraction coefficients, while the contraction scheme was held fixed at the original one of the LANL2DZ basis functions. The performance of the recontracted basis sets was analyzed by direct comparison between calculated and experimental excitation and ionization energies. Results reported here compared with those obtained using the original basis sets show clearly an improvement in the reproduction of the corresponding experimental gaps.
Rocca, Dario
2014-05-14
A new ab initio approach is introduced to compute the correlation energy within the adiabatic connection fluctuation dissipation theorem in the random phase approximation. First, an optimally small basis set to represent the response functions is obtained by diagonalizing an approximate dielectric matrix containing the kinetic energy contribution only. Then, the Lanczos algorithm is used to compute the full dynamical dielectric matrix and the correlation energy. The convergence issues with respect to the number of empty states or the dimension of the basis set are avoided and the dynamical effects are easily kept into account. To demonstrate the accuracy and efficiency of this approach the binding curves for three different configurations of the benzene dimer are computed: T-shaped, sandwich, and slipped parallel.
Boström, Jonas; Delcey, Mickaël G; Aquilante, Francesco; Serrano-Andrés, Luis; Pedersen, Thomas Bondo; Lindh, Roland
2010-03-09
The accuracy of auxiliary basis sets derived from Cholesky decomposition of two-electron integrals is assessed for excitation energies calculated at the state-average complete active space self-consistent field (CASSCF) and multiconfigurational second order perturbation theory (CASPT2) levels of theory using segmented as well as generally contracted atomic orbital basis sets. Based on 196 valence excitations in 26 organic molecules and 72 Rydberg excitations in 3 organic molecules, the results show that Cholesky auxiliary basis sets can be used without compromising the accuracy of the multiconfigurational methods. Specifically, with a decomposition threshold of 10(-4) au, the mean error due to the Cholesky auxiliary basis set is 0.001 eV, or smaller, decreasing with increasing atomic orbital basis set quality.
Efficient basis sets for non-covalent interactions in XDM-corrected density-functional theory.
Johnson, Erin R; Otero-de-la-Roza, Alberto; Dale, Stephen G; DiLabio, Gino A
2013-12-07
In the development and application of dispersion-corrected density-functional theory, the effects of basis set incompleteness have been largely mitigated through the use of very large, nearly-complete basis sets. However, the use of such large basis sets makes application of these methods inefficient for large systems. In this work, we examine a series of basis sets, including Pople-style, correlation-consistent, and polarization-consistent bases, for their ability to efficiently and accurately predict non-covalent interactions when used in conjunction with the exchange-hole dipole moment (XDM) dispersion model. We find that the polarization-consistent 2 (pc-2) basis sets, and two modifications thereof with some diffuse functions removed, give performance of comparable quality to that obtained with aug-cc-pVTZ basis sets, while being roughly 12 to 23 times faster computationally. The behavior is explained, in part, by the role of diffuse functions in recovering small density changes in the intermolecular region. The general performance of the modified basis sets is tested by application of XDM to standard intermolecular benchmark sets at, and away from, equilibrium.
Basis set generation for quantum dynamics simulations using simple trajectory-based methods.
Saller, Maximilian A C; Habershon, Scott
2015-01-13
Methods for solving the time-dependent Schrödinger equation generally employ either a global static basis set, which is fixed at the outset, or a dynamic basis set, which evolves according to classical-like or variational equations of motion; the former approach results in the well-known exponential scaling with system size, while the latter can suffer from challenging numerical problems, such as singular matrices, as well as violation of energy conservation. Here, we suggest a middle road: building a basis set using trajectories to place time-independent basis functions in the regions of phase space relevant to wave function propagation. This simple approach, which potentially circumvents many of the problems traditionally associated with global or dynamic basis sets, is successfully demonstrated for two challenging benchmark problems in quantum dynamics, namely, relaxation dynamics following photoexcitation in pyrazine, and the spin Boson model.
Behavior of the Sapporo-nZP-2012 basis set family
Weber, Rebecca; Hovda, Benjamin; Schoendorff, George; Wilson, Angela K.
2015-09-01
The behavior of Sapporo-nZP-2012 (n = D, T, Q) basis sets for 3d atoms is investigated. It is shown that total atomic energies obtained using Sapporo sets of increasing quality converge to a limit. Several schemes are used to determine these limits and comparisons are made to numerical Hartree-Fock energies and to limits obtained with correlation consistent sets (cc-pVnZ, n = T, Q, 5). While differences in energy relative to numerical HF are larger for Sapporo-nZP-2012 sets (16-40 mEh) than for correlation consistent basis sets (∼0.005 mEh), the systematic nature of the Sapporo-nZP-2012 sets may provide a reasonable alternative when the correlation consistent basis sets are not available.
Tekarli, Sammer M; Drummond, Michael L; Williams, T Gavin; Cundari, Thomas R; Wilson, Angela K
2009-07-30
The performance of 44 density functionals used in conjunction with the correlation consistent basis sets (cc-pVnZ where n = T and Q) has been assessed for the gas-phase enthalpies of formation at 298.15 K of 3d transition metal (TM) containing systems. Nineteen molecules were examined: ScS, VO, VO(2), Cr(CO)(6), MnS, MnCl(2), Mn(CO)(5)Cl, FeCl(3), Fe(CO)(5), CoH(CO)(4), NiCl(2), Ni(CO)(4), CuH, CuF, CuCl, ZnH, ZnO, ZnCl, and Zn(CH(3))(2). Of the functionals examined, the functionals that resulted in the smallest mean absolute deviation (MAD, in parentheses, kcal mol(-1)) from experiment were B97-1 (6.9), PBE1KCIS (8.1), TPSS1KCIS (9.6), B97-2 (9.7), and B98 (10.7). All five of these functionals include some degree of Hartree-Fock (HF) exchange. The impact of increasing the basis set from cc-pVTZ to cc-pVQZ was found to be slight for the generalized gradient approximation (GGA) and meta-GGA (MGGA) functionals studied, indicating basis set saturation at the triple-zeta level. By contrast, for most of the generalized gradient exchange (GGE), hybrid GGA (HGGA), and hybrid meta-GGA (HMGGA) functionals considered, improvements in the average MAD of 2-3 kcal mol(-1) were seen upon progressing to a quadruple-zeta level basis set. Overall, it was found that the functionals that include Hartree-Fock exchange performed best overall, but those with greater than 40% HF exchange exhibit significantly poor performance for the prediction of enthalpies of formation for 3d TM complexes. Carbonyl-containing complexes, a mainstay in organometallic TM chemistry, are demonstrated to be exceedingly difficult to describe accurately with all but 2 of the 44 functionals considered. The most accurate functional, for both CO-containing and CO-free compounds, is B97-1/cc-pVQZ, which is shown to be capable of yielding results within 1 kcal mol(-1) of high-level ab initio composite methodologies.
Mackie, Iain D.; DiLabio, Gino A.
2011-10-01
The first-principles calculation of non-covalent (particularly dispersion) interactions between molecules is a considerable challenge. In this work we studied the binding energies for ten small non-covalently bonded dimers with several combinations of correlation methods (MP2, coupled-cluster single double, coupled-cluster single double (triple) (CCSD(T))), correlation-consistent basis sets (aug-cc-pVXZ, X = D, T, Q), two-point complete basis set energy extrapolations, and counterpoise corrections. For this work, complete basis set results were estimated from averaged counterpoise and non-counterpoise-corrected CCSD(T) binding energies obtained from extrapolations with aug-cc-pVQZ and aug-cc-pVTZ basis sets. It is demonstrated that, in almost all cases, binding energies converge more rapidly to the basis set limit by averaging the counterpoise and non-counterpoise corrected values than by using either counterpoise or non-counterpoise methods alone. Examination of the effect of basis set size and electron correlation shows that the triples contribution to the CCSD(T) binding energies is fairly constant with the basis set size, with a slight underestimation with CCSD(T)/aug-cc-pVDZ compared to the value at the (estimated) complete basis set limit, and that contributions to the binding energies obtained by MP2 generally overestimate the analogous CCSD(T) contributions. Taking these factors together, we conclude that the binding energies for non-covalently bonded systems can be accurately determined using a composite method that combines CCSD(T)/aug-cc-pVDZ with energy corrections obtained using basis set extrapolated MP2 (utilizing aug-cc-pVQZ and aug-cc-pVTZ basis sets), if all of the components are obtained by averaging the counterpoise and non-counterpoise energies. With such an approach, binding energies for the set of ten dimers are predicted with a mean absolute deviation of 0.02 kcal/mol, a maximum absolute deviation of 0.05 kcal/mol, and a mean percent
Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory
Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.
1990-01-01
New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.
Calaminici, Patrizia; Janetzko, Florian; Köster, Andreas M; Mejia-Olvera, Roberto; Zuniga-Gutierrez, Bernardo
2007-01-28
Density functional theory optimized basis sets for gradient corrected functionals for 3d transition metal atoms are presented. Double zeta valence polarization and triple zeta valence polarization basis sets are optimized with the PW86 functional. The performance of the newly optimized basis sets is tested in atomic and molecular calculations. Excitation energies of 3d transition metal atoms, as well as electronic configurations, structural parameters, dissociation energies, and harmonic vibrational frequencies of a large number of molecules containing 3d transition metal elements, are presented. The obtained results are compared with available experimental data as well as with other theoretical data from the literature.
Pseudospectral sampling of Gaussian basis sets as a new avenue to high-dimensional quantum dynamics
Heaps, Charles
This thesis presents a novel approach to modeling quantum molecular dynamics (QMD). Theoretical approaches to QMD are essential to understanding and predicting chemical reactivity and spectroscopy. We implement a method based on a trajectory-guided basis set. In this case, the nuclei are propagated in time using classical mechanics. Each nuclear configuration corresponds to a basis function in the quantum mechanical expansion. Using the time-dependent configurations as a basis set, we are able to evolve in time using relatively little information at each time step. We use a basis set of moving frozen (time-independent width) Gaussian functions that are well-known to provide a simple and efficient basis set for nuclear dynamics. We introduce a new perspective to trajectory-guided Gaussian basis sets based on existing numerical methods. The distinction is based on the Galerkin and collocation methods. In the former, the basis set is tested using basis functions, projecting the solution onto the functional space of the problem and requiring integration over all space. In the collocation method, the Dirac delta function tests the basis set, projecting the solution onto discrete points in space. This effectively reduces the integral evaluation to function evaluation, a fundamental characteristic of pseudospectral methods. We adopt this idea for independent trajectory-guided Gaussian basis functions. We investigate a series of anharmonic vibrational models describing dynamics in up to six dimensions. The pseudospectral sampling is found to be as accurate as full integral evaluation, while the former method is fully general and integration is only possible on very particular model potential energy surfaces. Nonadiabatic dynamics are also investigated in models of photodissociation and collinear triatomic vibronic coupling. Using Ehrenfest trajectories to guide the basis set on multiple surfaces, we observe convergence to exact results using hundreds of basis functions
Haghdani, Shokouh; Åstrand, Per-Olof; Koch, Henrik
2016-02-01
We have calculated the electronic optical rotation of seven molecules using coupled cluster singles-doubles (CCSD) and the second-order approximation (CC2) employing the aug-cc-pVXZ (X = D, T, or Q) basis sets. We have also compared to time-dependent density functional theory (TDDFT) by utilizing two functionals B3LYP and CAM-B3LYP and the same basis sets. Using relative and absolute error schemes, our calculations demonstrate that the CAM-B3LYP functional predicts optical rotation with the minimum deviations compared to CCSD at λ = 355 and 589.3 nm. Furthermore, our results illustrate that the aug-cc-pVDZ basis set provides the optical rotation in good agreement with the larger basis sets for molecules not possessing small-angle optical rotation at λ = 589.3 nm. We have also performed several two-point inverse power extrapolations for the basis set convergence, i.e., OR(∞) + AX(-n), using the CC2 model at λ = 355 and 589.3 nm. Our results reveal that a two-point inverse power extrapolation with the aug-cc-pVTZ and aug-cc-pVQZ basis sets at n = 5 provides optical rotation deviations similar to those of aug-cc-pV5Z with respect to the basis limit.
Adapting DFT+U for the Chemically Motivated Correction of Minimal Basis Set Incompleteness.
Kulik, Heather J; Seelam, Natasha; Mar, Brendan D; Martínez, Todd J
2016-07-28
Recent algorithmic and hardware advances have enabled the application of electronic structure methods to the study of large-scale systems such as proteins with O(10(3)) atoms. Most such methods benefit greatly from the use of reduced basis sets to further enhance their speed, but truly minimal basis sets are well-known to suffer from incompleteness error that gives rise to incorrect descriptions of chemical bonding, preventing minimal basis set use in production calculations. We present a strategy for improving these well-known shortcomings in minimal basis sets by selectively tuning the energetics and bonding of nitrogen and oxygen atoms within proteins and small molecules to reproduce polarized double-ζ basis set geometries at minimal basis set cost. We borrow the well-known +U correction from the density functional theory community normally employed for self-interaction errors and demonstrate its power in the context of correcting basis set incompleteness within a formally self-interaction-free Hartree-Fock framework. We tune the Hubbard U parameters for nitrogen and oxygen atoms on small-molecule tautomers (e.g., cytosine), demonstrate the applicability of the approach on a number of amide-containing molecules (e.g., formamide, alanine tripeptide), and test our strategy on a 10 protein test set where anomalous proton transfer events are reduced by 90% from RHF/STO-3G to RHF/STO-3G+U, bringing the latter into quantitative agreement with RHF/6-31G* results. Although developed with the study of biological molecules in mind, this empirically tuned U approach shows promise as an alternative strategy for correction of basis set incompleteness errors.
Booth, George H; Alavi, Ali; Tew, David P
2012-01-01
By performing a stochastic dynamic in a space of Slater determinants, the Full Configuration Interaction Quantum Monte Carlo (FCIQMC) method has been able to obtain energies which are essentially free from systematic error to the basis set correlation energy, within small and systematically improvable errorbars. However, the weakly exponential scaling with basis size makes converging the energy with respect to basis set costly and in larger systems, impossible. To ameliorate these basis set issues, here we use perturbation theory to couple the FCIQMC wave function to an explicitly correlated strongly orthogonal basis of geminals, following the [2]_{\\textrm{R12}} approach of Valeev {\\em et al.}. The required one- and two-particle density matrices are computed on-the-fly during the FCIQMC dynamic, using a sampling procedure which incurs relatively little additional computation expense. The F12 energy corrections are shown to converge rapidly as a function of sampling, both in imaginary time, and number of walke...
Large-basis ab initio no-core shell model and its application to {sup 12}C
Energy Technology Data Exchange (ETDEWEB)
Navratil, P.; Vary, J. P.; Barrett, B. R.
2000-11-01
We present the framework for the ab initio no-core nuclear shell model and apply it to obtain properties of {sup 12}C. We derive two-body effective interactions microscopically for specific model spaces from the realistic CD-Bonn and the Argonne V8' nucleon-nucleon (NN) potentials. We then evaluate binding energies, excitation spectra, radii, and electromagnetic transitions in the 0{Dirac_h}{Omega}, 2{Dirac_h}{Omega}, and 4{Dirac_h}{Omega} model spaces for the positive-parity states and the 1{Dirac_h}{Omega}, 3{Dirac_h}{Omega}, and 5{Dirac_h}{Omega} model spaces for the negative-parity states. Dependence on the model-space size, on the harmonic-oscillator frequency, and on the type of the NN potential, used for the effective interaction derivation, are studied. In addition, electromagnetic and weak neutral elastic charge form factors are calculated in the impulse approximation. Sensitivity of the form-factor ratios to the strangeness one-body form-factor parameters and to the influence of isospin-symmetry violation is evaluated and discussed. Agreement between theory and experiment is favorable for many observables, while others require yet larger model spaces and/or three-body forces. The limitations of the present results are easily understood by virtue of the trends established and previous phenomenological results.
Oberhofer, Harald; Blumberger, Jochen
2010-12-01
We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q-) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, ( { } )^{1/2} = 6.7 {mH}, is significantly higher than the value obtained for the minimum energy structure, | {H_ab } | = 3.8 {mH}. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q- in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level.
Improved Segmented All-Electron Relativistically Contracted Basis Sets for the Lanthanides.
Aravena, Daniel; Neese, Frank; Pantazis, Dimitrios A
2016-03-08
Improved versions of the segmented all-electron relativistically contracted (SARC) basis sets for the lanthanides are presented. The second-generation SARC2 basis sets maintain efficient construction of their predecessors and their individual adaptation to the DKH2 and ZORA Hamiltonians, but feature exponents optimized with a completely new orbital shape fitting procedure and a slightly expanded f space that results in sizable improvement in CASSCF energies and in significantly more accurate prediction of spin-orbit coupling parameters. Additionally, an extended set of polarization/correlation functions is constructed that is appropriate for multireference correlated calculations and new auxiliary basis sets for use in resolution-of-identity (density-fitting) approximations in combination with both DFT and wave function based treatments. Thus, the SARC2 basis sets extend the applicability of the first-generation DFT-oriented basis sets to routine all-electron wave function-based treatments of lanthanide complexes. The new basis sets are benchmarked with respect to excitation energies, radial distribution functions, optimized geometries, orbital eigenvalues, ionization potentials, and spin-orbit coupling parameters of lanthanide systems and are shown to be suitable for the description of magnetic and spectroscopic properties using both DFT and multireference wave function-based methods.
Gidofalvi, Gergely
2014-01-01
Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multi-referenced) electrons. We use a low-cost approximate solution of the anti-Hermitian contracted Schr{\\"o}dinger equation (ACSE) for the one- and two-electron reduced density matrices (RDMs) to generate an approximate set of natural orbitals for strongly correlated quantum systems. The natural-orbital basis set is truncated to generate a molecule-optimized basis set whose rank matches that of a standard correlation-consistent basis set optimized for the atoms. We show that basis-set truncation by approximate natural orbitals can be viewed as a one-electron unitary transformation of the Hamiltonian operator and suggest an extension of approximate natural-orbital truncations through two-electron unitary transformations of the Hamiltonian operator, such as those employed in the solution of the ACSE. The molecule-optimized basis set from the ACS...
A Hartree–Fock study of the confined helium atom: Local and global basis set approaches
Energy Technology Data Exchange (ETDEWEB)
Young, Toby D., E-mail: tyoung@ippt.pan.pl [Zakład Metod Komputerowych, Instytut Podstawowych Prolemów Techniki Polskiej Akademia Nauk, ul. Pawińskiego 5b, 02-106 Warszawa (Poland); Vargas, Rubicelia [Universidad Autónoma Metropolitana Iztapalapa, División de Ciencias Básicas e Ingenierías, Departamento de Química, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, D.F. C.P. 09340, México (Mexico); Garza, Jorge, E-mail: jgo@xanum.uam.mx [Universidad Autónoma Metropolitana Iztapalapa, División de Ciencias Básicas e Ingenierías, Departamento de Química, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, D.F. C.P. 09340, México (Mexico)
2016-02-15
Two different basis set methods are used to calculate atomic energy within Hartree–Fock theory. The first is a local basis set approach using high-order real-space finite elements and the second is a global basis set approach using modified Slater-type orbitals. These two approaches are applied to the confined helium atom and are compared by calculating one- and two-electron contributions to the total energy. As a measure of the quality of the electron density, the cusp condition is analyzed. - Highlights: • Two different basis set methods for atomic Hartree–Fock theory. • Galerkin finite element method and modified Slater-type orbitals. • Confined atom model (helium) under small-to-extreme confinement radii. • Detailed analysis of the electron wave-function and the cusp condition.
DEFF Research Database (Denmark)
Hedegård, Erik D.; Jensen, Frank; Kongsted, Jacob
2012-01-01
of the optical rotation to the basis set limits for nine small or medium sized molecules, using basis sets developed specifically for DFT and magnetic properties (aug-pcS-n series). We suggest that assignment of absolute configuration by comparisons between theoretical and experimental optical rotations may......Even for pure substances, the deduction of the absolute configuration is not always straightforward since there is no direct link between the magnitude and sign of the optical rotation and the absolute configuration. It would be very useful to use computations of the optical rotation to link...... experimentally measured optical rotations to an absolute configuration. Such electronic structure calculations of the optical rotation typically employ regular energy optimized basis sets from wave function theory, and especially the aug-cc-pVDZ basis set has been popular. Here, we have carried out extrapolation...
The Bethe Sum Rule and Basis Set Selection in the Calculation of Generalized Oscillator Strengths
DEFF Research Database (Denmark)
Cabrera-Trujillo, Remigio; Sabin, John R.; Oddershede, Jens;
1999-01-01
Fulfillment of the Bethe sum rule may be construed as a measure of basis set quality for atomic and molecular properties involving the generalized oscillator strength distribution. It is first shown that, in the case of a complete basis, the Bethe sum rule is fulfilled exactly in the random phase...
Paschoal, Diego; Marcial, Bruna L; Lopes, Juliana Fedoce; De Almeida, Wagner B; Dos Santos, Hélio F
2012-11-05
In this article, we conducted an extensive ab initio study on the importance of the level of theory and the basis set for theoretical predictions of the structure and reactivity of cisplatin [cis-diamminedichloroplatinum(II) (cDDP)]. Initially, the role of the basis set for the Pt atom was assessed using 24 different basis sets, including three all-electron basis sets (ABS). In addition, a modified all-electron double zeta polarized basis set (mDZP) was proposed by adding a set of diffuse d functions onto the existing DZP basis set. The energy barrier and the rate constant for the first chloride/water exchange ligand process, namely, the aquation reaction, were taken as benchmarks for which reliable experimental data are available. At the B3LYP/mDZP/6-31+G(d) level (the first basis set is for Pt and the last set is for all of the light atoms), the energy barrier was 22.8 kcal mol(-1), which is in agreement with the average experimental value, 22.9 ± 0.4 kcal mol(-1). For the other accessible ABS (DZP and ADZP), the corresponding values were 15.4 and 24.5 kcal mol(-1), respectively. The ADZP and mDZP are notably similar, raising the importance of diffuse d functions for the prediction of the kinetic properties of cDDP. In this article, we also analyze the ligand basis set and the level of theory effects by considering 36 basis sets at distinct levels of theory, namely, Hartree-Fock, MP2, and several DFT functionals. From a survey of the data, we recommend the mPW1PW91/mDZP/6-31+G(d) or B3PW91/mDZP/6-31+G(d) levels to describe the structure and reactivity of cDDP and its small derivatives. Conversely, for large molecules containing a cisplatin motif (for example, the cDDP-DNA complex), the lower levels B3LYP/LANL2DZ/6-31+G(d) and B3LYP/SBKJC-VDZ/6-31+G(d) are suggested. At these levels of theory, the predicted energy barrier was 26.0 and 25.9 kcal mol(-1), respectively, which is only 13% higher than the actual value.
New basis set for the prediction of the specific rotation in flexible biological molecules
DEFF Research Database (Denmark)
Baranowska-Łaczkowska, Angelika; Z. Łaczkowski, Krzysztof Z. Łaczkowski; Henriksen, Christian
2016-01-01
Using a novel method based on increasingly accurate calculations, we obtain the main conformers of a set of flexible molecules. We then employ the recently developed ORP basis set for calculating the specific rotation of the found set carried out at the TD-DFT level of theory. The results...... presented for the investigated chiral azido alcohols are to our knowledge the first estimations of their specific rotations....... are compared to those obtained with the (d-)aug-cc-pVXZ (X = D, T and Q) basis sets of Dunning et al. The ORP values are in good overall agreement with the aug-cc-pVTZ results making the ORP a good basis set for routine TD-DFT optical rotation calculations of conformationally flexible molecules. The results...
On sets of vectors of a finite vector space in which every subset of basis size is a basis II
Ball, Simeon
2012-01-01
This article contains a proof of the MDS conjecture for $k \\leq 2p-2$. That is, that if $S$ is a set of vectors of ${\\mathbb F}_q^k$ in which every subset of $S$ of size $k$ is a basis, where $q=p^h$, $p$ is prime and $q$ is not and $k \\leq 2p-2$, then $|S| \\leq q+1$. It also contains a short proof of the same fact for $k\\leq p$, for all $q$.
A novel Gaussian-Sinc mixed basis set for electronic structure calculations
Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.
2015-08-01
A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree-Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the "localized" and "delocalized" regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the "delocalized" regions and the atom-centered Gaussian functions are used to represent the "localized" regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definable and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree-Fock energies for atoms up to neon, the diatomic systems H2, O2, and N2, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.
Magnetic properties with multiwavelets and DFT: the complete basis set limit achieved.
Jensen, Stig Rune; Flå, Tor; Jonsson, Dan; Monstad, Rune Sørland; Ruud, Kenneth; Frediani, Luca
2016-08-01
Multiwavelets are emerging as an attractive alternative to traditional basis sets such as Gaussian-type orbitals and plane waves. One of their distinctive properties is the ability to reach the basis set limit (often a chimera for traditional approaches) reliably and consistently by fixing the desired precision ε. We present our multiwavelet implementation of the linear response formalism, applied to static magnetic properties, at the self-consistent field level of theory (both for Hartree-Fock and density functional theories). We demonstrate that the multiwavelets consistently improve the accuracy of the results when increasing the desired precision, yielding results that have four to five digits precision, thus providing a very useful benchmark which could otherwise only be estimated by extrapolation methods. Our results show that magnetizabilities obtained with the augmented quadruple-ζ basis (aug-cc-pCVQZ) are practically at the basis set limit, whereas absolute nuclear magnetic resonance shielding tensors are more challenging: even by making use of a standard extrapolation method, the accuracy is not substantially improved. In contrast, our results provide a benchmark that: (1) confirms the validity of the extrapolation ansatz; (2) can be used as a reference to achieve a property-specific extrapolation scheme, thus providing a means to obtain much better extrapolated results; (3) allows us to separate functional-specific errors from basis-set ones and thus to assess the level of cancellation between basis set and functional errors often exploited in density functional theory.
Peverati, Roberto; Baldridge, Kim K
2009-10-13
The implementation, optimization, and performance of DFT-D, including the effects of solvation, has been tested on applications of polar processes in solution, where dispersion and hydrogen bonding is known to be involved. Solvent effects are included using our ab initio continuum solvation strategy, COSab, a conductor-like continuum solvation model, modified for ab initio in the quantum chemistry program GAMESS. Structure and properties are investigated across various functionals to evaluate their ability to properly model dispersion and solvation effects. The commonly used S22 set with accurate interaction energies of organic complexes has been used for parametrization studies of dispersion parameters and relevant solvation parameters. Dunning's correlation consistent basis sets, cc-pVnZ (n = D, T), are used in the optimization, together with the Grimme B97-D exchange-correlation functional. Both water (ε = 78.4) and ether (ε = 4.33) environments are considered. Optimized semiempirical dispersion correction parameters and solvent extent radii are proposed for several functionals. We find that special parametrization of the semiempirical dispersion correction when used together in the DFT-D/COSab approach is not necessary. The global performance is quite acceptable in terms of chemical accuracy and suggests that this approach is a reliable as well as economical method for evaluation of solvent effects in systems with dispersive interactions. The resulting theory is applied to a group of push-pull pyrrole systems to illustrate the effects of donor/acceptor and solvation on their conformational and energetic properties.
Efficient calculation of integrals in mixed ramp-Gaussian basis sets
Energy Technology Data Exchange (ETDEWEB)
McKemmish, Laura K., E-mail: laura.mckemmish@gmail.com [Department of Physics and Astronomy, University College London, London (United Kingdom); Research School of Chemistry, Australian National University, Canberra (Australia)
2015-04-07
Algorithms for the efficient calculation of two-electron integrals in the newly developed mixed ramp-Gaussian basis sets are presented, alongside a Fortran90 implementation of these algorithms, RAMPITUP. These new basis sets have significant potential to (1) give some speed-up (estimated at up to 20% for large molecules in fully optimised code) to general-purpose Hartree-Fock (HF) and density functional theory quantum chemistry calculations, replacing all-Gaussian basis sets, and (2) give very large speed-ups for calculations of core-dependent properties, such as electron density at the nucleus, NMR parameters, relativistic corrections, and total energies, replacing the current use of Slater basis functions or very large specialised all-Gaussian basis sets for these purposes. This initial implementation already demonstrates roughly 10% speed-ups in HF/R-31G calculations compared to HF/6-31G calculations for large linear molecules, demonstrating the promise of this methodology, particularly for the second application. As well as the reduction in the total primitive number in R-31G compared to 6-31G, this timing advantage can be attributed to the significant reduction in the number of mathematically complex intermediate integrals after modelling each ramp-Gaussian basis-function-pair as a sum of ramps on a single atomic centre.
Basis set effects on the Hartree-Fock description of confined many-electron atoms
Garza, Jorge; Hernández-Pérez, Julio M.; Ramírez, José-Zeferino; Vargas, Rubicelia
2012-01-01
In this work, the basis sets designed by Clementi, Bunge and Thakkar, for atomic systems, have been used to obtain the electronic structure of confined many-electron atoms by using Roothaan's approach in the Hartree-Fock context with a new code written in C, which uses the message-passing interface library. The confinement was imposed as Ludeña suggested to simulate walls with infinity potential. For closed-shell atoms, the Thakkar basis set functions give the best total energies (TE) as a function of the confinement radius, obtaining the following ordering: TE(Thakkar) Clementi). However, for few open-shell atoms this ordering is not preserved and a trend, for the basis sets, is not observed. Although there are differences between the TE predicted by these basis set functions, the corresponding pressures are similar to each other; it means that changes in the total energy are described almost in the same way by using any of these basis sets. By analysing the total energy as a function of the inverse of the volume we propose an equation of state; for regions of small volumes, this equation predicts that the pressure is inversely proportional to the square of the volume.
Mao, Yuezhi; Horn, Paul R; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin
2016-07-28
Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces set limit can be even better reproduced. With further improvement to its implementation, MAB-SCF (PC) is a promising lower-cost substitute for conventional large-basis calculations as a method to approach the basis set limit of modern density functionals.
Mao, Yuezhi; Horn, Paul R.; Mardirossian, Narbe; Head-Gordon, Teresa; Skylaris, Chris-Kriton; Head-Gordon, Martin
2016-07-01
Recently developed density functionals have good accuracy for both thermochemistry (TC) and non-covalent interactions (NC) if very large atomic orbital basis sets are used. To approach the basis set limit with potentially lower computational cost, a new self-consistent field (SCF) scheme is presented that employs minimal adaptive basis (MAB) functions. The MAB functions are optimized on each atomic site by minimizing a surrogate function. High accuracy is obtained by applying a perturbative correction (PC) to the MAB calculation, similar to dual basis approaches. Compared to exact SCF results, using this MAB-SCF (PC) approach with the same large target basis set produces modern density functionals.
Basis set convergence on static electric dipole polarizability calculations of alkali-metal clusters
Energy Technology Data Exchange (ETDEWEB)
Souza, Fabio A. L. de; Jorge, Francisco E., E-mail: jorge@cce.ufes.br [Departamento de Fisica, Universidade Federal do Espirito Santo, 29060-900 Vitoria-ES (Brazil)
2013-07-15
A hierarchical sequence of all-electron segmented contracted basis sets of double, triple and quadruple zeta valence qualities plus polarization functions augmented with diffuse functions for the atoms from H to Ar was constructed. A systematic study of basis sets required to obtain reliable and accurate values of static dipole polarizabilities of lithium and sodium clusters (n = 2, 4, 6 and 8) at their optimized equilibrium geometries is reported. Three methods are examined: Hartree-Fock (HF), second-order Moeller-Plesset perturbation theory (MP2), and density functional theory (DFT). By direct calculations or by fitting the directly calculated values through one extrapolation scheme, estimates of the HF, MP2 and DFT complete basis set limits were obtained. Comparison with experimental and theoretical data reported previously in the literature is done (author)
On the basis set convergence of electron-electron entanglement measures: helium-like systems.
Hofer, Thomas S
2013-01-01
A systematic investigation of three different electron-electron entanglement measures, namely the von Neumann, the linear and the occupation number entropy at full configuration interaction level has been performed for the four helium-like systems hydride, helium, Li(+) and Be(2+) using a large number of different basis sets. The convergence behavior of the resulting energies and entropies revealed that the latter do in general not show the expected strictly monotonic increase upon increase of the one-electron basis. Overall, the three different entanglement measures show good agreement among each other, the largest deviations being observed for small basis sets. The data clearly demonstrates that it is important to consider the nature of the chemical system when investigating entanglement phenomena in the framework of Gaussian type basis sets: while in case of hydride the use of augmentation functions is crucial, the application of core functions greatly improves the accuracy in case of cationic systems such as Li(+) and Be(2+). In addition, numerical derivatives of the entanglement measures with respect to the nucleic charge have been determined, which proved to be a very sensitive probe of the convergence leading to qualitatively wrong results (i.e., the wrong sign) if too small basis sets are used.
On the basis set convergence of electron-electron entanglement measures: helium-like systems
Directory of Open Access Journals (Sweden)
Thomas S. Hofer
2013-11-01
Full Text Available A systematic investigation of three different electron--electron entanglement measures, namely the von Neumann, the linear and the occupation number entropy at full configuration interaction level has been performed for the four helium-like systems hydride, helium, lithium(I and beryllium(II using a large number of different basis sets. The convergence behaviour of the resulting energies and entropies was revealed that the latter do in general not show monotonic convergence upon increase of the one--electron basis. Overall, the three different entanglement measures show good agreement among each other, the largest deviations being observed for small basis sets. The data clearly demonstrates that it is important to consider the nature of the chemical system when investigating entanglement phenomena in the framework of Gaussian type basis sets: while in case of hydride the use of augmentation functions is crucial, the application of core functions greatly improves the accuracy in case of cationic systems such as lithium(I and beryllium(II.In addition, numerical derivatives of the entanglement measures with respect to the nucleic charge have been determined, which proved to be a very sensitive probe of the convergence leading to qualitatively wrong results if inadequate basis sets are used.
Papajak, Ewa; Truhlar, Donald G
2011-01-11
We present sets of convergent, partially augmented basis set levels corresponding to subsets of the augmented "aug-cc-pV(n+d)Z" basis sets of Dunning and co-workers. We show that for many molecular properties a basis set fully augmented with diffuse functions is computationally expensive and almost always unnecessary. On the other hand, unaugmented cc-pV(n+d)Z basis sets are insufficient for many properties that require diffuse functions. Therefore, we propose using intermediate basis sets. We developed an efficient strategy for partial augmentation, and in this article, we test it and validate it. Sequentially deleting diffuse basis functions from the "aug" basis sets yields the "jul", "jun", "may", "apr", etc. basis sets. Tests of these basis sets for Møller-Plesset second-order perturbation theory (MP2) show the advantages of using these partially augmented basis sets and allow us to recommend which basis sets offer the best accuracy for a given number of basis functions for calculations on large systems. Similar truncations in the diffuse space can be performed for the aug-cc-pVxZ, aug-cc-pCVxZ, etc. basis sets.
Strategies for reducing basis set superposition error (BSSE) in O/AU and O/Ni
Shuttleworth, I.G.
2015-11-01
© 2015 Elsevier Ltd. All rights reserved. The effect of basis set superposition error (BSSE) and effective strategies for the minimisation have been investigated using the SIESTA-LCAO DFT package. Variation of the energy shift parameter ΔEPAO has been shown to reduce BSSE for bulk Au and Ni and across their oxygenated surfaces. Alternative strategies based on either the expansion or contraction of the basis set have been shown to be ineffective in reducing BSSE. Comparison of the binding energies for the surface systems obtained using LCAO were compared with BSSE-free plane wave energies.
Hübener, Hannes; Pérez-Osorio, Miguel A.; Ordejón, Pablo; Giustino, Feliciano
2012-06-01
We develop a first-principles computational method for investigating the dielectric screening in extended systems using the self-consistent Sternheimer equation and localized nonorthogonal basis sets. Our approach does not require the explicit calculation of unoccupied electronic states, uses only two-center integrals, and has a theoretical scaling of order O(N3). We demonstrate this method by comparing our calculations for silicon, germanium, diamond, and LiCl with reference plane-wave calculations. We show that accuracy comparable to that of plane-wave calculations can be achieved via a systematic optimization of the basis set.
Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set.
Paschoal, D; Guerra, C Fonseca; de Oliveira, M A L; Ramalho, T C; Dos Santos, H F
2016-10-01
Predicting NMR properties is a valuable tool to assist the experimentalists in the characterization of molecular structure. For heavy metals, such as Pt-195, only a few computational protocols are available. In the present contribution, all-electron Gaussian basis sets, suitable to calculate the Pt-195 NMR chemical shift, are presented for Pt and all elements commonly found as Pt-ligands. The new basis sets identified as NMR-DKH were partially contracted as a triple-zeta doubly polarized scheme with all coefficients obtained from a Douglas-Kroll-Hess (DKH) second-order scalar relativistic calculation. The Pt-195 chemical shift was predicted through empirical models fitted to reproduce experimental data for a set of 183 Pt(II) complexes which NMR sign ranges from -1000 to -6000 ppm. Furthermore, the models were validated using a new set of 75 Pt(II) complexes, not included in the descriptive set. The models were constructed using non-relativistic Hamiltonian at density functional theory (DFT-PBEPBE) level with NMR-DKH basis set for all atoms. For the best model, the mean absolute deviation (MAD) and the mean relative deviation (MRD) were 150 ppm and 6%, respectively, for the validation set (75 Pt-complexes) and 168 ppm (MAD) and 5% (MRD) for all 258 Pt(II) complexes. These results were comparable with relativistic DFT calculation, 200 ppm (MAD) and 6% (MRD). © 2016 Wiley Periodicals, Inc.
Gidopoulos, Nikitas I.; Lathiotakis, Nektarios N.
2013-10-01
The Comment by Friedrich does not dispute the central result of our paper [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.85.052508 85, 052508 (2012)] that nonanalytic behavior is present in long-established mathematical pathologies arising in the solution of finite basis optimized effective potential (OEP) equations. In the Comment, the terms “balancing of basis sets” and “basis-set convergence” imply a particular order towards the limit of a large orbital basis sets where the large-orbital-base limit is always taken first, before the large-auxiliary-base limit, until overall convergence is achieved, at a high computational cost. The authors claim that, on physical grounds, this order of limits is not only sufficient, but also necessary in order to avoid the mathematical pathologies. In response to the Comment, we remark that it is already written in our paper that the nonanalyticity trivially disappears with large orbital basis sets. We point out that the authors of the Comment give an incorrect proof of this statement. We also show that the order of limits towards convergence of the potential is immaterial. A recent paper by the authors of the Comment proposes a partial correction for the incomplete orbital basis error in the full-potential linearized augmented-plane-wave method. Similar to the correction developed in our paper, this correction also benefits from an effectively complete orbital basis, even though only a finite orbital basis is employed in the calculation. This shows that it is unnecessary to take, in practice, the limit of an infinite orbital basis in order to avoid mathematical pathologies in the OEP. Our paper is a significant contribution in that direction with general applicability to any choice of basis sets. Finally, contrary to an allusion in the abstract and assertions in the main text of the Comment that unphysical oscillations of the OEP are supposedly attributed to the common energy denominator approximation, in fact, such
$\\it{Ab}$ $\\it{initio}$ nuclear many-body perturbation calculations in the Hartree-Fock basis
Hu, Baishan; Sun, Zhonghao; Vary, James P; Li, Tong
2016-01-01
Starting from realistic nuclear forces, the chiral N$^3$LO and JISP16, we have applied many-body perturbation theory (MBPT) to the structure of closed-shell nuclei, $^4$He and $^{16}$O. The two-body N$^3$LO interaction is softened by a similarity renormalization group transformation while JISP16 is adopted without renormalization. The MBPT calculations are performed within the Hartree-Fock (HF) bases. The angular momentum coupled scheme is used, which can reduce the computational task. Corrections up to the third order in energy and up to the second order in radius are evaluated. Higher-order corrections in the HF basis are small relative to the leading-order perturbative result. Using the anti-symmetrized Goldstone diagram expansions of the wave function, we directly correct the one-body density for the calculation of the radius, rather than calculate corrections to the occupation propabilities of single-particle orbits as found in other treatments. We compare our results with other methods where available a...
On the use of Locally Dense Basis Sets in the Calculation of EPR Hyperfine Couplings
DEFF Research Database (Denmark)
Hedegård, Erik D.; Sauer, Stephan P. A.; Milhøj, Birgitte O.
2013-01-01
The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site in the c...
On the use of locally dense basis sets in the calculation of EPR hyperfine couplings
DEFF Research Database (Denmark)
Milhøj, Birgitte Olai; Hedegård, Erik D.; Sauer, Stephan P. A.
2013-01-01
The usage of locally dense basis sets in the calculation of Electron Paramagnetic Resonance (EPR) hyperne coupling constants is investigated at the level of Density Functional Theory (DFT) for two model systems of biologically important transition metal complexes: One for the active site in the c...
Continuum contributions to dipole oscillator-strength sum rules for hydrogen in finite basis sets
DEFF Research Database (Denmark)
Oddershede, Jens; Ogilvie, John F.; Sauer, Stephan P. A.;
2017-01-01
Calculations of the continuum contributions to dipole oscillator sum rules for hydrogen are performed using both exact and basis-set representations of the stick spectra of the continuum wave function. We show that the same results are obtained for the sum rules in both cases, but that the conver...
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.
Laury, Marie L; Carlson, Matthew J; Wilson, Angela K
2012-11-15
Calculated harmonic vibrational frequencies systematically deviate from experimental vibrational frequencies. The observed deviation can be corrected by applying a scale factor. Scale factors for: (i) harmonic vibrational frequencies [categorized into low (1000 cm(-1))], (ii) vibrational contributions to enthalpy and entropy, and (iii) zero-point vibrational energies (ZPVEs) have been determined for widely used density functionals in combination with polarization consistent basis sets (pc-n, n = 0,1,2,3,4). The density functionals include pure functionals (BP86, BPW91, BLYP, HCTH93, PBEPBE), hybrid functionals with Hartree-Fock exchange (B3LYP, B3P86, B3PW91, PBE1PBE, mPW1K, BH&HLYP), hybrid meta functionals with the kinetic energy density gradient (M05, M06, M05-2X, M06-2X), a double hybrid functional with Møller-Plesset correlation (B2GP-PLYP), and a dispersion corrected functional (B97-D). The experimental frequencies for calibration were from 41 organic molecules and the ZPVEs for comparison were from 24 small molecules (diatomics, triatomics). For this family of basis sets, the scale factors for each property are more dependent on the functional selection than on basis set level, and thus allow for a suggested scale factor for each density functional when employing polarization consistent basis sets (pc-n, n = 1,2,3,4). A separate scale factor is recommended when the un-polarized basis set, pc-0, is used in combination with the density functionals.
Accurate calculation of the intensity dependence of the refractive index using polarized basis sets
Baranowska-Łączkowska, Angelika; Łączkowski, Krzysztof Z.; Fernández, Berta
2012-01-01
Using the single and double excitation coupled cluster level of theory (CCSD) and the density functional theory/Becke 3-parameter Lee-Yang and Parr (DFT/B3LYP) methods, we test the performance of the Pol, ZPol, and LPol-n (n = ds, dl, fs, fl) basis sets in the accurate description of the intensity dependence of the refractive index in the Ne atom, and the N2 and the CO molecules. Additionally, we test the aug-pc-n (n = 1, 2) basis sets of Jensen, and the SVPD, TZVPD, and QZVPD bases by Rappoport and Furche. Tests involve calculations of dynamic polarizabilities and frequency dependent second hyperpolarizabilities. The results are interpreted in terms of the medium constants entering the expressions for optically induced birefringences. In all achiral systems, the performance of the LPol-n sets is very good. Also the aug-pc-2 set yields promising results. Accurate CCSD results available in the literature allow us to select the best basis sets in order to carry out DFT/B3LYP calculations of medium constants in larger molecules. As applications, we show results for (R)-fluoro-oxirane and (R)-methyloxirane.
Robust Periodic Hartree-Fock Exchange for Large-Scale Simulations Using Gaussian Basis Sets.
Guidon, Manuel; Hutter, Jürg; VandeVondele, Joost
2009-11-10
Hartree-Fock exchange with a truncated Coulomb operator has recently been discussed in the context of periodic plane-waves calculations [Spencer, J.; Alavi, A. Phys. Rev. B: Solid State, 2008, 77, 193110]. In this work, this approach is extended to Gaussian basis sets, leading to a stable and accurate procedure for evaluating Hartree-Fock exchange at the Γ-point. Furthermore, it has been found that standard hybrid functionals can be transformed into short-range functionals without loss of accuracy. The well-defined short-range nature of the truncated exchange operator can naturally be exploited in integral screening procedures and makes this approach interesting for both condensed phase and gas phase systems. The presented Hartree-Fock implementation is massively parallel and scales up to ten thousands of cores. This makes it feasible to perform highly accurate calculations on systems containing thousands of atoms or ten thousands of basis functions. The applicability of this scheme is demonstrated by calculating the cohesive energy of a LiH crystal close to the Hartree-Fock basis set limit and by performing an electronic structure calculation of a complete protein (rubredoxin) in solution with a large and flexible basis set.
Noncovalent Interactions by Quantum Monte Carlo: A Speedup by a Smart Basis Set Reduction
Dubecký, Matúš
2015-01-01
A fixed-node diffusion Monte Carlo (FN-DMC) method provides a promising alternative to the commonly used coupled-cluster (CC) methods, in the domain of benchmark noncovalent interaction energy calculations. This is mainly true for a low-order polynomial CPU cost scaling of FN-DMC and favorable FN error cancellation leading to benchmark interaction energies accurate to 0.1 kcal/mol. While it is empirically accepted that the FN-DMC results depend weakly on the one-particle basis sets used to expand the guiding functions, limits of this assumption remain elusive. Our recent work indicates that augmented triple zeta basis sets are sufficient to achieve a benchmark level of 0.1 kcal/mol. Here we report on a possibility of significant truncation of the one-particle basis sets without any visible bias on the overall accuracy of the final FN-DMC energy differences. The approach is tested on a set of seven small noncovalent closed-shell complexes including a water dimer. The reported findings enable cheaper high-quali...
Swart, M; Snijders, JG
The geometries of a set of small molecules were optimized using eight different exchange-correlation (xc) potentials in a few different basis sets of Slater-type orbitals, ranging from a minimal basis (I) to a triple-zeta valence basis plus double polarization functions (VII). This enables a
Structural Identification of Nonlinear Static System on Basis of Analysis Sector Sets
Directory of Open Access Journals (Sweden)
Nikolay Karabutov
2013-12-01
Full Text Available Methods of structural identification of static systems with a vector input and several nonlinearities in the conditions of uncertainty are considered. We consider inputs irregular. The concept of structural space is introduced. In this space special structures (virtual portraits are analyzed. The Holder condition is applied to construction of sector set, to which belongs a virtual portrait of system of identification. Criteria of decision-making on a class of nonlinear functions on the basis of the analysis of proximity of sector sets are described. Procedures of an estimation of structural parameters of two classes of nonlinearities are stated: power and a hysteresis.
Basis set limit geometries for ammonia at the SCF and MP2 levels of theory
Defrees, D. J.; Mclean, A. D.
1984-01-01
The controversy over the Hartree-Fock bond angle of NH3 is resolved and the convergence of the geometry for the molecule as the basis set is systematically improved with both SCF and correlated MP2 wave functions. The results of the geometrical optimizations, carried out in four stages with a series of uncontracted bases sets, are shown. The obtained structure for NH3 supports the results of Radom and Rodwell (1980) that the Hartree-Fock limit angle is significantly greater than was previously believed.
First-principle modelling of forsterite surface properties: Accuracy of methods and basis sets.
Demichelis, Raffaella; Bruno, Marco; Massaro, Francesco R; Prencipe, Mauro; De La Pierre, Marco; Nestola, Fabrizio
2015-07-15
The seven main crystal surfaces of forsterite (Mg2 SiO4 ) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor s of the dispersion formulation. An estimation for the surface energy is provided through adopting C6 coefficients that are more suitable than the standard ones to describe O-O interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface.
2012-01-01
We develop a first-principles computational method for investigating the dielectric screening in extended systems using the self-consistent Sternheimer equation and localized non-orthogonal basis sets. Our approach does not require the explicit calculation of unoccupied electronic states, only uses two-center integrals, and has a theoretical scaling of order O(N^3). We demonstrate this method by comparing our calculations for silicon, germanium, diamond, and LiCl with reference planewaves cal...
Tesch, Carmen M; de Vivie-Riedle, Regina
2004-12-22
The phase of quantum gates is one key issue for the implementation of quantum algorithms. In this paper we first investigate the phase evolution of global molecular quantum gates, which are realized by optimally shaped femtosecond laser pulses. The specific laser fields are calculated using the multitarget optimal control algorithm, our modification of the optimal control theory relevant for application in quantum computing. As qubit system we use vibrational modes of polyatomic molecules, here the two IR-active modes of acetylene. Exemplarily, we present our results for a Pi gate, which shows a strong dependence on the phase, leading to a significant decrease in quantum yield. To correct for this unwanted behavior we include pressure on the quantum phase in our multitarget approach. In addition the accuracy of these phase corrected global quantum gates is enhanced. Furthermore we could show that in our molecular approach phase corrected quantum gates and basis set independence are directly linked. Basis set independence is also another property highly required for the performance of quantum algorithms. By realizing the Deutsch-Jozsa algorithm in our two qubit molecular model system, we demonstrate the good performance of our phase corrected and basis set independent quantum gates.
Geminal embedding scheme for optimal atomic basis set construction in correlated calculations
Energy Technology Data Exchange (ETDEWEB)
Sorella, S., E-mail: sorella@sissa.it [International School for Advanced Studies (SISSA), Via Beirut 2-4, 34014 Trieste, Italy and INFM Democritos National Simulation Center, Trieste (Italy); Devaux, N.; Dagrada, M., E-mail: mario.dagrada@impmc.upmc.fr [Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Case 115, 4 Place Jussieu, 75252 Paris Cedex 05 (France); Mazzola, G., E-mail: gmazzola@phys.ethz.ch [Theoretische Physik, ETH Zurich, 8093 Zurich (Switzerland); Casula, M., E-mail: michele.casula@impmc.upmc.fr [CNRS and Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Case 115, 4 Place Jussieu, 75252 Paris Cedex 05 (France)
2015-12-28
We introduce an efficient method to construct optimal and system adaptive basis sets for use in electronic structure and quantum Monte Carlo calculations. The method is based on an embedding scheme in which a reference atom is singled out from its environment, while the entire system (atom and environment) is described by a Slater determinant or its antisymmetrized geminal power (AGP) extension. The embedding procedure described here allows for the systematic and consistent contraction of the primitive basis set into geminal embedded orbitals (GEOs), with a dramatic reduction of the number of variational parameters necessary to represent the many-body wave function, for a chosen target accuracy. Within the variational Monte Carlo method, the Slater or AGP part is determined by a variational minimization of the energy of the whole system in presence of a flexible and accurate Jastrow factor, representing most of the dynamical electronic correlation. The resulting GEO basis set opens the way for a fully controlled optimization of many-body wave functions in electronic structure calculation of bulk materials, namely, containing a large number of electrons and atoms. We present applications on the water molecule, the volume collapse transition in cerium, and the high-pressure liquid hydrogen.
Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin
2017-06-01
With the aim of mitigating the basis set error in density functional theory (DFT) calculations employing local basis sets, we herein develop two empirical corrections for basis set superposition error (BSSE) in the def2-SVPD basis, a basis which—when stripped of BSSE—is capable of providing near-complete-basis DFT results for non-covalent interactions. Specifically, we adapt the existing pairwise geometrical counterpoise (gCP) approach to the def2-SVPD basis, and we develop a beyond-pairwise approach, DFT-C, which we parameterize across a small set of intermolecular interactions. Both gCP and DFT-C are evaluated against the traditional Boys-Bernardi counterpoise correction across a set of 3402 non-covalent binding energies and isomerization energies. We find that the DFT-C method represents a significant improvement over gCP, particularly for non-covalently-interacting molecular clusters. Moreover, DFT-C is transferable among density functionals and can be combined with existing functionals—such as B97M-V—to recover large-basis results at a fraction of the cost.
Hellweg, Arnim; Rappoport, Dmitrij
2015-01-14
We report optimized auxiliary basis sets for use with the Karlsruhe segmented contracted basis sets including moderately diffuse basis functions (Rappoport and Furche, J. Chem. Phys., 2010, 133, 134105) in resolution-of-the-identity (RI) post-self-consistent field (post-SCF) computations for the elements H-Rn (except lanthanides). The errors of the RI approximation using optimized auxiliary basis sets are analyzed on a comprehensive test set of molecules containing the most common oxidation states of each element and do not exceed those of the corresponding unaugmented basis sets. During these studies an unsatisfying performance of the def2-SVP and def2-QZVPP auxiliary basis sets for Barium was found and improved sets are provided. We establish the versatility of the def2-SVPD, def2-TZVPPD, and def2-QZVPPD basis sets for RI-MP2 and RI-CC (coupled-cluster) energy and property calculations. The influence of diffuse basis functions on correlation energy, basis set superposition error, atomic electron affinity, dipole moments, and computational timings is evaluated at different levels of theory using benchmark sets and showcase examples.
Correlation consistent basis sets for actinides. II. The atoms Ac and Np-Lr
Feng, Rulin; Peterson, Kirk A.
2017-08-01
New correlation consistent basis sets optimized using the all-electron third-order Douglas-Kroll-Hess (DKH3) scalar relativistic Hamiltonian are reported for the actinide elements Ac and Np through Lr. These complete the series of sets reported previously for Th-U [K. A. Peterson, J. Chem. Phys. 142, 074105 (2015); M. Vasiliu et al., J. Phys. Chem. A 119, 11422 (2015)]. The new sets range in size from double- to quadruple-zeta and encompass both those optimized for valence (6s6p5f7s6d) and outer-core electron correlations (valence + 5s5p5d). The final sets have been contracted for both the DKH3 and eXact 2-component (X2C) Hamiltonians, yielding cc-pVnZ-DK3/cc-pVnZ-X2C sets for valence correlation and cc-pwCVnZ-DK3/cc-pwCVnZ-X2C sets for outer-core correlation (n = D, T, Q in each case). In order to test the effectiveness of the new basis sets, both atomic and molecular benchmark calculations have been carried out. In the first case, the first three atomic ionization potentials (IPs) of all the actinide elements Ac-Lr have been calculated using the Feller-Peterson-Dixon (FPD) composite approach, primarily with the multireference configuration interaction (MRCI) method. Excellent convergence towards the respective complete basis set (CBS) limits is achieved with the new sets, leading to good agreement with experiment, where these exist, after accurately accounting for spin-orbit effects using the 4-component Dirac-Hartree-Fock method. For a molecular test, the IP and atomization energy (AE) of PuO2 have been calculated also using the FPD method but using a coupled cluster approach with spin-orbit coupling accounted for using the 4-component MRCI. The present calculations yield an IP0 for PuO2 of 159.8 kcal/mol, which is in excellent agreement with the experimental electron transfer bracketing value of 162 ± 3 kcal/mol. Likewise, the calculated 0 K AE of 305.6 kcal/mol is in very good agreement with the currently accepted experimental value of 303.1 ± 5 kcal
DEFF Research Database (Denmark)
Silva-Junior, Mario R.; Sauer, Stephan P. A.; Schreiber, Marko;
2010-01-01
to those obtained previously with the smaller TZVP basis set. For each of the three coupled cluster methods, a correlation coefficient greater than 0.994 is found between the vertical excitation energies computed with the two basis sets. The deviations of the CC2 and CCSDR(3) results from the CC3 reference...... strengths and excited-state dipole moments, CC2 calculations with the aug-cc-pVTZ and TZVP basis sets give correlation coefficients of 0.966 and 0.833, respectively, implying that basis set convergence is slower for these one-electron properties....
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
Energy Technology Data Exchange (ETDEWEB)
Makhov, Dmitry V.; Shalashilin, Dmitrii V. [Department of Chemistry, University of Leeds, Leeds LS2 9JT (United Kingdom); Glover, William J.; Martinez, Todd J. [Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)
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.
Directory of Open Access Journals (Sweden)
Vesko Drašković
2008-08-01
Full Text Available According to the World Health Organization’s data, obesity is one of the main risk factors for the human health, especially in so called “mature age”, that is in forties and fiftees of the human’s life. There are many causes of obesity, and the most common ones are unadequate or excessive nutrition, low quality food rich in fats and highly caloric sweetener, unsufficient physical activity – hypokinesy, but also technical and technological development of the modern World (TV, cell phones, elevators, cars etc.. The objective of this research is to define the obesity of adults living in the urban settings through BMI (body mass index and to create, on the basis of these findings, the basis for different applications of the recreational sports programme.
Champagne, Benoı̂t; Botek, Edith; Nakano, Masayoshi; Nitta, Tomoshige; Yamaguchi, Kizashi
2005-03-01
The basis set and electron correlation effects on the static polarizability (α) and second hyperpolarizability (γ) are investigated ab initio for two model open-shell π-conjugated systems, the C5H7 radical and the C6H8 radical cation in their doublet state. Basis set investigations evidence that the linear and nonlinear responses of the radical cation necessitate the use of a less extended basis set than its neutral analog. Indeed, double-zeta-type basis sets supplemented by a set of d polarization functions but no diffuse functions already provide accurate (hyper)polarizabilities for C6H8 whereas diffuse functions are compulsory for C5H7, in particular, p diffuse functions. In addition to the 6-31G*+pd basis set, basis sets resulting from removing not necessary diffuse functions from the augmented correlation consistent polarized valence double zeta basis set have been shown to provide (hyper)polarizability values of similar quality as more extended basis sets such as augmented correlation consistent polarized valence triple zeta and doubly augmented correlation consistent polarized valence double zeta. Using the selected atomic basis sets, the (hyper)polarizabilities of these two model compounds are calculated at different levels of approximation in order to assess the impact of including electron correlation. As a function of the method of calculation antiparallel and parallel variations have been demonstrated for α and γ of the two model compounds, respectively. For the polarizability, the unrestricted Hartree-Fock and unrestricted second-order Møller-Plesset methods bracket the reference value obtained at the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples level whereas the projected unrestricted second-order Møller-Plesset results are in much closer agreement with the unrestricted coupled cluster singles and doubles with a perturbative inclusion of the triples values than the projected unrestricted Hartree
Gaspari, Roberto; Rapallo, Arnaldo
2008-06-28
In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum
Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas
2015-08-01
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods
Grimme, Stefan; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas
2015-08-07
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods
Energy Technology Data Exchange (ETDEWEB)
Grimme, Stefan, E-mail: grimme@thch.uni-bonn.de; Brandenburg, Jan Gerit; Bannwarth, Christoph; Hansen, Andreas [Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn (Germany)
2015-08-07
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of “low-cost” electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT
Symmetry-adapted basis sets automatic generation for problems in chemistry and physics
Avery, John Scales; Avery, James Emil
2012-01-01
In theoretical physics, theoretical chemistry and engineering, one often wishes to solve partial differential equations subject to a set of boundary conditions. This gives rise to eigenvalue problems of which some solutions may be very difficult to find. For example, the problem of finding eigenfunctions and eigenvalues for the Hamiltonian of a many-particle system is usually so difficult that it requires approximate methods, the most common of which is expansion of the eigenfunctions in terms of basis functions that obey the boundary conditions of the problem. The computational effort needed
Correlation consistent basis sets for lanthanides: The atoms La-Lu.
Lu, Qing; Peterson, Kirk A
2016-08-07
Using the 3rd-order Douglas-Kroll-Hess (DKH3) Hamiltonian, all-electron correlation consistent basis sets of double-, triple-, and quadruple-zeta quality have been developed for the lanthanide elements La through Lu. Basis sets designed for the recovery of valence correlation (defined here as 4f5s5p5d6s), cc-pVnZ-DK3, and outer-core correlation (valence + 4s4p4d), cc-pwCVnZ-DK3, are reported (n = D, T, and Q). Systematic convergence of both Hartree-Fock and correlation energies towards their respective complete basis set (CBS) limits are observed. Benchmark calculations of the first three ionization potentials (IPs) of La through Lu are reported at the DKH3 coupled cluster singles and doubles with perturbative triples, CCSD(T), level of theory, including effects of correlation down through the 4s electrons. Spin-orbit coupling is treated at the 2-component HF level. After extrapolation to the CBS limit, the average errors with respect to experiment were just 0.52, 1.14, and 4.24 kcal/mol for the 1st, 2nd, and 3rd IPs, respectively, compared to the average experimental uncertainties of 0.03, 1.78, and 2.65 kcal/mol, respectively. The new basis sets are also used in CCSD(T) benchmark calculations of the equilibrium geometries, atomization energies, and heats of formation for Gd2, GdF, and GdF3. Except for the equilibrium geometry and harmonic frequency of GdF, which are accurately known from experiment, all other calculated quantities represent significant improvements compared to the existing experimental quantities. With estimated uncertainties of about ±3 kcal/mol, the 0 K atomization energies (298 K heats of formation) are calculated to be (all in kcal/mol): 33.2 (160.1) for Gd2, 151.7 (-36.6) for GdF, and 447.1 (-295.2) for GdF3.
Roscioni, Otello M; Lee, Edmond P F; Dyke, John M
2012-10-05
We present a set of effective core potential (ECP) basis sets for rhodium atoms which are of reasonable size for use in electronic structure calculations. In these ECP basis sets, the Los Alamos ECP is used to simulate the effect of the core electrons while an optimized set of Gaussian functions, which includes polarization and diffuse functions, is used to describe the valence electrons. These basis sets were optimized to reproduce the ionization energy and electron affinity of atomic rhodium. They were also tested by computing the electronic ground state geometry and harmonic frequencies of [Rh(CO)(2) μ-Cl](2) , Rh(CO)(2) ClPy, and RhCO (neutral and its positive, and negative ions) as well as the enthalpy of the reaction of [Rh(CO)(2) μ-Cl](2) with pyridine (Py) to give Rh(CO)(2) ClPy, at different levels of theory. Good agreement with experimental values was obtained. Although the number of basis functions used in our ECP basis sets is smaller than those of other ECP basis sets of comparable quality, we show that the newly developed ECP basis sets provide the flexibility and precision required to reproduce a wide range of chemical and physical properties of rhodium compounds. Therefore, we recommend the use of these compact yet accurate ECP basis sets for electronic structure calculations on molecules involving rhodium atoms. Copyright © 2012 Wiley Periodicals, Inc.
Solving One-Electron Systems in a Novel Gaussian-Sinc Mixed Basis Set
Jerke, Jonathan L; Tymczak, C J
2014-01-01
We introduce a novel Gaussian-Sinc mixed basis set for the calculation of the electronic structure of one-electron systems within a uniform magnetic field in three dimensions. As opposed to traditional grid based methods, the Sinc basis is unbiased and invariant to the choice of the grids origin. This is shown to be due to the transformation properties of the Sinc basis functions under translations. The entire method is translational invariant and the potentials are properly calculated and are necessarily off diagonal, as well as variationally bounded. With this method, it was generally found that under arbitrary configurations of the protons that four to six significant digits in the ground state energy accuracy was achievable. This technology was then applied to calculate the ground state energy of H, $H_{2}^{+}$ ion and $H_{3}^{2+}$ ion in magnetic fields up to a magnetic field strength of 1.18x$10^9$ T (5000 au). From this it can be shown that $H_{3}^(2+}$ ion is unstable up to the maximum magnetic field ...
Corsetti, Fabiano
2014-01-01
The implementation of the orbital minimization method (OMM) for solving the self-consistent Kohn-Sham (KS) problem for electronic structure calculations in a basis of non-orthogonal numerical atomic orbitals of finite-range is reported. We explore the possibilities for using the OMM as an exact cubic-scaling solver for the KS problem, and compare its performance with that of explicit diagonalization in realistic systems. We analyze the efficiency of the method depending on the choice of line search algorithm and on two free parameters, the scale of the kinetic energy preconditioning and the eigenspectrum shift. The results of several timing tests are then discussed, showing that the OMM can achieve a noticeable speedup with respect to diagonalization even for minimal basis sets for which the number of occupied eigenstates represents a significant fraction of the total basis size (>15%). We investigate the hard and soft parallel scaling of the method on multiple cores, finding a performance equal to or better ...
2010-10-01
... physician services in a teaching setting. 415.170 Section 415.170 Public Health CENTERS FOR MEDICARE... BY PHYSICIANS IN PROVIDERS, SUPERVISING PHYSICIANS IN TEACHING SETTINGS, AND RESIDENTS IN CERTAIN SETTINGS Physician Services in Teaching Settings § 415.170 Conditions for payment on a fee schedule basis...
Green's function multiple-scattering theory with a truncated basis set: An augmented-KKR formalism
Alam, Aftab; Khan, Suffian N.; Smirnov, A. V.; Nicholson, D. M.; Johnson, Duane D.
2014-11-01
The Korringa-Kohn-Rostoker (KKR) Green's function, multiple-scattering theory is an efficient site-centered, electronic-structure technique for addressing an assembly of N scatterers. Wave functions are expanded in a spherical-wave basis on each scattering center and indexed up to a maximum orbital and azimuthal number Lmax=(l,mmax), while scattering matrices, which determine spectral properties, are truncated at Lt r=(l,mt r) where phase shifts δl >ltr are negligible. Historically, Lmax is set equal to Lt r, which is correct for large enough Lmax but not computationally expedient; a better procedure retains higher-order (free-electron and single-site) contributions for Lmax>Lt r with δl >ltr set to zero [X.-G. Zhang and W. H. Butler, Phys. Rev. B 46, 7433 (1992), 10.1103/PhysRevB.46.7433]. We present a numerically efficient and accurate augmented-KKR Green's function formalism that solves the KKR equations by exact matrix inversion [R3 process with rank N (ltr+1 ) 2 ] and includes higher-L contributions via linear algebra [R2 process with rank N (lmax+1) 2 ]. The augmented-KKR approach yields properly normalized wave functions, numerically cheaper basis-set convergence, and a total charge density and electron count that agrees with Lloyd's formula. We apply our formalism to fcc Cu, bcc Fe, and L 1 0 CoPt and present the numerical results for accuracy and for the convergence of the total energies, Fermi energies, and magnetic moments versus Lmax for a given Lt r.
Mackie, Iain D; Dilabio, Gino A
2010-06-21
B971, PBE and PBE1 density functionals with 6-31G(d) basis sets are shown to accurately describe the binding in dispersion bound dimers. This is achieved through the use of dispersion-correcting potentials (DCPs) in conjunction with counterpoise corrections. DCPs resemble and are applied like conventional effective core potentials that can be used with most computational chemistry programs without code modification. Rather, DCPs are implemented by simple appendage to the input files for these types of programs. Binding energies are predicted to within ca. 11% and monomer separations to within ca. 0.06 A of high-level wavefunction data using B971/6-31G(d)-DCP. Similar results are obtained for PBE and PBE1 with the 6-31G(d) basis sets and DCPs. Although results found using the 3-21G(d) are not as impressive, they never-the-less show promise as a means of initial study for a wide variety of dimers, including those dominated by dispersion, hydrogen-bonding and a mixture of interactions. Notable improvement is found in comparison to M06-2X/6-31G(d) data, e.g., mean absolute deviations for the S22-set of dimers of ca. 13.6 and 16.5% for B971/6-31G(d)-DCP and M06-2X, respectively. However, it should be pointed out that the latter data were obtained using a larger integration grid size since a smaller grid results in different binding energies and geometries for simple dispersion-bound dimers such as methane and ethene.
Lan, Tran Nguyen; Zgid, Dominika
2016-01-01
We present a detailed discussion of self-energy embedding theory (SEET) which is a quantum embedding scheme allowing us to describe a chosen subsystem very accurately while keeping the description of the environment at a lower cost. We apply SEET to molecular examples where commonly our chosen subsystem is made out of a set of strongly correlated orbitals while the weakly correlated orbitals constitute an environment. Such a self-energy separation is very general and to make this procedure applicable to multiple systems a detailed and practical procedure for the evaluation of the system and environment self-energy is necessary. We list all the intricacies for one of the possible procedures while focusing our discussion on many practical implementation aspects such as the choice of best orbital basis, impurity solver, and many steps necessary to reach chemical accuracy. Finally, on a set of carefully chosen molecular examples, we demonstrate that SEET which is a controlled, systematically improvable Green's fu...
Kawashima, Yukio; Hirao, Kimihiko
2017-02-24
We introduced two methods to correct the singularity in the calculation of long-range Hartree-Fock (HF) exchange for long-range-corrected density functional theory (LC-DFT) calculations in plane-wave basis sets. The first method introduces an auxiliary function to cancel out the singularity. The second method introduces a truncated long-range Coulomb potential, which has no singularity. We assessed the introduced methods using the LC-BLYP functional by applying it to isolated systems of naphthalene and pyridine. We first compared the total energies and the HOMO energies of the singularity-corrected and uncorrected calculations and confirmed that singularity correction is essential for LC-DFT calculations using plane-wave basis sets. The LC-DFT calculation results converged rapidly with respect to the cell size as the other functionals, and their results were in good agreement with the calculated results obtained using Gaussian basis sets. LC-DFT succeeded in obtaining accurate orbital energies and excitation energies. We next applied LC-DFT with singularity correction methods to the electronic structure calculations of the extended systems, Si and SiC. We confirmed that singularity correction is important for calculations of extended systems as well. The calculation results of the valence and conduction bands by LC-BLYP showed good convergence with respect to the number of k points sampled. The introduced methods succeeded in overcoming the singularity problem in HF exchange calculation. We investigated the effect of the singularity correction on the excitation state calculation and found that careful treatment of the singularities is required compared to ground-state calculations. We finally examined the excitonic effect on the band gap of the extended systems. We calculated the excitation energies to the first excited state of the extended systems using a supercell model at the Γ point and found that the excitonic binding energy, supposed to be small for
GAUSSIAN 76: An ab initio Molecular Orbital Program
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.
A two-dimensional volatility basis set – Part 3: Prognostic modeling and NOx dependence
Directory of Open Access Journals (Sweden)
W. K. Chuang
2015-06-01
Full Text Available When NOx is introduced to organic emissions, aerosol production is sometimes, but not always, reduced. Under certain conditions, these interactions will instead increase aerosol concentrations. We expanded the two-dimensional volatility basis set (2-D-VBS to include the effects of NOx on aerosol formation. This includes the formation of organonitrates, where the addition of a nitrate group contributes to a decrease of 2.5 orders of magnitude in volatility. With this refinement, we model outputs from experimental results, such as the atomic N : C ratio, organonitrate mass, and nitrate fragments in AMS measurements. We also discuss the mathematical methods underlying the implementation of the 2-D-VBS and provide the complete code in the Supplemental material. A developer version is available on Bitbucket, an online community repository.
Phosgene at the complete basis set limit of CCSDT(Q): Molecular structure and rovibrational analysis
Murphy, Kevin V.; Schaefer, Henry F.; Agarwal, Jay
2017-09-01
The ground-state (X∼1A″) equilibrium geometry of phosgene is examined with coupled-cluster theory, using derivatives extrapolated to the complete basis set (CBS) limit of CCSDT(Q). The C-O and C-Cl bond lengths are predicted to be 1.1768 Å and 1.7374 Å, respectively; the Cl-C-Cl bond angle is 124.03° and the O-C-Cl bond angle is 111.93°. Anharmonic frequencies are determined with VPT2, using CCSD(T)/cc-pCVQZ cubic and quartic force-fields and a CCSDT(Q)/CBS quadratic force field: ν1 = 1832.9 ; ν2 = 570.5 ; ν3 = 301.2 ; ν4 = 576.3 ; ν5 = 849.4 ; and ν6 = 438.9 cm-1.
Accurate Hartree-Fock energy of extended systems using large Gaussian basis sets
Paier, Joachim; Diaconu, Cristian V.; Scuseria, Gustavo E.; Guidon, Manuel; Vandevondele, Joost; Hutter, Jürg
2009-11-01
Calculating highly accurate thermochemical properties of condensed matter via wave-function-based approaches (such as, e.g., Hartree-Fock or hybrid functionals) has recently attracted much interest. We here present two strategies providing accurate Hartree-Fock energies for solid LiH in a large Gaussian basis set and applying periodic boundary conditions. The total energies were obtained using two different approaches, namely, a supercell evaluation of Hartree-Fock exchange using a truncated Coulomb operator and an extrapolation toward the full-range Hartree-Fock limit of a Padé fit to a series of short-range screened Hartree-Fock calculations. These two techniques agreed to significant precision. We also present the Hartree-Fock cohesive energy of LiH (converged to within sub-millielectron volt) at the experimental equilibrium volume as well as the Hartree-Fock equilibrium lattice constant and bulk modulus.
Rohmer, Jeremy
2016-04-01
Predicting the temporal evolution of landslides is typically supported by numerical modelling. Dynamic sensitivity analysis aims at assessing the influence of the landslide properties on the time-dependent predictions (e.g., time series of landslide displacements). Yet two major difficulties arise: 1. Global sensitivity analysis require running the landslide model a high number of times (> 1000), which may become impracticable when the landslide model has a high computation time cost (> several hours); 2. Landslide model outputs are not scalar, but function of time, i.e. they are n-dimensional vectors with n usually ranging from 100 to 1000. In this article, I explore the use of a basis set expansion, such as principal component analysis, to reduce the output dimensionality to a few components, each of them being interpreted as a dominant mode of variation in the overall structure of the temporal evolution. The computationally intensive calculation of the Sobol' indices for each of these components are then achieved through meta-modelling, i.e. by replacing the landslide model by a "costless-to-evaluate" approximation (e.g., a projection pursuit regression model). The methodology combining "basis set expansion - meta-model - Sobol' indices" is then applied to the La Frasse landslide to investigate the dynamic sensitivity analysis of the surface horizontal displacements to the slip surface properties during the pore pressure changes. I show how to extract information on the sensitivity of each main modes of temporal behaviour using a limited number (a few tens) of long running simulations. In particular, I identify the parameters, which trigger the occurrence of a turning point marking a shift between a regime of low values of landslide displacements and one of high values.
Hsu, Po Jen; Lai, S K; Rapallo, Arnaldo
2014-03-14
Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit
Trail-Needs pseudopotentials in quantum Monte Carlo calculations with plane-wave/blip basis sets
Drummond, N. D.; Trail, J. R.; Needs, R. J.
2016-10-01
We report a systematic analysis of the performance of a widely used set of Dirac-Fock pseudopotentials for quantum Monte Carlo (QMC) calculations. We study each atom in the periodic table from hydrogen (Z =1 ) to mercury (Z =80 ), with the exception of the 4 f elements (57 ≤Z ≤70 ). We demonstrate that ghost states are a potentially serious problem when plane-wave basis sets are used in density functional theory (DFT) orbital-generation calculations, but that this problem can be almost entirely eliminated by choosing the s channel to be local in the DFT calculation; the d channel can then be chosen to be local in subsequent QMC calculations, which generally leads to more accurate results. We investigate the achievable energy variance per electron with different levels of trial wave function and we determine appropriate plane-wave cutoff energies for DFT calculations for each pseudopotential. We demonstrate that the so-called "T-move" scheme in diffusion Monte Carlo is essential for many elements. We investigate the optimal choice of spherical integration rule for pseudopotential projectors in QMC calculations. The information reported here will prove crucial in the planning and execution of QMC projects involving beyond-first-row elements.
Duke, Brian J.; Havenith, Remco W. A.
2016-01-01
The use of larger basis sets to approach the complete basis limit, now common in quantum chemistry, is applied for the first time to a range of valence bond functions for the simplest case of molecular hydrogen. Good convergence of the energy is slow due to difficulty in getting a correct cusp near
European air quality modelled by CAMx including the volatility basis set scheme
Directory of Open Access Journals (Sweden)
G. Ciarelli
2015-12-01
Full Text Available Four periods of EMEP (European Monitoring and Evaluation Programme intensive measurement campaigns (June 2006, January 2007, September–October 2008 and February–March 2009 were modelled using the regional air quality model CAMx with VBS (Volatility Basis Set approach for the first time in Europe within the framework of the EURODELTA-III model intercomparison exercise. More detailed analysis and sensitivity tests were performed for the period of February–March 2009 and June 2006 to investigate the uncertainties in emissions as well as to improve the modelling of organic aerosols (OA. Model performance for selected gas phase species and PM2.5 was evaluated using the European air quality database Airbase. Sulfur dioxide (SO2 and ozone (O3 were found to be overestimated for all the four periods with O3 having the largest mean bias during June 2006 and January–February 2007 periods (8.93 and 12.30 ppb mean biases, respectively. In contrast, nitrogen dioxide (NO2 and carbon monoxide (CO were found to be underestimated for all the four periods. CAMx reproduced both total concentrations and monthly variations of PM2.5 very well for all the four periods with average biases ranging from −2.13 to 1.04 μg m-3. Comparisons with AMS (Aerosol Mass Spectrometer measurements at different sites in Europe during February–March 2009, showed that in general the model over-predicts the inorganic aerosol fraction and under-predicts the organic one, such that the good agreement for PM2.5 is partly due to compensation of errors. The effect of the choice of volatility basis set scheme (VBS on OA was investigated as well. Two sensitivity tests with volatility distributions based on previous chamber and ambient measurements data were performed. For February–March 2009 the chamber-case reduced the total OA concentrations by about 43 % on average. On the other hand, a test based on ambient measurement data increased OA concentrations by about 47 % for the same
Energy Technology Data Exchange (ETDEWEB)
Holden, Zachary C.; Richard, Ryan M.; Herbert, John M., E-mail: herbert@chemistry.ohio-state.edu [Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210 (United States)
2013-12-28
An implementation of Ewald summation for use in mixed quantum mechanics/molecular mechanics (QM/MM) calculations is presented, which builds upon previous work by others that was limited to semi-empirical electronic structure for the QM region. Unlike previous work, our implementation describes the wave function's periodic images using “ChElPG” atomic charges, which are determined by fitting to the QM electrostatic potential evaluated on a real-space grid. This implementation is stable even for large Gaussian basis sets with diffuse exponents, and is thus appropriate when the QM region is described by a correlated wave function. Derivatives of the ChElPG charges with respect to the QM density matrix are a potentially serious bottleneck in this approach, so we introduce a ChElPG algorithm based on atom-centered Lebedev grids. The ChElPG charges thus obtained exhibit good rotational invariance even for sparse grids, enabling significant cost savings. Detailed analysis of the optimal choice of user-selected Ewald parameters, as well as timing breakdowns, is presented.
Culpitt, Tanner; Brorsen, Kurt R.; Hammes-Schiffer, Sharon
2017-06-01
Density functional theory (DFT) embedding approaches have generated considerable interest in the field of computational chemistry because they enable calculations on larger systems by treating subsystems at different levels of theory. To circumvent the calculation of the non-additive kinetic potential, various projector methods have been developed to ensure the orthogonality of molecular orbitals between subsystems. Herein the orthogonality constrained basis set expansion (OCBSE) procedure is implemented to enforce this subsystem orbital orthogonality without requiring a level shifting parameter. This scheme is a simple alternative to existing parameter-free projector-based schemes, such as the Huzinaga equation. The main advantage of the OCBSE procedure is that excellent convergence behavior is attained for DFT-in-DFT embedding without freezing any of the subsystem densities. For the three chemical systems studied, the level of accuracy is comparable to or higher than that obtained with the Huzinaga scheme with frozen subsystem densities. Allowing both the high-level and low-level DFT densities to respond to each other during DFT-in-DFT embedding calculations provides more flexibility and renders this approach more generally applicable to chemical systems. It could also be useful for future extensions to embedding approaches combining wavefunction theories and DFT.
Entanglement Patterns in Mutually Unbiased Basis Sets for N Prime-state Particles
Lawrence, Jay
2011-01-01
A few simply-stated rules govern the entanglement patterns that can occur in mutually unbiased basis sets (MUBs), and constrain the combinations of such patterns that can coexist (ie, the stoichiometry) in full complements of p^N+1 MUBs. We consider Hilbert spaces of prime power dimension (as realized by systems of N prime-state particles, or qupits), where full complements are known to exist, and we assume only that MUBs are eigenbases of Pauli operators, without using a particular construction. The general rules include the following: 1) In any MUB, a particular qupit appears either in a pure state, or totally entangled, and 2) in any full MUB complement, each qupit is pure in p+1 bases (not necessarily the same ones), and totally entangled in the remaining p^N-p. It follows that the maximum number of product bases is p+1, and when this number is realized, all remaining p^N-p bases in the complement are characterized by the total entanglement of every qupit. This "standard distribution" is inescapable for t...
Indian Academy of Sciences (India)
Sarvesh Kumar Pandey; Prasanta Das; Puspendu K Das; Elangannan Arunan; Sadasivam Manogaran
2015-06-01
It has been shown earlier1 that the relaxed force constants (RFCs) could be used as a measure of bond strength only when the bonds form a part of the complete valence internal coordinates (VIC) basis. However, if the bond is not a part of the complete VIC basis, its RFC is not necessarily a measure of bond strength. Sometimes, it is possible to have a complete VIC basis that does not contain the intramolecular hydrogen bond (IMHB) as part of the basis. This means the RFC of IMHB is not necessarily a measure of bond strength. However, we know that IMHB is a weak bond and hence its RFC has to be a measure of bond strength. We resolve this problem of IMHB not being part of the complete basis by postulating `equivalent’ basis sets where IMHB is part of the basis at least in one of the equivalent sets of VIC. As long as a given IMHB appears in one of the equivalent complete VIC basis sets, its RFC could be used as a measure of bond strength parameter.
On the Use of a Mixed Gaussian/Finite-Element Basis Set for the Calculation of Rydberg States
Thuemmel, Helmar T.; Langhoff, Stephen (Technical Monitor)
1996-01-01
Configuration-interaction studies are reported for the Rydberg states of the helium atom using mixed Gaussian/finite-element (GTO/FE) one particle basis sets. Standard Gaussian valence basis sets are employed, like those, used extensively in quantum chemistry calculations. It is shown that the term values for high-lying Rydberg states of the helium atom can be obtained accurately (within 1 cm -1), even for a small GTO set, by augmenting the n-particle space with configurations, where orthonormalized interpolation polynomials are singly occupied.
Hill, J Grant
2013-09-30
Auxiliary basis sets (ABS) specifically matched to the cc-pwCVnZ-PP and aug-cc-pwCVnZ-PP orbital basis sets (OBS) have been developed and optimized for the 4d elements Y-Pd at the second-order Møller-Plesset perturbation theory level. Calculation of the core-valence electron correlation energies for small to medium sized transition metal complexes demonstrates that the error due to the use of these new sets in density fitting is three to four orders of magnitude smaller than that due to the OBS incompleteness, and hence is considered negligible. Utilizing the ABSs in the resolution-of-the-identity component of explicitly correlated calculations is also investigated, where it is shown that i-type functions are important to produce well-controlled errors in both integrals and correlation energy. Benchmarking at the explicitly correlated coupled cluster with single, double, and perturbative triple excitations level indicates impressive convergence with respect to basis set size for the spectroscopic constants of 4d monofluorides; explicitly correlated double-ζ calculations produce results close to conventional quadruple-ζ, and triple-ζ is within chemical accuracy of the complete basis set limit.
Simulating the oxygen content of ambient organic aerosol with the 2D volatility basis set
Murphy, B. N.; Donahue, N. M.; Fountoukis, C.; Pandis, S. N.
2011-08-01
A module predicting the oxidation state of organic aerosol (OA) has been developed using the two-dimensional volatility basis set (2D-VBS) framework. This model is an extension of the 1D-VBS framework and tracks saturation concentration and oxygen content of organic species during their atmospheric lifetime. The host model, a one-dimensional Lagrangian transport model, is used to simulate air parcels arriving at Finokalia, Greece during the Finokalia Aerosol Measurement Experiment in May 2008 (FAME-08). Extensive observations were collected during this campaign using an aerosol mass spectrometer (AMS) and a thermodenuder to determine the chemical composition and volatility, respectively, of the ambient OA. Although there are several uncertain model parameters, the consistently high oxygen content of OA measured during FAME-08 (O:C = 0.8) can help constrain these parameters and elucidate OA formation and aging processes that are necessary for achieving the high degree of oxygenation observed. The base-case model reproduces observed OA mass concentrations (measured mean = 3.1 μg m-3, predicted mean = 3.3 μg m-3) and O:C (predicted O:C = 0.78) accurately. A suite of sensitivity studies explore uncertainties due to (1) the anthropogenic secondary OA (SOA) aging rate constant, (2) assumed enthalpies of vaporization, (3) the volatility change and number of oxygen atoms added for each generation of aging, (4) heterogeneous chemistry, (5) the oxidation state of the first generation of compounds formed from SOA precursor oxidation, and (6) biogenic SOA aging. Perturbations in most of these parameters do impact the ability of the model to predict O:C well throughout the simulation period. By comparing measurements of the O:C from FAME-08, several sensitivity cases including a high oxygenation case, a low oxygenation case, and biogenic SOA aging case are found to unreasonably depict OA aging, keeping in mind that this study does not consider possibly important processes
Friese, Daniel H; Ringholm, Magnus; Gao, Bin; Ruud, Kenneth
2015-10-13
We present theory, implementation, and applications of a recursive scheme for the calculation of single residues of response functions that can treat perturbations that affect the basis set. This scheme enables the calculation of nonlinear light absorption properties to arbitrary order for other perturbations than an electric field. We apply this scheme for the first treatment of two-photon circular dichroism (TPCD) using London orbitals at the Hartree-Fock level of theory. In general, TPCD calculations suffer from the problem of origin dependence, which has so far been solved by using the velocity gauge for the electric dipole operator. This work now enables comparison of results from London orbital and velocity gauge based TPCD calculations. We find that the results from the two approaches both exhibit strong basis set dependence but that they are very similar with respect to their basis set convergence.
DEFF Research Database (Denmark)
Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian
2012-01-01
We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set ...
Brorsen, Kurt R.; Sirjoosingh, Andrew; Pak, Michael V.; Hammes-Schiffer, Sharon
2015-06-01
The nuclear electronic orbital (NEO) reduced explicitly correlated Hartree-Fock (RXCHF) approach couples select electronic orbitals to the nuclear orbital via Gaussian-type geminal functions. This approach is extended to enable the use of a restricted basis set for the explicitly correlated electronic orbitals and an open-shell treatment for the other electronic orbitals. The working equations are derived and the implementation is discussed for both extensions. The RXCHF method with a restricted basis set is applied to HCN and FHF- and is shown to agree quantitatively with results from RXCHF calculations with a full basis set. The number of many-particle integrals that must be calculated for these two molecules is reduced by over an order of magnitude with essentially no loss in accuracy, and the reduction factor will increase substantially for larger systems. Typically, the computational cost of RXCHF calculations with restricted basis sets will scale in terms of the number of basis functions centered on the quantum nucleus and the covalently bonded neighbor(s). In addition, the RXCHF method with an odd number of electrons that are not explicitly correlated to the nuclear orbital is implemented using a restricted open-shell formalism for these electrons. This method is applied to HCN+, and the nuclear densities are in qualitative agreement with grid-based calculations. Future work will focus on the significance of nonadiabatic effects in molecular systems and the further enhancement of the NEO-RXCHF approach to accurately describe such effects.
Reuter, Matthew G; Harrison, Robert J
2013-09-21
We revisit the derivation of electron transport theories with a focus on the projection operators chosen to partition the system. The prevailing choice of assigning each computational basis function to a region causes two problems. First, this choice generally results in oblique projection operators, which are non-Hermitian and violate implicit assumptions in the derivation. Second, these operators are defined with the physically insignificant basis set and, as such, preclude a well-defined basis set limit. We thus advocate for the selection of physically motivated, orthogonal projection operators (which are Hermitian) and present an operator-based derivation of electron transport theories. Unlike the conventional, matrix-based approaches, this derivation requires no knowledge of the computational basis set. In this process, we also find that common transport formalisms for nonorthogonal basis sets improperly decouple the exterior regions, leading to a short circuit through the system. We finally discuss the implications of these results for first-principles calculations of electron transport.
Directory of Open Access Journals (Sweden)
CASTRO EUSTÁQUIO V. R. DE
2001-01-01
Full Text Available The generator coordinate Hartree-Fock method is used to generate adapted Gaussian basis sets for the atoms from Li (Z=3 through Xe (Z=54. In this method the Griffin-Hill-Wheeler-Hartree-Fock equations are integrated through the integral discretization technique. The wave functions generated in this work are compared with the widely used Roothaan-Hartree-Fock wave functions of Clementi and Roetti (1974, and with other basis sets reported in the literature. For all atoms studied, the errors in our total energy values relatively to the numerical Hartree-Fock limits are always less than 7.426 mhartree.
Kollmar, Christian; Neese, Frank
2014-10-07
The role of the static Kohn-Sham (KS) response function describing the response of the electron density to a change of the local KS potential is discussed in both the theory of the optimized effective potential (OEP) and the so-called inverse Kohn-Sham problem involving the task to find the local KS potential for a given electron density. In a general discussion of the integral equation to be solved in both cases, it is argued that a unique solution of this equation can be found even in case of finite atomic orbital basis sets. It is shown how a matrix representation of the response function can be obtained if the exchange-correlation potential is expanded in terms of a Schmidt-orthogonalized basis comprising orbitals products of occupied and virtual orbitals. The viability of this approach in both OEP theory and the inverse KS problem is illustrated by numerical examples.
Simulating the oxygen content of ambient organic aerosol with the 2D volatility basis set
Directory of Open Access Journals (Sweden)
B. N. Murphy
2011-08-01
Full Text Available A module predicting the oxidation state of organic aerosol (OA has been developed using the two-dimensional volatility basis set (2D-VBS framework. This model is an extension of the 1D-VBS framework and tracks saturation concentration and oxygen content of organic species during their atmospheric lifetime. The host model, a one-dimensional Lagrangian transport model, is used to simulate air parcels arriving at Finokalia, Greece during the Finokalia Aerosol Measurement Experiment in May 2008 (FAME-08. Extensive observations were collected during this campaign using an aerosol mass spectrometer (AMS and a thermodenuder to determine the chemical composition and volatility, respectively, of the ambient OA. Although there are several uncertain model parameters, the consistently high oxygen content of OA measured during FAME-08 (O:C = 0.8 can help constrain these parameters and elucidate OA formation and aging processes that are necessary for achieving the high degree of oxygenation observed. The base-case model reproduces observed OA mass concentrations (measured mean = 3.1 μg m^{−3}, predicted mean = 3.3 μg m^{−3} and O:C (predicted O:C = 0.78 accurately. A suite of sensitivity studies explore uncertainties due to (1 the anthropogenic secondary OA (SOA aging rate constant, (2 assumed enthalpies of vaporization, (3 the volatility change and number of oxygen atoms added for each generation of aging, (4 heterogeneous chemistry, (5 the oxidation state of the first generation of compounds formed from SOA precursor oxidation, and (6 biogenic SOA aging. Perturbations in most of these parameters do impact the ability of the model to predict O:C well throughout the simulation period. By comparing measurements of the O:C from FAME-08, several sensitivity cases including a high oxygenation case, a low oxygenation case, and biogenic SOA aging case are found to unreasonably depict OA aging, keeping in mind that this study does not consider
Witte, Jonathon; Neaton, Jeffrey B.; Head-Gordon, Martin
2016-05-01
With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions—noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms—with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.
Witte, Jonathon; Neaton, Jeffrey B; Head-Gordon, Martin
2016-05-21
With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions-noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms-with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.
Heaps, Charles W
2016-01-01
Quantum molecular dynamics requires an accurate representation of the molecular potential energy surface from a minimal number of electronic structure calculations, particularly for nonadiabatic dynamics where excited states are required. In this paper, we employ pseudospectral sampling of time-dependent Gaussian basis functions for the simulation of non-adiabatic dynamics. Unlike other methods, the pseudospectral Gaussian molecular dynamics tests the Schr\\"{o}dinger equation with $N$ Dirac delta functions located at the centers of the Gaussian functions reducing the scaling of potential energy evaluations from $\\mathcal{O}(N^2)$ to $\\mathcal{O}(N)$. By projecting the Gaussian basis onto discrete points in space, the method is capable of efficiently and quantitatively describing nonadiabatic population transfer and intra-surface quantum coherence. We investigate three model systems; the photodissociation of three coupled Morse oscillators, the bound state dynamics of two coupled Morse oscillators, and a two-d...
Brandenburg, Jan Gerit; Alessio, Maristella; Civalleri, Bartolomeo; Peintinger, Michael F; Bredow, Thomas; Grimme, Stefan
2013-09-26
We extend the previously developed geometrical correction for the inter- and intramolecular basis set superposition error (gCP) to periodic density functional theory (DFT) calculations. We report gCP results compared to those from the standard Boys-Bernardi counterpoise correction scheme and large basis set calculations. The applicability of the method to molecular crystals as the main target is tested for the benchmark set X23. It consists of 23 noncovalently bound crystals as introduced by Johnson et al. (J. Chem. Phys. 2012, 137, 054103) and refined by Tkatchenko et al. (J. Chem. Phys. 2013, 139, 024705). In order to accurately describe long-range electron correlation effects, we use the standard atom-pairwise dispersion correction scheme DFT-D3. We show that a combination of DFT energies with small atom-centered basis sets, the D3 dispersion correction, and the gCP correction can accurately describe van der Waals and hydrogen-bonded crystals. Mean absolute deviations of the X23 sublimation energies can be reduced by more than 70% and 80% for the standard functionals PBE and B3LYP, respectively, to small residual mean absolute deviations of about 2 kcal/mol (corresponding to 13% of the average sublimation energy). As a further test, we compute the interlayer interaction of graphite for varying distances and obtain a good equilibrium distance and interaction energy of 6.75 Å and -43.0 meV/atom at the PBE-D3-gCP/SVP level. We fit the gCP scheme for a recently developed pob-TZVP solid-state basis set and obtain reasonable results for the X23 benchmark set and the potential energy curve for water adsorption on a nickel (110) surface.
Chan, Bun; Radom, Leo
2011-09-13
A variety of combinations of B-LYP-based double-hybrid density functional theory (DHDFT) procedures and basis sets have been examined. A general observation is that the optimal combination of exchange contributions is in the proximity of 30% Becke 1988 (B88) exchange and 70% Hartree-Fock (HF) exchange, while for the correlation contributions, the use of independently optimized spin-component-scaled Møller-Plesset second-order perturbation theory (SCS-MP2) parameters (MP2OS and MP2SS) is beneficial. The triple-ζ Dunning aug'-cc-pVTZ+d and Pople 6-311+G(3df,2p)+d basis sets are found to be cost-effective for DHDFT methods. As a result, we have formulated the DuT-D3 DHDFT procedure, which employs the aug'-cc-pVTZ+d basis set and includes 30% B88 and 70% HF exchange energies, 59% LYP, 47% MP2OS, and 36% MP2SS correlation energies, and a D3 dispersion correction with the parameters s6 = 0.5, sr,6 = 1.569, and s8 = 0.35. Likewise, the PoT-D3 DHDFT procedure was formulated with the 6-311+G(3df,2p)+d basis set and has 32% B88 and 68% HF exchange energies, 63% LYP, 46% MP2OS, and 27% MP2SS correlation energies, and the D3 parameters s6 = 0.5, sr,6 = 1.569, and s8 = 0.30. Testing using the large E3 set of 740 energies demonstrates the robustness of these methods. Further comparisons show that the performance of these methods, particularly DuT-D3, compares favorably with the previously reported DSD-B-LYP and DSD-B-LYP-D3 methods used in conjunction with quadruple-ζ aug'-pc3+d and aug'-def2-QZVP basis sets but at lower computational expense. The previously reported ωB97X-(LP)/6-311++G(3df,3pd) procedure also performs very well. Our findings highlight the cost-effectiveness of appropriate- and moderate-sized triple-ζ basis sets in the application of DHDFT procedures.
Linear scaling calculation of maximally localized Wannier functions with atomic basis set.
Xiang, H J; Li, Zhenyu; Liang, W Z; Yang, Jinlong; Hou, J G; Zhu, Qingshi
2006-06-21
We have developed a linear scaling algorithm for calculating maximally localized Wannier functions (MLWFs) using atomic orbital basis. An O(N) ground state calculation is carried out to get the density matrix (DM). Through a projection of the DM onto atomic orbitals and a subsequent O(N) orthogonalization, we obtain initial orthogonal localized orbitals. These orbitals can be maximally localized in linear scaling by simple Jacobi sweeps. Our O(N) method is validated by applying it to water molecule and wurtzite ZnO. The linear scaling behavior of the new method is demonstrated by computing the MLWFs of boron nitride nanotubes.
Astabatyan, R A; Kavalov, R L; Kugler, A; Kuznetsov, I V; Kushniruk, V F; Lobastov, S P; Lukyanov, S M; Markaryan, E R; Maslov, V A; Mikhailov, L; Penionzhkevich, Yu E; Poroshin, N O; Skobelev, N K; Smirnov, V I; Sobolev, Yu G; Ugryumov, V Yu
2002-01-01
A large-aperture set-up designed for nuclear physics experiments on beams of radioactive nuclei is described. The set-up includes Multiwire Proportional Chamber (MWPC) for measuring the beam profile, MWPC for measuring reaction product angular distributions, a CsI(Tl)-crystal detector and a longitudinal drift ionization chamber for identifying scattered particles and measuring their energy. The results of tests of coordinate MWPCs, particle identification on photon and ion beams, and preliminary measurements of the elastic scattering and the charge exchange reaction of 170 MeV ^{6}He on a CH_{2} target are presented.
Institute of Scientific and Technical Information of China (English)
DONG Li-xin; XIAO Deng-ming Xiao; LIU Yi-lu
2007-01-01
Rough set (RS) and radial basis function neural network (RBFNN) based insulation data mining fault diagnosis for power transformer is proposed. On the one hand rough set is used as front of RBFNN to simplify the input of RBFNN and mine the rules. The mined rules whose "confidence" and "support" is higher than requirement are used to offer fault diagnosis service for power transformer directly. On the other hand the mining samples corresponding to the mined rule, whose "confidence and support" is lower than requirement,are used to be training samples set of RBFNN and these samples are clustered by rough set. The center of each clustering set is used to be center of radial basis function, i.e. , as the hidden layer neuron. The RBFNN is structured with above base, which is used to diagnose the case that can not be diagnosed by mined simplified valuable rules based on rough set. The advantages and effectiveness of this method are verified by testing.
Accelerating wavefunction in density-functional-theory embedding by truncating the active basis set.
Bennie, Simon J; Stella, Martina; Miller, Thomas F; Manby, Frederick R
2015-07-14
Methods where an accurate wavefunction is embedded in a density-functional description of the surrounding environment have recently been simplified through the use of a projection operator to ensure orthogonality of orbital subspaces. Projector embedding already offers significant performance gains over conventional post-Hartree-Fock methods by reducing the number of correlated occupied orbitals. However, in our first applications of the method, we used the atomic-orbital basis for the full system, even for the correlated wavefunction calculation in a small, active subsystem. Here, we further develop our method for truncating the atomic-orbital basis to include only functions within or close to the active subsystem. The number of atomic orbitals in a calculation on a fixed active subsystem becomes asymptotically independent of the size of the environment, producing the required O(N(0)) scaling of cost of the calculation in the active subsystem, and accuracy is controlled by a single parameter. The applicability of this approach is demonstrated for the embedded many-body expansion of binding energies of water hexamers and calculation of reaction barriers of SN2 substitution of fluorine by chlorine in α-fluoroalkanes.
Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets
Miceli, Giacomo; Pasquarello, Alfredo
2016-01-01
We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions.
Salvador, P; Mayer, I
2004-04-01
The basis set superposition error-free second-order Møller-Plesset perturbation theory of intermolecular interactions, based on the "chemical Hamiltonian approach," which has been introduced in Part I, is applied here to open-shell systems by using a new, effective computer realization. The results of the numerical examples considered (CH(4) em leader HO, NO em leader HF) showed again the perfect performance of the method. Striking agreement has again been found with the results of the a posteriori counterpoise correction (CP) scheme in the case of large, well-balanced basis sets, which is also in agreement with a most recent formal theoretical analysis. The difficulties of the CP correction in open-shell systems are also discussed.
Bjornsson, Ragnar; Bühl, Michael
2010-06-14
Electric field gradients (EFGs) were computed for the first-row transition metal nuclei in Cr(C(6)H(6))(CO)(3), MnO(3)F, Mn(CO)(5)H, MnCp(CO)(3), Co(CO)(4)H, Co(CO)(3)(NO) and VCp(CO)(4), for which experimental gas-phase data (in form of nuclear quadrupole coupling constants) are available from microwave spectroscopy. A variety of exchange-correlation functionals were assessed, among which range-separated hybrids (such as CAM-B3LYP or LC-omegaPBE) perform best, followed by global hybrids (such as B3LYP and PBE0) and gradient-corrected functionals (such as BP86). While large basis sets are required on the metal atom for converged EFGs, smaller basis sets can be employed on the ligands. In most cases, EFGs show little sensitivity toward the geometrical parameters.
Buimaga-Iarinca, Luiza
2014-01-01
We compare the density functional theory (DFT) results on the adsorption of small aromatic molecules (benzene, pyridine and thiophene) on gold surfaces obtained by using three types of van der Waals exchange-correlation functionals and localized basis set calculations. We show that the value of the molecule surface binding energy depends on the interplay between the BSSE effect and the tendency of the exchange-correlation functionals to overestimate both the molecule-surface as well as the gold-gold distances within the relaxed systems. Consequently, we find that by using different types of LCAO basis sets or geometric models for the adsorption of the molecules on the surface, the binding energy can vary up to 100 %. A critical analysis of the physical parameters resulting from the calculations is presented for each exchange-correlation functional.
Core gene set as the basis of multilocus sequence analysis of the subclass Actinobacteridae.
Directory of Open Access Journals (Sweden)
Toïdi Adékambi
Full Text Available Comparative genomic sequencing is shedding new light on bacterial identification, taxonomy and phylogeny. An in silico assessment of a core gene set necessary for cellular functioning was made to determine a consensus set of genes that would be useful for the identification, taxonomy and phylogeny of the species belonging to the subclass Actinobacteridae which contained two orders Actinomycetales and Bifidobacteriales. The subclass Actinobacteridae comprised about 85% of the actinobacteria families. The following recommended criteria were used to establish a comprehensive gene set; the gene should (i be long enough to contain phylogenetically useful information, (ii not be subject to horizontal gene transfer, (iii be a single copy (iv have at least two regions sufficiently conserved that allow the design of amplification and sequencing primers and (v predict whole-genome relationships. We applied these constraints to 50 different Actinobacteridae genomes and made 1,224 pairwise comparisons of the genome conserved regions and gene fragments obtained by using Sequence VARiability Analysis Program (SVARAP, which allow designing the primers. Following a comparative statistical modeling phase, 3 gene fragments were selected, ychF, rpoB, and secY with R2>0.85. Selected sets of broad range primers were tested from the 3 gene fragments and were demonstrated to be useful for amplification and sequencing of 25 species belonging to 9 genera of Actinobacteridae. The intraspecies similarities were 96.3-100% for ychF, 97.8-100% for rpoB and 96.9-100% for secY among 73 strains belonging to 15 species of the subclass Actinobacteridae compare to 99.4-100% for 16S rRNA. The phylogenetic topology obtained from the combined datasets ychF+rpoB+secY was globally similar to that inferred from the 16S rRNA but with higher confidence. It was concluded that multi-locus sequence analysis using core gene set might represent the first consensus and valid approach for
2012-01-01
We present a systematic study of the performance of numerical pseudo-atomic orbital basis sets in the calculation of dielectric matrices of extended systems using the self-consistent Sternheimer approach of [F. Giustino et al., Phys. Rev. B 81 (11), 115105 (2010)]. In order to cover a range of systems, from more insulating to more metallic character, we discuss results for the three semiconductors diamond, silicon, and germanium. Dielectric matrices calculated using our method fall within 1-3...
Homeier, H. H. H.; Neef, M. D.
2000-01-01
The performance of the recently introduced $\\Pi$2 method [1] is investigated for some diatomic molecules. For this end, ground state energies are calculated at the MP4 level for various basis sets of increasing size. With negligible extra effort, the $\\Pi$2, F4, and [2/2] estimators are obtained, together with information on the reliability of the basic perturbation series [1]. The results are compared to more expensive CCSD(T) results. Also, electronic energy hypersurfaces are calculated at ...
Kolmann, Stephen J; Jordan, Meredith J T
2010-02-07
One of the largest remaining errors in thermochemical calculations is the determination of the zero-point energy (ZPE). The fully coupled, anharmonic ZPE and ground state nuclear wave function of the SSSH radical are calculated using quantum diffusion Monte Carlo on interpolated potential energy surfaces (PESs) constructed using a variety of method and basis set combinations. The ZPE of SSSH, which is approximately 29 kJ mol(-1) at the CCSD(T)/6-31G* level of theory, has a 4 kJ mol(-1) dependence on the treatment of electron correlation. The anharmonic ZPEs are consistently 0.3 kJ mol(-1) lower in energy than the harmonic ZPEs calculated at the Hartree-Fock and MP2 levels of theory, and 0.7 kJ mol(-1) lower in energy at the CCSD(T)/6-31G* level of theory. Ideally, for sub-kJ mol(-1) thermochemical accuracy, ZPEs should be calculated using correlated methods with as big a basis set as practicable. The ground state nuclear wave function of SSSH also has significant method and basis set dependence. The analysis of the nuclear wave function indicates that SSSH is localized to a single symmetry equivalent global minimum, despite having sufficient ZPE to be delocalized over both minima. As part of this work, modifications to the interpolated PES construction scheme of Collins and co-workers are presented.
Zhao, Yan; Truhlar, Donald G
2005-08-04
Benchmark stabilization energies for planar H-bonded and stacked structures of formic acid tetramers and formamide tetramers were determined as the sum of the infinite basis set limit of MP2 energies and a CCSD(T) correction term evaluated with the 6-31G*(0.25) basis set. The infinite basis (IB) set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and separate extrapolation of the Hartree-Fock and correlation energies with new IB parameters for augmented basis sets determined here. Final stabilization energies (kcal/mol) for the tetramer studied are in the range of 4.6 to approximately 6.7 kcal/mol and they were used as reference data to test 14 density functionals. Among the tested DFT methods, PWB6K gives the best performance with an average error equal to only 30% of the average binding energy. In contrast, the popular B3LYP functional has an average error of 85%. We recommend the PWB6K method for exploring the potential energy surfaces of organic complexes and clusters and supramolecular assemblies.
A new set of basis functions for the discrete geometric approach
Codecasa, Lorenzo; Specogna, Ruben; Trevisan, Francesco
2010-09-01
By exploiting the geometric structure behind Maxwell's equations, the so called discrete geometric approach allows to translate the physical laws of electromagnetism into discrete relations, involving circulations and fluxes associated with the geometric elements of a pair of interlocked grids: the primal grid and the dual grid. To form a finite dimensional system of equations, discrete counterparts of the constitutive relations must be introduced in addition. They are referred to as constitutive matrices which must comply with precise properties (symmetry, positive definiteness, consistency) in order to guarantee the stability and consistency of the overall finite dimensional system of equations. The aim of this work is to introduce a general and efficient set of vector functions associated with the edges and faces of a polyhedral primal grids or of a dual grid obtained from the barycentric subdivision of the boundary of the primal grid; these vector functions comply with precise specifications which allow to construct stable and consistent discrete constitutive equations for the discrete geometric approach in the framework of an energetic method.
Energy Technology Data Exchange (ETDEWEB)
Rossikhin, V.V.; Kuzmenko, V.V.; Voronkov, E.O.; Zaslavskaya, L.I. [Dnepropetrovsk State Technical University, 2 Acad. Lazaryan St., Dnepropetrovsk 10, 320010 (UKRAINE)
1995-04-01
An {ital ab initio} method is proposed to compute the components of polarizability and magnetizability tensors of polyatomic molecules with the closed shells. Test calculations for the ten-electron hydride molecules demonstrate applicability and efficiency of the suggested method in comparison with traditional ones. (AIP) {copyright}{ital 1995 American Institute of Physics}
DEFF Research Database (Denmark)
Kupka, Teobald; Stachów, Michal; Kaminsky, Jakub
2013-01-01
A linear correlation between isotropic nuclear magnetic shielding constants for seven model molecules (CH2O, H2O, HF, F2, HCN, SiH4 and H2S) calculated with 37 methods (34 density functionals, RHF, MP2 and CCSD(T) ), with affordable pcS-2 basis set and corresponding complete basis set results......, estimated from calculations with the family of polarizationconsistent pcS-n basis sets is reported. This dependence was also supported by inspection of profiles of deviation between CBS estimated nuclear shieldings and obtained with significantly smaller basis sets pcS-2 and aug-cc-pVTZ-J for the selected...
Energy Technology Data Exchange (ETDEWEB)
Kupka, T.; Ruscic, B.; Botto, R. E.; Chemistry
2003-05-01
The nuclear shielding anisotropy and shielding tensor components calculated using the hybrid density functional B3PW91 are reported for a model set of compounds comprised of N{sub 2}, NH{sub 3}, CH{sub 4}, C{sub 2}H{sub 4}, HCN and CH{sub 3}CN. An estimation of density functional theory (DFT) and Hartree-Fock complete basis-set limit (CBS) parameters from a 2 (3) point exact fit vs. least-squares fit was obtained with the cc-pVxZ and aug-cc-pVxZ basis sets (x=D, T, Q, 5, 6). Both Hartree-Fock- and DFT-predicted CBS shielding anisotropies and shielding tensor components of the model molecules were in reasonable agreement with available experimental data. The utility of using a limited CBS approach for calculating accurate anisotropic shielding parameters of larger molecules as complementary methods to solid-state NMR is proposed.
Zhang, Gaigong; Hu, Wei; Yang, Chao; Pask, John E
2015-01-01
Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracy required in practice. Since the adaptive local basis set has implicit dependence on a...
Simon, Sílvia; Duran, Miquel
1997-08-01
Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.
Institute of Scientific and Technical Information of China (English)
Zhang Yue-Xia; Meng Hui-Yan; Shi Ting-Yun
2008-01-01
The B-spline basis set plus complex scaling method is applied to the numerical calculation of the exact resonance parameters Er and I/2 of a hydrogen atom in parallel electric and magnetic fields.The method can calculate the ground and higher excited resonances accurately and efficiently.The resonance parameters with accuracies of 10-9 - 10-12 for hydrogen atom in parallel fields with different field strengths and symmetries are presented and compared with previous ones.Extension to the calculation of Rydberg atom in crossed electric and magnetic fields and of atomic double excited states in external electric fields is discussed.
Hübener, H.; Pérez-Osorio, M. A.; Ordejón, P.; Giustino, F.
2012-09-01
We present a systematic study of the performance of numerical pseudo-atomic orbital basis sets in the calculation of dielectric matrices of extended systems using the self-consistent Sternheimer approach of [F. Giustino et al., Phys. Rev. B 81, 115105 (2010)]. In order to cover a range of systems, from more insulating to more metallic character, we discuss results for the three semiconductors diamond, silicon, and germanium. Dielectric matrices of silicon and diamond calculated using our method fall within 1% of reference planewaves calculations, demonstrating that this method is promising. We find that polarization orbitals are critical for achieving good agreement with planewaves calculations, and that only a few additional ζ's are required for obtaining converged results, provided the split norm is properly optimized. Our present work establishes the validity of local orbital basis sets and the self-consistent Sternheimer approach for the calculation of dielectric matrices in extended systems, and prepares the ground for future studies of electronic excitations using these methods.
Teodoro, Tiago Quevedo; Visscher, Lucas; da Silva, Albérico Borges Ferreira; Haiduke, Roberto Luiz Andrade
2017-01-06
The f-block elements are addressed in this third part of a series of prolapse-free basis sets of quadruple-ζ quality (RPF-4Z). Relativistic adapted Gaussian basis sets (RAGBSs) are used as primitive sets of functions while correlating/polarization (C/P) functions are chosen by analyzing energy lowerings upon basis set increments in Dirac-Coulomb multireference configuration interaction calculations with single and double excitations of the valence spinors. These function exponents are obtained by applying the RAGBS parameters in a polynomial expression. Moreover, through the choice of C/P characteristic exponents from functions of lower angular momentum spaces, a reduction in the computational demand is attained in relativistic calculations based on the kinetic balance condition. The present study thus complements the RPF-4Z sets for the whole periodic table (Z ≤ 118). The sets are available as Supporting Information and can also be found at http://basis-sets.iqsc.usp.br .
On the Basis of the Elderly Care Settings%论老年监护设置依据
Institute of Scientific and Technical Information of China (English)
刘清生; 黄燕香
2016-01-01
老年监护设置不同于未成年人监护设置，设置依据是老年监护设置的前提条件，却为学界所忽视。对监护设置历史的追溯可以发现，监护设置依据自古包括智能和体能两因素，近现代国家民法中也多有体现。不同于未成年人体能和智能增长“从无到有”的过程，老年人因衰老而导致的体能与智能减损是一个“从有到无”的过程，年龄无法成为设置老年监护的直接依据。智能或体能减损致老年人无法“正常化”生活是老年监护设置的合理标准。%The academic research on elderly care is not based on the actual needs of the elderly individuals,which does not really deals with the issue of how to set elderly care. From the historical retrospective,we know that the system of guardianship settings is based on the factors of intelligent mental health and physical condition,stated in the laws of the modern countries. Because of the process of aging caused by physical and mental impairments,age can not be the basis of elderly guardianship basis. The weakening of mental and physical abilities should be the standards for elderly guardianship settings.
Hill, J. Grant; Mazumder, Shivnath; Peterson, Kirk A.
2010-02-01
Correlation consistent basis sets have been optimized for accurately describing core-core and core-valence correlation effects with explicitly correlated F12 methods. The new sets, denoted cc-pCVnZ-F12 (n =D, T, Q) and aug-cc-pCF12VnZ (n =D, T, Q, 5), were developed by augmenting the cc-pVnZ-F12 and aug-cc-pVnZ families of basis sets with additional functions whose exponents were optimized based on the difference between all-electron and valence-electron correlation energies. The number of augmented functions added is fewer, in general, than in the standard cc-pCVnZ and cc-pwCVnZ families of basis sets. Optimal values of the geminal Slater exponent for use with these basis sets in MP2-F12 calculations are presented and are also recommended for CCSD-F12b calculations. Auxiliary basis sets for use in the resolution of the identity approximation in explicitly correlated calculations have also been optimized and matched to the new cc-pCVnZ-F12 series of orbital basis sets. The cc-pCVnZ-F12 basis sets, along with the new auxiliary sets, were benchmarked in CCSD(T)-F12b calculations of spectroscopic properties on a series of homo- and heteronuclear first and second row diatomic molecules. Comparing the effects of correlating the outer core electrons in these molecules with those from conventional CCSD(T) at the complete basis set limit, which involved calculations with new cc-pCV6Z basis sets for the second row elements that were also developed in the course of this work, it is observed that the F12 values are reasonably well converged already at just the triple-ζ level.
Structure and binding energy of the H2S dimer at the CCSD(T) complete basis set limit
Lemke, Kono H.
2017-06-01
This study presents results for the binding energy and geometry of the H2S dimer which have been computed using Møller-Plesset perturbation theory (MP2, MP4) and coupled cluster (CCSD, CCSD(T)) calculations with basis sets up to aug-cc-pV5Z. Estimates of De, EZPE, Do, and dimer geometry have been obtained at each level of theory by taking advantage of the systematic convergence behavior toward the complete basis set (CBS) limit. The CBS limit binding energy values of De are 1.91 (MP2), 1.75 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD[T]). The most accurate values for the equilibrium S-S distance rSS (without counterpoise correction) are 4.080 (MP2/aug-cc-pV5Z), 4.131 (MP4/aug-cc-pVQZ), 4.225 (CCSD/aug-cc-pVQZ), and 4.146 Å (CCSD(T)/aug-cc-pVQZ). This study also evaluates the effect of counterpoise correction on the H2S dimer geometry and binding energy. As regards the structure of (H2S)2, MPn, CCSD, and CCSD(T) level values of rSS, obtained by performing geometry optimizations on the counterpoise-corrected potential energy surface, converge systematically to CBS limit values of 4.099 (MP2), 4.146 (MP4), 4.233 (CCSD), and 4.167 Å (CCSD(T)). The corresponding CBS limit values of the equilibrium binding energy De are 1.88 (MP2), 1.76 (MP4), 1.41 (CCSD), and 1.69 kcal/mol (CCSD(T)), the latter in excellent agreement with the measured binding energy value of 1.68 ± 0.02 kcal/mol reported by Ciaffoni et al. [Appl. Phys. B 92, 627 (2008)]. Combining CBS electronic binding energies De with EZPE predicted by CCSD(T) vibrational second-order perturbation theory calculations yields Do = 1.08 kcal/mol, which is around 0.6 kcal/mol smaller than the measured value of 1.7 ± 0.3 kcal/mol. Overall, the results presented here demonstrate that the application of high level calculations, in particular CCSD(T), in combination with augmented correlation consistent basis sets provides valuable insight into the structure and energetics of the hydrogen sulfide dimer.
Andrade, Xavier
2013-01-01
We discuss the application of graphical processing units (GPUs) to accelerate real-space density functional theory (DFT) calculations. To make our implementation efficient, we have developed a scheme to expose the data parallelism available in the DFT approach; this is applied to the different procedures required for a real-space DFT calculation. We present results for current-generation GPUs from AMD and Nvidia, which show that our scheme, implemented in the free code OCTOPUS, can reach a sustained performance of up to 90 GFlops for a single GPU, representing an important speed-up when compared to the CPU version of the code. Moreover, for some systems our implementation can outperform a GPU Gaussian basis set code, showing that the real-space approach is a competitive alternative for DFT simulations on GPUs.
Andrade, Xavier; Aspuru-Guzik, Alán
2013-10-01
We discuss the application of graphical processing units (GPUs) to accelerate real-space density functional theory (DFT) calculations. To make our implementation efficient, we have developed a scheme to expose the data parallelism available in the DFT approach; this is applied to the different procedures required for a real-space DFT calculation. We present results for current-generation GPUs from AMD and Nvidia, which show that our scheme, implemented in the free code Octopus, can reach a sustained performance of up to 90 GFlops for a single GPU, representing a significant speed-up when compared to the CPU version of the code. Moreover, for some systems, our implementation can outperform a GPU Gaussian basis set code, showing that the real-space approach is a competitive alternative for DFT simulations on GPUs.
Guan, Qingze; Blume, Doerte
2016-05-01
The explicit correlated Gaussian (ECG) basis set expansion approach is a variational approach that has been used in various areas, including molecular, nuclear, atomic, and chemical physics. In the world of cold atoms, e.g., the ECG approach has been used to calculate the eigenenergies and eigenstates of few-body systems governed by Efimov physics. Since the first experimental realization of synthesized gauge fields, few-body systems with spin-orbit coupling have attracted a great deal of attention. Here, the ECG approach is customized to few-body systems with both short-range interactions and spin-orbit couplings. Benchmark tests and a performance analysis will be presented. Support by the NSF is gratefully acknowledged.
Many-body basis-set reduction applied to the two-dimensional t-Jz model
Riera, J.; Dagotto, E.
1993-06-01
A simple variation of the Lanczos method is discussed. The technique is based on a systematic reduction of the size of the Hilbert space of the model under consideration, and it has many similarities with the basis-set-reduction approach recently introduced by Wenzel and Wilson in the context of quantum chemistry. As an example, the two-dimensional t-Jz model of strongly correlated electrons is studied. Accurate results for the ground-state energy can be obtained on clusters of up to 50 sites, which are unreachable by conventional Lanczos approaches. In particular, the energy of one and two holes is analyzed as a function of Jz/t. In the bulk limit, the numerical results suggest that a finite coupling Jz/t]c~0.18 is necessary to induce ``binding'' of holes in the model.
New STO(II-3Gmag family basis sets for the calculations of the molecules magnetic properties
Directory of Open Access Journals (Sweden)
Karina Kapusta
2015-10-01
Full Text Available An efficient approach for construction of physically justified STO(II-3Gmag family basis sets for calculation of molecules magnetic properties has been proposed. The procedure of construction based upon the taken into account the second order of perturbation theory in the magnetic field case. Analytical form of correction functions has been obtained using the closed representation of the Green functions by the solution of nonhomogeneous Schrödinger equation for the model problem of "one-electron atom in the external uniform magnetic field". Their performance has been evaluated for the DFT level calculations carried out with a number of functionals. The test calculations of magnetic susceptibility and 1H nuclear magnetic shielding tensors demonstrated a good agreement of the calculated values with the experimental data.
Daramola, Damilola A; Muthuvel, Madhivanan; Botte, Gerardine G
2010-07-29
Geometry and vibration properties for monoclinic zirconium oxide were studied using Gaussian basis sets and LDA, GGA, and B3LYP functionals. Bond angles, bond lengths, lattice parameters, and Raman frequencies were calculated and compared to experimental values. Bond angles and lengths were found to agree within experimental standard deviations. The B3LYP gave the best performance of all three functionals with a percent error of 1.35% for the lattice parameters while the average difference between experimental and calculated Raman frequency values was -3 cm(-1). The B3LYP functional was then used to assign the atomic vibrations causing each frequency mode using isotopic substitution of (93.40)Zr for (91.22)Zr and (18.00)O for (16.00)O. This resulted in seven modes assigned to the Zr atom, ten modes to the O atom, and one mode being a mixture of both.
Khvostichenko, Daria; Choi, Andrew; Boulatov, Roman
2008-04-24
We investigated the effect of several computational variables, including the choice of the basis set, application of symmetry constraints, and zero-point energy (ZPE) corrections, on the structural parameters and predicted ground electronic state of model 5-coordinate hemes (iron(II) porphines axially coordinated by a single imidazole or 2-methylimidazole). We studied the performance of B3LYP and B3PW91 with eight Pople-style basis sets (up to 6-311+G*) and B97-1, OLYP, and TPSS functionals with 6-31G and 6-31G* basis sets. Only hybrid functionals B3LYP, B3PW91, and B97-1 reproduced the quintet ground state of the model hemes. With a given functional, the choice of the basis set caused up to 2.7 kcal/mol variation of the quintet-triplet electronic energy gap (DeltaEel), in several cases, resulting in the inversion of the sign of DeltaEel. Single-point energy calculations with triple-zeta basis sets of the Pople (up to 6-311G++(2d,2p)), Ahlrichs (TZVP and TZVPP), and Dunning (cc-pVTZ) families showed the same trend. The zero-point energy of the quintet state was approximately 1 kcal/mol lower than that of the triplet, and accounting for ZPE corrections was crucial for establishing the ground state if the electronic energy of the triplet state was approximately 1 kcal/mol less than that of the quintet. Within a given model chemistry, effects of symmetry constraints and of a "tense" structure of the iron porphine fragment coordinated to 2-methylimidazole on DeltaEel were limited to 0.3 kcal/mol. For both model hemes the best agreement with crystallographic structural data was achieved with small 6-31G and 6-31G* basis sets. Deviation of the computed frequency of the Fe-Im stretching mode from the experimental value with the basis set decreased in the order: nonaugmented basis sets, basis sets with polarization functions, and basis sets with polarization and diffuse functions. Contraction of Pople-style basis sets (double-zeta or triple-zeta) affected the results
Directory of Open Access Journals (Sweden)
Fabien Cignetti
2016-07-01
Full Text Available Conventional analysis of functional magnetic resonance imaging (fMRI data using the general linear model (GLM employs a neural model convolved with a canonical hemodynamic response function (HRF peaking 5s after stimulation. Incorporation of a further basis function, namely the canonical HRF temporal derivative, accounts for delays in the hemodynamic response to neural activity. A population that may benefit from this flexible approach is children whose hemodynamic response is not yet mature. Here, we examined the effects of using the set based on the canonical HRF plus its temporal derivative on both first- and second-level GLM analyses, through simulations and using developmental data (an fMRI dataset on proprioceptive mapping in children and adults. Simulations of delayed fMRI first-level data emphasized the benefit of carrying forward to the second-level a derivative boost that combines derivative and nonderivative beta estimates. In the experimental data, second-level analysis using a paired t-test showed increased mean amplitude estimate (i.e., increased group contrast mean in several brain regions related to proprioceptive processing when using the derivative boost compared to using only the nonderivative term. This was true especially in children. However, carrying forward to the second-level the individual derivative boosts had adverse consequences on random-effects analysis that implemented one-sample t-test, yielding increased between-subject variance, thus affecting group-level statistic. Boosted data also presented a lower level of smoothness that had implication for the detection of group average activation. Imposing soft constraints on the derivative boost by limiting the time-to-peak range of the modelled response within a specified range (i.e., 4-6s mitigated these issues. These findings support the notion that there are pros and cons to using the informed basis set with developmental data.
Cignetti, Fabien; Salvia, Emilie; Anton, Jean-Luc; Grosbras, Marie-Hélène; Assaiante, Christine
2016-01-01
Conventional analysis of functional magnetic resonance imaging (fMRI) data using the general linear model (GLM) employs a neural model convolved with a canonical hemodynamic response function (HRF) peaking 5 s after stimulation. Incorporation of a further basis function, namely the canonical HRF temporal derivative, accounts for delays in the hemodynamic response to neural activity. A population that may benefit from this flexible approach is children whose hemodynamic response is not yet mature. Here, we examined the effects of using the set based on the canonical HRF plus its temporal derivative on both first- and second-level GLM analyses, through simulations and using developmental data (an fMRI dataset on proprioceptive mapping in children and adults). Simulations of delayed fMRI first-level data emphasized the benefit of carrying forward to the second-level a derivative boost that combines derivative and nonderivative beta estimates. In the experimental data, second-level analysis using a paired t-test showed increased mean amplitude estimate (i.e., increased group contrast mean) in several brain regions related to proprioceptive processing when using the derivative boost compared to using only the nonderivative term. This was true especially in children. However, carrying forward to the second-level the individual derivative boosts had adverse consequences on random-effects analysis that implemented one-sample t-test, yielding increased between-subject variance, thus affecting group-level statistic. Boosted data also presented a lower level of smoothness that had implication for the detection of group average activation. Imposing soft constraints on the derivative boost by limiting the time-to-peak range of the modeled response within a specified range (i.e., 4-6 s) mitigated these issues. These findings support the notion that there are pros and cons to using the informed basis set with developmental data.
Mackenzie, Anne I.; Baginski, Michael E.; Rao, Sadasiva M.
2008-01-01
In this work, we present an alternate set of basis functions, each defined over a pair of planar triangular patches, for the method of moments solution of electromagnetic scattering and radiation problems associated with arbitrarily-shaped, closed, conducting surfaces. The present basis functions are point-wise orthogonal to the pulse basis functions previously defined. The prime motivation to develop the present set of basis functions is to utilize them for the electromagnetic solution of dielectric bodies using a surface integral equation formulation which involves both electric and magnetic cur- rents. However, in the present work, only the conducting body solution is presented and compared with other data.
Ab initio molecular dynamics simulations of the Li4F4 cluster
Heidenreich, A.; Sauer, J.
1995-12-01
Molecular dynamics simulations have been performed directly on the ab initio potential energy surface of Li4F4, which was generated within the Hartree-Fock approximation using a Gaussian basis set (split valence contraction). Trajectories at different temperatures yield the temperature dependence of the infrared spectra and the photoelectron spectra. For the infrared spectra comparison is made with MD results using a shell model ion pair potential function.
AB initio calculations of the structure and stability of the non-rigid LiBF 4 molecule
Zakzhevzskii, V. G.; Boldyrev, A. I.; Charkin, O. P.
1980-07-01
Ab initio calculations of the potential energy surface, equilibrium geometry and energetic stability of the non-rigid LiBF4 molecule have been performed using the basis sets of Roos and Siegbahn, and Huzinaga and Dunning in a doublezeta contraction. The results are compared with similar ab initio data for LiBH 4, LiAlH 4, LiBeH -4, LiCH +4, Li 2 F 2, and LiBeF 3 ‡The geometry of the most disadvantageous configuration (m) was not optimized completely
Dattani, Nikesh S.; Sharma, Sandeep; Alavi, Ali
2016-06-01
Being the simplest uncharged homonuclear dimer after H_2 that has a stable ground state, Li_2 is one of the most important benchmark systems for theory and experiment. In 1930, Delbruck used Li_2 to test his theory of homopolar binding, and it was used again and again as a prototype to test what have now become some of the most ubiquitous concepts in molecular physics (LCAO, SCF, MO, just to name a few). Experimentally, Roscoe and Schuster studied alkali dimers back in 1874. At the dawn of quantum mechanics, the emerging types of spectroscopic analyses we now use today, were tested on Li_2 in the labs of Wurm (1928), Harvey (1929), Lewis (1931), and many others, independently. Li_2 was at the centre of the development of PFOODR in the 80s, and PAS in the 90s; and Lithium Bose-Einstein condensates were announced only 1 month after the Nobel Prize winning BEC announcement in 1995. Even now in the 2010s, numerous experimental and theoretical studies on Li have tested QED up to the 7th power of the fine structure constant. Li_2 has also been of interest to sub-atomic physicists, as it was spectroscopic measurements on ^7Li_2 that determined the spin of ^7Li to be 3/2 in 1931; and Li_2 has been proposed in 2014 as a candidate for the first ``halo nucleonic molecule". The lowest triplet state a(1^3Σ_u^+) is an excellent benchmark system for all newly emerging ab initio techniques because it has only 6e^-, its potential is only 334 cm-1 deep, it avoids harsh complications from spin-orbit coupling, and it is the deepest potential for which all predicted vibrational energy levels have been observed with 0.0001 cm-1 precision. However the current best ab initio potentials do not even yield all vibrational energy spacings correct to within 1 cm-1. This could be because the calculation was only done on a cc-pV5Z basis set, or because the QCISD(T,full) method that the authors used, only considered triple excitations while a full CI calculation should include up to hexuple
Howard, J Coleman; Tschumper, Gregory S
2015-05-12
A series of (H2O)n clusters ranging from the dimer to the hexamer have been characterized with the CCSD(T) and the 2-body:Many-body CCSD(T):MP2 methods near the complete basis set (CBS) limit to generate benchmark-quality optimized structures and harmonic vibrational frequencies for these important systems. Quadruple-ζ correlation-consistent basis sets that augment the O atoms with diffuse functions have been employed in the analytic computation of harmonic vibrational frequencies for the global minima of the dimer, trimer, tetramer, and pentamer as well as the ring, book, cage, and prism isomers of the hexamer. Prior calibration [J. Chem. Phys. 2013, 139, 184113 and J. Chem. Theory Comput. 2014, 10, 5426] suggests that harmonic frequencies computed with this approach will lie within a few cm(-1) of the canonical CCSD(T) CBS limit. These data are used as reference values to gauge the performance of harmonic frequencies obtained with other ab initio methods (e.g., LCCSD(T) and MP2) and water potentials (e.g., TTM3-F and WHBB). This comparison reveals that it is far more challenging to converge harmonic vibrational frequencies for the bound OH stretching modes in these (H2O)n clusters to the CCSD(T) CBS limit than the free OH stretches, the n intramonomer HOH bending modes and even the 6n - 6 intermonomer modes. Deviations associated with the bound OH stretching harmonic frequencies increase rapidly with the size of the cluster for all methods and potentials examined, as do the corresponding frequency shifts relative to the monomer OH stretches.
Dunn, Meghan E; Pokon, Emma K; Shields, George C
2004-03-03
The Gaussian-2, Gaussian-3, complete basis set- (CBS-) QB3, and CBS-APNO methods have been used to calculate Delta H degrees and Delta G degrees values for neutral clusters of water, (H(2)O)(n), where n = 2-6. The structures are similar to those determined from experiment and from previous high-level calculations. The thermodynamic calculations by the G2, G3, and CBS-APNO methods compare well against the estimated MP2(CBS) limit. The cyclic pentamer and hexamer structures release the most heat per hydrogen bond formed of any of the clusters. While the cage and prism forms of the hexamer are the lowest energy structures at very low temperatures, as temperature is increased the cyclic structure is favored. The free energies of cluster formation at different temperatures reveal interesting insights, the most striking being that the cyclic trimer, cyclic tetramer, and cyclic pentamer, like the dimer, should be detectable in the lower troposphere. We predict water dimer concentrations of 9 x 10(14) molecules/cm(3), water trimer concentrations of 2.6 x 10(12) molecules/cm(3), tetramer concentrations of approximately 5.8 x 10(11) molecules/cm(3), and pentamer concentrations of approximately 3.5 x 10(10) molecules/cm(3) in saturated air at 298 K. These results have important implications for understanding the gas-phase chemistry of the lower troposphere.
DEFF Research Database (Denmark)
Faber, Rasmus; Buczek, Aneta; Kupka, Teobald;
2016-01-01
convergence of the vibrational corrections is not monotonic and that very large basis sets are needed before a reasonable extrapolation to the basis set limit can be performed. Furthermore, our results suggest that coupled cluster methods and a decent basis set are required before the error of the electronic......The method and basis set dependence of zero-point vibrational corrections (ZPVC) to NMR shielding constants and anisotropies has been investigated using water as a test system. A systematic comparison has been made using the Hartree-Fock (HF), second-order Møller-Plesset perturbation theory (MP2......), coupled cluster singles and doubles (CCSD), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)) and Kohn-Sham density functional theory (DFT) with the B3LYP exchange-correlation functional methods in combination with the second order vibrational perturbation theory (VPT2...
Petit, Laurence; Maldivi, Pascale; Adamo, Carlo
2005-09-01
The calculation of the absorption spectra of four families of transition-metal complexes (Ni(CO)4, MnO4(-), MF6 (M = Cr, Mo, W) and CpM(CO)2 (M = Rh, Ir)) has been undertaken to unravel the influence of basis sets onto excitation energies, oscillator strengths, and assignments. Three among the most common pseudopotentials, with the corresponding valence basis sets, and two all-electron basis sets have been used for the metal center description in the framework of the time dependent Density Functional Theory (TD-DFT). Our results show that this approach does not particularly depend on the basis set used on the metal atoms. Furthermore, the chosen functional PBE0 provides transitions in good agreement with experiments, and it provides an accuracy of about 0.3 eV, comparable to that of refined post-Hartree-Fock methods.
Duijnen, P.Th. van; Thole, B.Th.; Broer, Ria; Nieuwpoort, W.C.
1980-01-01
Ab initio MO calculations, using both minimal (STO-3G) and extended (Roos-Siegbahn) basis sets are reported for the systems methanethiol-imidazole, methanethiol-imidazole-formaldehyde, and methanethiol-imidazole-formamide, which, together with a point-change representation of a long α-helix, form mo
Buczek, Aneta; Kupka, Teobald; Broda, Małgorzata A; Żyła, Adriana
2016-01-01
In this work, regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit are demonstrated for the first time. The performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with two Pople basis sets (6-311++G** and 6-311++G(3df,2pd)), the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, 6) was tested.The BLYP-calculated harmonic frequencies were found to be markedly closer than the B3LYP-calculated harmonic frequencies to the experimentally derived values, while the calculated anharmonic frequencies consistently underestimated the observed wavenumbers. The different basis set families gave very similar estimated values for the CBS parameters. The anharmonic frequencies calculated with B3LYP/aug-pc-3 were consistently significantly higher than those obtained with the pc-3 basis set; applying the aug-pcseg-n basis set family alleviated this problem. Utilization of B3LYP/aug-pcseg-n basis sets instead of B3LYP/aug-cc-pVXZ, which is computationally less expensive, is suggested for medium-sized molecules. Harmonic BLYP/pc-2 calculations produced fairly accurate ethylene frequencies. Graphical Abstract In this study, the performance of the VPT2 scheme implemented using density functional theory (DFT-BLYP and DFT-B3LYP) in combination with the polarization-consistent basis sets pc-n, aug-pc-n, and pcseg-n (n = 0, 1, 2, 3, 4), and the correlation-consistent basis sets cc-pVXZ and aug-cc-pVXZ (X = D, T, Q, 5, and 6) was tested. For the first time, we demonstrated regular convergence patterns of the structural, harmonic, and VPT2-calculated anharmonic vibrational parameters of ethylene towards the Kohn-Sham complete basis set (KS CBS) limit.
Computational probes into the basis of silver ion chromatography. II. Silver(I)-olefin complexes
Kaneti, J.; Smet, de L.C.P.M.; Boom, R.M.; Zuilhof, H.; Sudhölter, E.J.R.
2002-01-01
Alkene complexes of silver(I) are studied by four computational methodologies: ab initio RHF, MP2, and MP4 computations, and density functional B3LYP computations, with a variety of all-electron and effective core potential basis sets. Methodological studies indicate that MP2/SBK(d) computations can
Directory of Open Access Journals (Sweden)
Claudio Amovilli
2016-02-01
Full Text Available In this work, we present a simple decomposition scheme of the Kohn-Sham optimized orbitals which is able to provide a reduced basis set, made of localized polycentric orbitals, specifically designed for Quantum Monte Carlo. The decomposition follows a standard Density functional theory (DFT calculation and is based on atomic connectivity and shell structure. The new orbitals are used to construct a compact correlated wave function of the Slater–Jastrow form which is optimized at the Variational Monte Carlo level and then used as the trial wave function for a final Diffusion Monte Carlo accurate energy calculation. We are able, in this way, to capture the basic information on the real system brought by the Kohn-Sham orbitals and use it for the calculation of the ground state energy within a strictly variational method. Here, we show test calculations performed on some small selected systems to assess the validity of the proposed approach in a molecular fragmentation, in the calculation of a barrier height of a chemical reaction and in the determination of intermolecular potentials. The final Diffusion Monte Carlo energies are in very good agreement with the best literature data within chemical accuracy.
Wang, Yang; Liu, Qingzhu; Qiu, Ling; Wang, Tengfei; Yuan, Haoliang; Lin, Jianguo; Luo, Shineng
2015-01-01
Three different density functional theory (DFT) methods were employed to study the molecular structures of cis-diamminedichloroplatinum(II) (CDDP) and trans-diamminedichloroplatinum(II) (TDDP). The basis set effect on the structure was also investigated. By comparing the optimized structures with the experimental data, a relatively more accurate method was chosen for further study of the IR spectra and other properties as well as the solvent effect. Nineteen characteristic vibrational bands of the title compounds were assigned and compared with available experimental data. The number of characteristic peaks for the asymmetric stretching and deformation vibrations of N-H can serve as a judgment for the isomer between CDDP and TDDP. Significant solvent effect was observed on the molecular structures and IR spectra. The reduced density gradient analysis was performed to study the intramolecular interactions of CDDP and TDDP, and the nature of changes in the structures caused by the solvent was illustrated. Several descriptors determined from the energies of frontier molecular orbitals (HOMO and LUMO) were applied to describe the chemical reactivity of the title compounds. The molecular electrostatic potential (MESP) surfaces showed that the amino groups were the most favorable sites that nucleophilic reagents tend to attack, and CDDP was easier to be attacked by nucleophilic reagents than TDDP.
Boström, Jonas; Pitoňák, Michal; Aquilante, Francesco; Neogrády, Pavel; Pedersen, Thomas Bondo; Lindh, Roland
2012-06-12
We compute noncovalent intermolecular interaction energies for the S22 test set [Phys. Chem. Chem. Phys.2006, 8, 1985-1993] of molecules at the Møller-Plesset and coupled cluster levels of supermolecular theory using density fitting (DF) to approximate all two-electron integrals. The error due to the DF approximation is analyzed for a range of auxiliary basis sets derived from Cholesky decomposition (CD) in conjunction with correlation consistent and atomic natural orbital valence basis sets. A Cholesky decomposition threshold of 10(-4)Eh for full molecular CD and its one-center approximation (1C-CD) generally yields errors below 0.03 kcal/mol, whereas 10(-3)Eh is sufficient to obtain the same level of accuracy or better with the atomic CD (aCD) and atomic compact CD (acCD) auxiliary basis sets. Comparing to commonly used predefined auxiliary basis sets, we find that while the aCD and acCD sets are larger by a factor of 2-4 with triple-ζ AO basis sets, they provide results 1-2 orders of magnitude more accurate.
Li, Ji-Lai; Mata, Ricardo A; Ryde, Ulf
2013-03-12
The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated. Basis sets of at least triple-ζ quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration toward local CCSD(T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBE0, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results.
Martin, J M L; Martin, Jan M.L.; Sundermann, Andreas
2001-01-01
We propose large-core correlation-consistent pseudopotential basis sets for the heavy p-block elements Ga-Kr and In-Xe. The basis sets are of cc-pVTZ and cc-pVQZ quality, and have been optimized for use with the large-core (valence-electrons only) Stuttgart-Dresden-Bonn relativistic pseudopotentials. Validation calculations on a variety of third-row and fourth-row diatomics suggest them to be comparable in quality to the all-electron cc-pVTZ and cc-pVQZ basis sets for lighter elements. Especially the SDB-cc-pVQZ basis set in conjunction with a core polarization potential (CPP) yields excellent agreement with experiment for compounds of the later heavy p-block elements. For accurate calculations on Ga (and, to a lesser extent, Ge) compounds, explicit treatment of 13 valence electrons appears to be desirable, while it seems inevitable for In compounds. For Ga and Ge, we propose correlation consistent basis sets extended for (3d) correlation. For accurate calculations on organometallic complexes of interest to h...
{\\it Ab initio} nuclear structure - the large sparse matrix eigenvalue problem
Vary, James P; Ng, Esmond; Yang, Chao; Sosonkina, Masha
2009-01-01
The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several {\\it ab initio} methods have now emerged that provide nearly exact solutions for some nuclear properties. The {\\it ab initio} no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds $10^{10}$ and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving t...
Directory of Open Access Journals (Sweden)
M. Shrivastava
2011-07-01
Full Text Available The Weather Research and Forecasting model coupled with chemistry (WRF-Chem is modified to include a volatility basis set (VBS treatment of secondary organic aerosol formation. The VBS approach, coupled with SAPRC-99 gas-phase chemistry mechanism, is used to model gas-particle partitioning and multiple generations of gas-phase oxidation of organic vapors. In addition to the detailed 9-species VBS, a simplified mechanism using 2 volatility species (2-species VBS is developed and tested for similarity to the 9-species VBS in terms of both mass and oxygen-to-carbon ratios of organic aerosols in the atmosphere. WRF-Chem results are evaluated against field measurements of organic aerosols collected during the MILAGRO 2006 campaign in the vicinity of Mexico City. The simplified 2-species mechanism reduces the computational cost by a factor of 2 as compared to 9-species VBS. Both ground site and aircraft measurements suggest that the 9-species and 2-species VBS predictions of total organic aerosol mass as well as individual organic aerosol components including primary, secondary, and biomass burning are comparable in magnitude. In addition, oxygen-to-carbon ratio predictions from both approaches agree within 25 %, providing evidence that the 2-species VBS is well suited to represent the complex evolution of organic aerosols. Model sensitivity to amount of anthropogenic semi-volatile and intermediate volatility (S/IVOC precursor emissions is also examined by doubling the default emissions. Both the emission cases significantly under-predict primary organic aerosols in the city center and along aircraft flight transects. Secondary organic aerosols are predicted reasonably well along flight tracks surrounding the city, but are consistently over-predicted downwind of the city. Also, oxygen-to-carbon ratio predictions are significantly improved compared to prior studies by adding 15 % oxygen mass per generation of oxidation; however, all modeling cases
López Arvizu, Gregorio; Calaminici, Patrizia
2007-05-21
Density functional calculations have been performed for small nickel clusters, Ni(n), Ni(n) (+), and Ni(n)(-) (ntheory approach. Newly developed nickel all-electron basis sets optimized for generalized gradient approximation (GGA) as well as an all-electron basis set optimized for the local density approximation were employed. For both neutral and charged systems, several isomers and different multiplicities were studied in order to determine the lowest energy structures. A vibrational analysis was performed in order to characterize these isomers. Structural parameters, harmonic frequencies, binding energies, ionization potentials, and electron affinities are reported. This work shows that the employed GGA basis sets for the nickel atom are important for the correct prediction of the ground state structures of small nickel clusters and that the structural assignment of these systems can be performed, with a good resolution, over the ionization potential.
Mazziotti, David A
2007-05-14
Two-electron reduced density matrices (2-RDMs) have recently been directly determined from the solution of the anti-Hermitian contracted Schrodinger equation (ACSE) to obtain 95%-100% of the ground-state correlation energy of atoms and molecules, which significantly improves upon the accuracy of the contracted Schrodinger equation (CSE) [D. A. Mazziotti, Phys. Rev. Lett. 97, 143002 (2006)]. Two subsets of the CSE, the ACSE and the contraction of the CSE onto the one-particle space, known as the 1,3-CSE, have two important properties: (i) dependence upon only the 3-RDM and (ii) inclusion of all second-order terms when the 3-RDM is reconstructed as only a first-order functional of the 2-RDM. The error in the 1,3-CSE has an important role as a stopping criterion in solving the ACSE for the 2-RDM. Using a computationally more efficient implementation of the ACSE, the author treats a variety of molecules, including H2O, NH3, HCN, and HO3-, in larger basis sets such as correlation-consistent polarized double- and triple-zeta. The ground-state energy of neon is also calculated in a polarized quadruple-zeta basis set with extrapolation to the complete basis-set limit, and the equilibrium bond length and harmonic frequency of N2 are computed with comparison to experimental values. The author observes that increasing the basis set enhances the ability of the ACSE to capture correlation effects in ground-state energies and properties. In the triple-zeta basis set, for example, the ACSE yields energies and properties that are closer in accuracy to coupled cluster with single, double, and triple excitations than to coupled cluster with single and double excitations. In all basis sets, the computed 2-RDMs very closely satisfy known N-representability conditions.
Reuter, Matthew G; Harrison, Robert J
2014-05-01
The thesis of Brandbyge's comment [J. Chem. Phys. 140, 177103 (2014)] is that our operator decoupling condition is immaterial to transport theories, and it appeals to discussions of nonorthogonal basis sets in transport calculations in its arguments. We maintain that the operator condition is to be preferred over the usual matrix conditions and subsequently detail problems in the existing approaches. From this operator perspective, we conclude that nonorthogonal projectors cannot be used and that the projectors must be selected to satisfy the operator decoupling condition. Because these conclusions pertain to operators, the choice of basis set is not germane.
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Nguyen Thanh Duoc
2015-12-01
Full Text Available The results presented in this paper are the ab initio intermolecular potentials and the second virial coefficient, B2 (T of the dimer Cl2-Cl2. These ab initio potentials were proposed by the quantum chemical calculations at high level of theory CCSD (T with basis sets of Dunning’s valence correlation-consistent aug-cc-pVmZ (m = 2, 3; these results were extrapolated to complete basis set limit aug-cc-pV23Z. The ab initio energies of complete basis set limit aug-cc-pV23Z resulted from the exponential extrapolation were used to construct the 5-site pair potential functions. The second virial coefficients for this dimer were predicted from those with four-dimensional integration. The second virial coefficients were also corrected to first-order quantum effects. The results turn out to be in good agreement with experimental data, if available, or with those from empirical correlation. The quality of ab initio 5-site potentials proved the reliability for prediction of molecular thermodynamic properties.
Al-Saidi, W A; Krakauer, Henry; Zhang, Shiwei
2007-05-21
The authors present phaseless auxiliary-field (AF) quantum Monte Carlo (QMC) calculations of the ground states of some hydrogen-bonded systems. These systems were selected to test and benchmark different aspects of the new phaseless AF QMC method. They include the transition state of H+H(2) near the equilibrium geometry and in the van der Walls limit, as well as the H(2)O, OH, and H(2)O(2) molecules. Most of these systems present significant challenges for traditional independent-particle electronic structure approaches, and many also have exact results available. The phaseless AF QMC method is used either with a plane wave basis with pseudopotentials or with all-electron Gaussian basis sets. For some systems, calculations are done with both to compare and characterize the performance of AF QMC under different basis sets and different Hubbard-Stratonovich decompositions. Excellent results are obtained using as input single Slater determinant wave functions taken from independent-particle calculations. Comparisons of the Gaussian based AF QMC results with exact full configuration interaction show that the errors from controlling the phase problem with the phaseless approximation are small. At the large basis-size limit, the AF QMC results using both types of basis sets are in good agreement with each other and with experimental values.
Convergence from cluster to surface:ab initio calculations of Pd_n clusters
Institute of Scientific and Technical Information of China (English)
徐昕; 王南钦; 吕鑫; 陈明旦; 张乾二
1995-01-01
The"Metallic State Principle"and a way to constitute the metallic basis set are proposed,the latter is a modification of atomic basis set based on the free electron theory in solid state physics.Pd_n dusters have been carefully studied by means of ab initio calculations with atomic and metallic basis sets.Three rules,namely the"Ground State Principle",the"Lowest-Spin State Principle"and the"Metallic StatePrinciple"have been investigated and the calculation results based on these three rules are compared with eachother in terms of metallic configuration of bulk Pd,d-band width,Fermi level,etc.The calculation resultsdemonstrate that the characteristic properties of bulk Pd may be reproduced to some extent even with a smallduster if the"Metallic State Principle"is adopted.
Ab initio and DFT studies on vibrational spectra of some halides of group IIIB elements
Zhang, Yu; Zhao, Jianying; Tang, Guodong; Zhu, Longgen
2005-11-01
The vibrational spectra of some group IIIB elements halides MX 3 and their dimmers, M 2X 6 (M = Sc(III), Y(III), La(III); X = F, Cl, Br, I), have been systematically investigated by ab initio restricted Hartree-Fock (RHF) and density functional B3LYP methods with LanL2DZ and SDD basis sets. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational frequencies, calculated by two methods with different basis sets, are compared to each other. The effect of the methods and the basis sets used on the calculated vibrational frequencies are discussed. Some vibrational frequencies of these complexes are also predicted.
First fully ab initio potential energy surface of methane with a spectroscopic accuracy
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.
Institute of Scientific and Technical Information of China (English)
G(U)M(U)(S), Sedat; (O)ZDO(G)AN, Telhat
2004-01-01
Hartree-Fock-Roothaan (HFR) calculations for ground states of some atoms, i.e. He, Be, Ne, Ar, and Kr have been performed using minimal basis sets of Slater type orbitals (STOs) with integer and noninteger principal quantum numbers (integer n-STOs and noninteger n-STOs). The obtained total energies for these atoms using minimal basis sets of integer n-STOs are in good agreement with those in the previous literature. On the other hand, for the case of minimal basis sets of noninteger n-STOs, although the calculated total energies of these atoms agree well with the results in literature, some striking results have been obtained for atoms Ar and Kr. Our computational results for the energies of atoms Ar and Kr are slightly better than those in literature, by amount of 0.00222 and 0.000054 a.u., respectively. The improvement in the energies of atoms Ar and Kr may result from the efficient calculations of one-center two-electron integrals over noninteger n-STOs. For some atomic ions in their ground state,HFR calculations have been carried out using minimal basis sets of noninteger n-STOs. The obtained total energies for these atomic ions are substantially lower than those available in literature.
DEFF Research Database (Denmark)
Brandbyge, Mads
2014-01-01
In a recent paper Reuter and Harrison [J. Chem. Phys.139, 114104 (2013)] question the widely used mean-field electron transport theories, which employ nonorthogonal localized basis sets. They claim these can violate an “implicit decoupling assumption,” leading to wrong results for the current...
Baesjou, PJ; Driessen, WL; Challa, G; Reedijk, J
1997-01-01
Ab initio unrestricted Hartree-Fock calculations with a 6-31G* basis set were performed on 2, 6-dimethylphenol (DMP or monomer) and 4-(2, 6-dimethylphenoxy)-2, 6-dimethylphenol (dimer) to gain more insight into the mechanism of the copper-catalyzed oxidative phenol coupling reaction. Atomic charges
A highly accurate {\\it ab initio} potential energy surface for methane
Owens, Alec; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2016-01-01
A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art \\textit{ab initio} theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include: core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of $^{12}$CH$_4$ reproduced with a root-mean-square error of $0.70{\\,}$cm$^{-1}$. The computed \\textit{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 e...
Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions
Energy Technology Data Exchange (ETDEWEB)
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.
Whitfield, T. W.; Crain, J.; Martyna, G. J.
2006-03-01
In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.
Ab initio simulations and neutron scattering studies of structure and dynamics in PdH
Totolici, I E
2001-01-01
The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...
Goldey, Matthew; Head-Gordon, Martin
2012-12-06
Second-order Møller-Plesset perturbation theory (MP2) treats electron correlation at low computational cost, but suffers from basis set superposition error (BSSE) and fundamental inaccuracies in long-range contributions. The cost differential between complete basis set (CBS) and small basis MP2 restricts system sizes where BSSE can be removed. Range-separation of MP2 could yield more tractable and/or accurate forms for short- and long-range correlation. Retaining only short-range contributions proves to be effective for MP2 in the small aug-cc-pVDZ (aDZ) basis. Using one range-separation parameter, superior behavior is obtained versus both MP2/aDZ and MP2/CBS for inter- and intramolecular test sets. Attenuation of the long-range helps to cancel both BSSE and intrinsic MP2 errors. Direct scaling of the MP2 correlation energy proves useful as well. The resulting SMP2/aDZ, MP2(erfc, aDZ), and MP2(terfc, aDZ) methods perform far better than MP2/aDZ across systems with hydrogen-bonding, dispersion, and mixed interactions at a fraction of MP2/CBS computational cost.
Hoggan, Philip E
2010-01-01
This paper advocates use of the atomic orbitals which have direct physical interpretation, i.e. Coulomb Sturmians and hydrogen-like orbitals. They are exponential type orbitals (ETOs). Their radial nodes are shown to be essential in obtaining accurate nuclear shielding tensors for NMR work. The present work builds on a 2003 French PhD and many numerical results were published by 2007. The improvements in this paper are noteworthy, the key being the actual basis function choice. Until 2008, their products on different atoms were difficult to manipulate for the evaluation of two-electron integrals. Coulomb resolutions provide an excellent approximation that reduces these integrals to a sum of one-electron overlap-like integral products that each involve orbitals on at most two centers. Such two-center integrals are separable in prolate spheroidal co-ordinates. They are thus readily evaluated. Only these integrals need to be re-evaluated to change basis functions. In this paper, a review of the translation proce...
Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan
2016-04-01
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.
Maschio, Lorenzo; Usvyat, Denis; Schütz, Martin; Civalleri, Bartolomeo
2010-04-07
We have calculated the equilibrium geometry, formation energy, and bulk modulus of two molecular bulk crystals, NH(3) and CO(2), at the periodic post-Hartree-Fock correlated level. The dependence of the results on the basis set has been analyzed, by employing basis sets up to aug-cc-pVQZ quality. In the calculations, we used the periodic local Møller-Plesset second order perturbation theory (LMP2), implemented in the CRYSCOR program. Multipolar expansion techniques, as well as density fitting, are employed in this code to reduce the number of and to factorize the required electron repulsion integrals; as a consequence of that, the computational cost for the correlation part of the calculations is comparable to that of the Hartree-Fock. Auxiliary calculations performed on molecular dimers are also reported to verify the accuracy of the LMP2 approach and of the basis sets used. Furthermore, the effect of spin-component scaling has been investigated for the two crystals. One intention of the present paper is also to lay out and specify the computational setup, which is generally applicable for accurate CRYSCOR calculations on molecular crystals.
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.
Directory of Open Access Journals (Sweden)
Zhenyu Mei
2012-01-01
Full Text Available The ongoing controversy about in what condition should we set the curb parking has few definitive answers because comprehensive research in this area has been lacking. Our goal is to present a set of heuristic urban street speed functions under mixed traffic flow by taking into account impacts of curb parking. Two impacts have been defined to classify and quantify the phenomena of motor vehicles' speed dynamics in terms of curb parking. The first impact is called Space impact, which is caused by the curb parking types. The other one is the Time impact, which results from the driver maneuvering in or out of parking space. In this paper, based on the empirical data collected from six typical urban streets in Nanjing, China, two models have been proposed to describe these phenomena for one-way traffic and two-way traffic, respectively. An intensive experiment has been conducted in order to calibrate and validate these proposed models, by taking into account the complexity of the model parameters. We also provide guidelines in terms of how to cluster and calculate those models' parameters. Results from these models demonstrated promising performance of modeling motor vehicles' speed for mixed traffic flow under the influence of curb parking.
Legler, C R; Brown, N R; Dunbar, R A; Harness, M D; Nguyen, K; Oyewole, O; Collier, W B
2015-06-15
The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.
Accurate calculation of the p Ka of trifluoroacetic acid using high-level ab initio calculations
Namazian, Mansoor; Zakery, Maryam; Noorbala, Mohammad R.; Coote, Michelle L.
2008-01-01
The p Ka value of trifluoroacetic acid has been successfully calculated using high-level ab initio methods such as G3 and CBS-QB3. Solvation energies have been calculated using CPCM continuum model of solvation at the HF and B3-LYP levels of theory with various basis sets. Excellent agreement with experiment (to within 0.4 p Ka units) was obtained using CPCM solvation energies at the B3-LYP/6-31+G(d) level (or larger) in conjunction with CBS-QB3 or G3 gas-phase energies of trifluoroacetic acid and its anion.
Ab initio adiabatic and quasidiabatic potential energy surfaces of H++ CN system
Indian Academy of Sciences (India)
Bhargava Anusuri; Sanjay Kumar
2016-02-01
We present restricted geometry (collinear and perpendicular approaches of proton) ab initio three dimensional potential energy surfaces for H++ CN system. The calculations were performed at the internally contracted multi-reference configuration interaction level of theory using Dunning’s correlation consistent polarized valence triple zeta basis set. Adiabatic and quasidiabatic surfaces have been computed for the ground and the first excited electronic states. Nonadiabatic effects arising from radial coupling have been analyzed in terms of nonadiabatic coupling matrix elements and coupling potentials.
Kashinski, D O; Chase, G M; Nelson, R G; Di Nallo, O E; Scales, A N; VanderLey, D L; Byrd, E F C
2017-03-23
We propose new approximate global multiplicative scaling factors for the DFT calculation of ground state harmonic vibrational frequencies using functionals from the TPSS, M06, and M11 functional families with standard correlation consistent cc-pVxZ and aug-cc-pVxZ (x = D, T, and Q), 6-311G split valence family, Sadlej and Sapporo polarized triple-ζ basis sets. Results for B3LYP, CAM-B3LYP, B3PW91, PBE, and PBE0 functionals with these basis sets are also reported. A total of 99 harmonic frequencies were calculated for 26 gas-phase organic and nonorganic molecules typically found in detonated solid propellant residue. Our proposed approximate multiplicative scaling factors are determined using a least-squares approach comparing the computed harmonic frequencies to experimental counterparts well established in the scientific literature. A comparison of our work to previously published global scaling factors is made to verify method reliability and the applicability of our molecular test set.
Rangel, T.; Caliste, D.; Genovese, L.; Torrent, M.
2016-11-01
We present a Projector Augmented-Wave (PAW) method based on a wavelet basis set. We implemented our wavelet-PAW method as a PAW library in the ABINIT package [http://www.abinit.org] and into BigDFT [http://www.bigdft.org]. We test our implementation in prototypical systems to illustrate the potential usage of our code. By using the wavelet-PAW method, we can simulate charged and special boundary condition systems with frozen-core all-electron precision. Furthermore, our work paves the way to large-scale and potentially order- N simulations within a PAW method.
Indian Academy of Sciences (India)
M Talebian; E Talebian; A Abdi
2012-05-01
We obtained an approximation of the force ﬁeld of -quartz crystal using a new idea of applying density functional theory [J Purton, R Jones, C R A Catlow and M Leslie, Phys. Chem. Minerals 19, 392 (1993)]. Our calculations were based on B3LYP Hamiltonian [A N Lazarev and A P Mirgorodsky, Phys. Chem. Minerals 18, 231 (1991)] in 6−311+G(2d) basis set for H16Si7O6 cluster and included a unit cell of the lattice. The advantage of our method is the increase in the speed of calculations and the better adaption of simulation results with the experimental data.
Rangel, Tonatiuh; Genovese, Luigi; Torrent, Marc
2016-01-01
We present a Projector Augmented-Wave~(PAW) method based on a wavelet basis set. We implemented our wavelet-PAW method as a PAW library in the ABINIT package [http://www.abinit.org] and into BigDFT [http://www.bigdft.org]. We test our implementation in prototypical systems to illustrate the potential usage of our code. By using the wavelet-PAW method, we can simulate charged and special boundary condition systems with frozen-core all-electron precision. Furthermore, our work paves the way to large-scale and potentially order-N simulations within a PAW method.
Hamel, Sébastien; Casida, Mark E.; Salahub, Dennis R.
2001-05-01
The Roothaan-Hartree-Fock (HF) method has been implemented in deMon-DynaRho within the resolution-of-the-identity (RI) auxiliary-function approximation. While previous studies have focused primarily upon the effect of the RI approximation on total energies, very little information has been available regarding the effect of the RI approximation on orbital energies, even though orbital energies play a central role in many theories of ionization and excitation. We fill this gap by testing the accuracy of the RI approximation against non-RI-HF calculations using the same basis sets, for the occupied orbital energies and an equal number of unoccupied orbital energies of five small molecules, namely CO, N2, CH2O, C2H4, and pyridine (in total 102 orbitals). These molecules have well-characterized excited states and so are commonly used to test and validate molecular excitation spectra computations. Of the deMon auxiliary basis sets tested, the best results are obtained with the (44) auxiliary basis sets, yielding orbital energies to within 0.05 eV, which is adequate for analyzing typical low resolution polyatomic molecule ionization and excitation spectra. Interestingly, we find that the error in orbital energies due to the RI approximation does not seem to increase with the number of electrons. The absolute RI error in the orbital energies is also roughly related to their absolute magnitude, being larger for the core orbitals where the magnitude of orbital energy is large and smallest where the molecular orbital energy is smallest. Two further approximations were also considered, namely uniterated ("zero-order") and single-iteration ("first-order") calculations of orbital energies beginning with a local density approximation initial guess. We find that zero- and first-order orbital energies are very similar for occupied but not for unoccupied orbitals, and that the first-order orbital energies are fairly close to the corresponding fully converged values. Typical root
Fábri, Csaba; Szidarovszky, Tamás; Magyarfalvi, Gábor; Tarczay, György
2011-05-12
Scaling factors for Pulay's scaled quantum mechanical (SQM) scheme have been determined for four different widely used DFT functionals (PBE, B3LYP, B3PW91, and M06-2X) and for two basis sets (6-31++G** and aug-cc-pVTZ) by fitting computed results to 347 fundamental experimental vibrational frequencies of 33 molecules. Measurements in the gas phase and in solid argon matrices were used independently in the fitting procedure in order to provide a simple method of estimating matrix shifts. The accuracy of the new scaling factors is demonstrated on test molecules including hydrogen-bonded systems and molecules containing chlorine and sulfur atoms.
Institute of Scientific and Technical Information of China (English)
John C.Gallagher; Michael W.Oppenheimer
2012-01-01
This paper introduces an improved evolvable and adaptive hardware oscillator design capable of supporting adaptation intended to restore control precision in damaged or imperfectly manufactured insect-scale flapping-wing micro air vehicles.It will also present preliminary experimental results demonstrating that previously used basis function sets may have been too large and that significantly improved learning times may be achieved by judiciously culling the oscillator search space.The paper will conclude with a discussion of the application of this adaptive,evolvable oscillator to full vehicle control as well as the consideration of longer term goals and requirements.
Ab initio atomic recombination reaction energetics on model heat shield surfaces
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.
Surface Tension of Ab Initio Liquid Water at the Water-Air Interface
Nagata, Yuki; Bonn, Mischa; Kühne, Thomas D
2016-01-01
We report calculations of the surface tension of the water-air interface using ab initio molecular dynamics (AIMD) simulations. We investigate the simulation cell size dependence of the surface tension of water from force field molecular dynamics (MD) simulations, which show that the calculated surface tension increases with increasing simulation cell size, thereby illustrating that a correction for finite size effects is required for the small system used in the AIMD simulation. The AIMD simulations reveal that the double-{\\xi} basis set overestimates the experimentally measured surface tension due to the Pulay stress, while the triple and quadruple-{\\xi} basis sets give similar results. We further demonstrate that the van der Waals corrections critically affect the surface tension. AIMD simulations without the van der Waals correction substantially underestimate the surface tension, while van der Waals correction with the Grimme's D2 technique results in the value for the surface tension that is too high. T...
Energy Technology Data Exchange (ETDEWEB)
Evarestov, R A; Panin, A I; Bandura, A V; Losev, M V [Department of Quantum Chemistry, St. Petersburg State University, University Prospect 26, Stary Peterghof, St. Petersburg, 198504 (Russian Federation)], E-mail: re1973@re1973.spb.edu
2008-06-01
The results of LCAO DFT calculations of lattice parameters, cohesive energy and bulk modulus of the crystalline uranium nitrides UN, U{sub 2}N{sub 3} and UN{sub 2} are presented and discussed. The LCAO computer codes Gaussian03 and Crystal06 are applied. The calculations are made with the uranium atom relativistic effective small core potential by Stuttgart-Cologne group (60 electrons in the core). The calculations include the U atom basis set optimization. Powell, Hooke-Jeeves, conjugated gradient and Box methods are implemented in the author's optimization package, being external to the codes for molecular and periodic calculations. The basis set optimization in LCAO calculations improves the agreement of the lattice parameter and bulk modulus of UN crystal with the experimental data, the change of the cohesive energy due to the optimization is small. The mixed metallic-covalent chemical bonding is found both in LCAO calculations of UN and U{sub 2}N{sub 3} crystals; UN{sub 2} crystal has the semiconducting nature.
Zen, Andrea; Luo, Ye; Sorella, Sandro; Guidoni, Leonardo
2013-10-08
Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely, the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Through a systematic study, we provide a useful guide to the choice of the wave function, the pseudopotential, and the basis set for QMC calculations. We also introduce a new method for the computation of forces with finite variance on open systems and a new strategy for the definition of the atomic orbitals involved in the Jastrow-Antisymmetrised Geminal power wave function, in order to drastically reduce the number of variational parameters. This scheme significantly improves the efficiency of QMC energy minimization in case of large basis sets.
HN2(2A') electronic manifold. I. A global ab initio study of first two states.
Mota, Vinícius C; Varandas, António J C
2007-10-18
A detailed ab initio multireference configuration interaction calculation with a standard aug-cc-pVTZ basis set is reported for the 1(2)A' and 2(2)A' states of the title system. The aim is to establish the dissociation scheme of all channels, while revealing the 2(2)A'/3(2)A' seam of conical intersections consistent with the crossings in the diatomic fragments. An ab initio mapping of linear NNH and T-shaped and linear NHN loci of conical intersections is also reported, jointly with a discussion of the topological features associated to a newly reported 2(2)A'/3(2)A' crossing seam.
Energy Technology Data Exchange (ETDEWEB)
Borges, P. D., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu; Scolfaro, L., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu [Department of Physics, Texas State University, San Marcos, Texas 78666 (United States)
2014-12-14
The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.
Löptien, U.; Dietze, H.
2014-06-01
The Baltic Sea is a seasonally ice-covered, marginal sea, situated in central northern Europe. It is an essential waterway connecting highly industrialised countries. Because ship traffic is intermittently hindered by sea ice, the local weather services have been monitoring sea ice conditions for decades. In the present study we revisit a historical monitoring data set, covering the winters 1960/1961. This data set, dubbed Data Bank for Baltic Sea Ice and Sea Surface Temperatures (BASIS) ice, is based on hand-drawn maps that were collected and then digitised 1981 in a joint project of the Finnish Institute of Marine Research (today Finish Meteorological Institute (FMI)) and the Swedish Meteorological and Hydrological Institute (SMHI). BASIS ice was designed for storage on punch cards and all ice information is encoded by five digits. This makes the data hard to access. Here we present a post-processed product based on the original five-digit code. Specifically, we convert to standard ice quantities (including information on ice types), which we distribute in the current and free Network Common Data Format (NetCDF). Our post-processed data set will help to assess numerical ice models and provide easy-to-access unique historical reference material for sea ice in the Baltic Sea. In addition we provide statistics showcasing the data quality. The website www.baltic-ocean.org hosts the post-prossed data and the conversion code. The data are also archived at the Data Publisher for Earth & Environmental Science PANGEA (doi:10.1594/PANGEA.832353).
Löptien, U.; Dietze, H.
2014-12-01
The Baltic Sea is a seasonally ice-covered, marginal sea in central northern Europe. It is an essential waterway connecting highly industrialised countries. Because ship traffic is intermittently hindered by sea ice, the local weather services have been monitoring sea ice conditions for decades. In the present study we revisit a historical monitoring data set, covering the winters 1960/1961 to 1978/1979. This data set, dubbed Data Bank for Baltic Sea Ice and Sea Surface Temperatures (BASIS) ice, is based on hand-drawn maps that were collected and then digitised in 1981 in a joint project of the Finnish Institute of Marine Research (today the Finnish Meteorological Institute (FMI)) and the Swedish Meteorological and Hydrological Institute (SMHI). BASIS ice was designed for storage on punch cards and all ice information is encoded by five digits. This makes the data hard to access. Here we present a post-processed product based on the original five-digit code. Specifically, we convert to standard ice quantities (including information on ice types), which we distribute in the current and free Network Common Data Format (NetCDF). Our post-processed data set will help to assess numerical ice models and provide easy-to-access unique historical reference material for sea ice in the Baltic Sea. In addition we provide statistics showcasing the data quality. The website http://www.baltic-ocean.org hosts the post-processed data and the conversion code. The data are also archived at the Data Publisher for Earth & Environmental Science, PANGAEA (doi:10.1594/PANGAEA.832353).
Maltsev, I A; Tupitsyn, I I; Shabaev, V M; Kozhedub, Y S; Plunien, G; Stoehlker, Th
2013-01-01
A new approach for solving the time-dependent two-center Dirac equation is presented. The method is based on using the finite basis set of cubic Hermite splines on a two-dimensional lattice. The Dirac equation is treated in rotating reference frame. The collision of U92+ (as a projectile) and U91+ (as a target) is considered at energy E_lab=6 MeV/u. The charge transfer probabilities are calculated for different values of the impact parameter. The obtained results are compared with the previous calculations [I. I. Tupitsyn et al., Phys. Rev. A 82, 042701 (2010)], where a method based on atomic-like Dirac-Sturm orbitals was employed. This work can provide a new tool for investigation of quantum electrodynamics effects in heavy-ion collisions near the supercritical regime.
Schmitz, G. J.
2016-01-01
The importance of microstructure simulation in integrated computational materials engineering settings in relation to the added value provided for macroscopic process simulation, as well as the contribution this kind of simulation can make in predicting material properties, are discussed. The roles of microstructure simulation in integrating scales ranging from component/process scales down to atomistic scales, and also in integrating experimental and virtual worlds, are highlighted. The hierarchical data format (HDF5) as a basis for enhancing the interoperability of the heterogeneous range of simulation tools and experimental datasets in the area of computational materials engineering is discussed. Several ongoing developments indicate that HDF5 might evolve into a de facto standard for digital microstructure representation of all length scales.
Thorvaldsen, Andreas J.; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia
2008-12-01
A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.
Thorvaldsen, Andreas J; Ruud, Kenneth; Kristensen, Kasper; Jørgensen, Poul; Coriani, Sonia
2008-12-07
A general method is presented for the calculation of molecular properties to arbitrary order at the Kohn-Sham density functional level of theory. The quasienergy and Lagrangian formalisms are combined to derive response functions and their residues by straightforward differentiation of the quasienergy derivative Lagrangian using the elements of the density matrix in the atomic orbital representation as variational parameters. Response functions and response equations are expressed in the atomic orbital basis, allowing recent advances in the field of linear-scaling methodology to be used. Time-dependent and static perturbations are treated on an equal footing, and atomic basis sets that depend on the applied frequency-dependent perturbations may be used, e.g., frequency-dependent London atomic orbitals. The 2n+1 rule may be applied if computationally favorable, but alternative formulations using higher-order perturbed density matrices are also derived. These may be advantageous in order to minimize the number of response equations that needs to be solved, for instance, when one of the perturbations has many components, as is the case for the first-order geometrical derivative of the hyperpolarizability.
Highly scalable Ab initio genomic motif identification
Marchand, Benoit
2011-01-01
We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.
Kalemos, Apostolos; Prosmiti, Rita
2014-09-14
We present for the first time a coherent ab initio study of 39 states of valence, Rydberg, and ion-pair character of the diatomic interhalogen ICl species through large scale multireference variational methods including spin-orbit effects coupled with quantitative basis sets. Various avoided crossings are responsible for a non-adiabatic behaviour creating a wonderful vista for its theoretical description. Our molecular constants are compared with all available experimental data with the aim to assist experimentalists especially in the high energy regime of up to ~95,000 cm(-1).
Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A
2008-12-07
This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.
Sanz-Vicario, José Luis; Pérez-Torres, Jhon Fredy; Moreno-Polo, Germán
2017-08-01
We compute the entanglement between the electronic and vibrational motions in the simplest molecular system, the hydrogen molecular ion, considering the molecule as a bipartite system, electron and vibrational motion. For that purpose we compute an accurate total non-Born-Oppenheimer wave function in terms of a huge expansion using nonorthogonal B-spline basis sets that expand separately the electronic and nuclear wave functions. According to the Schmidt decomposition theorem for bipartite systems, widely used in quantum-information theory, it is possible to find a much shorter but equivalent expansion in terms of the natural orbitals or Schmidt bases for the electronic and nuclear half spaces. Here we extend the Schmidt decomposition theorem to the case in which nonorthogonal bases are used to span the partitioned Hilbert spaces. This extension is first illustrated with two simple coupled systems, the former without an exact solution and the latter exactly solvable. In these model systems of distinguishable coupled particles it is shown that the entanglement content does not increase monotonically with the excitation energy, but only within the manifold of states that belong to an existing excitation mode, if any. In the hydrogen molecular ion the entanglement content for each non-Born-Oppenheimer vibronic state is quantified through the von Neumann and linear entropies and we show that entanglement serves as a witness to distinguish vibronic states related to different Born-Oppenheimer molecular energy curves or electronic excitation modes.
Goerigk, Lars; Collyer, Charles A; Reimers, Jeffrey R
2014-12-18
We demonstrate the importance of properly accounting for London dispersion and basis-set-superposition error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serve as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but also, for the first time, demonstrate how London dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme's recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density functional theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also the convergence behavior is much better. In particular, we show that the BP86/6-31G* approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. Using HF-D3-gCP is technically straightforward, and we therefore encourage users of quantum-chemical methods to adopt this approach in future applications.
Energy Technology Data Exchange (ETDEWEB)
Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M.; Vargas, Rubicelia; Garza, Jorge, E-mail: jgo@xanum.uam.mx [Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa C. P. 09340, México D. F., México (Mexico)
2015-07-21
In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.
Richard, Ryan M.
2016-01-05
© 2016 American Chemical Society. In designing organic materials for electronics applications, particularly for organic photovoltaics (OPV), the ionization potential (IP) of the donor and the electron affinity (EA) of the acceptor play key roles. This makes OPV design an appealing application for computational chemistry since IPs and EAs are readily calculable from most electronic structure methods. Unfortunately reliable, high-accuracy wave function methods, such as coupled cluster theory with single, double, and perturbative triples [CCSD(T)] in the complete basis set (CBS) limit are too expensive for routine applications to this problem for any but the smallest of systems. One solution is to calibrate approximate, less computationally expensive methods against a database of high-accuracy IP/EA values; however, to our knowledge, no such database exists for systems related to OPV design. The present work is the first of a multipart study whose overarching goal is to determine which computational methods can be used to reliably compute IPs and EAs of electron acceptors. This part introduces a database of 24 known organic electron acceptors and provides high-accuracy vertical IP and EA values expected to be within ±0.03 eV of the true non-relativistic, vertical CCSD(T)/CBS limit. Convergence of IP and EA values toward the CBS limit is studied systematically for the Hartree-Fock, MP2 correlation, and beyond-MP2 coupled cluster contributions to the focal point estimates.
Third-Order Incremental Dual-Basis Set Zero-Buffer Approach for Large High-Spin Open-Shell Systems.
Zhang, Jun; Dolg, Michael
2015-03-10
The third-order incremental dual-basis set zero-buffer approach (inc3-db-B0) is an efficient, accurate, and black-box quantum chemical method for obtaining correlation energies of large systems, and it has been successfully applied to many real chemical problems. In this work, we extend this approach to high-spin open-shell systems. In the open-shell approach, we will first decompose the occupied orbitals of a system into several domains by a K-means clustering algorithm. The essential part is that we preserve the active (singly occupied) orbitals in all the calculations of the domain correlation energies. The duplicated contributions of the active orbitals to the correlation energy are subtracted from the incremental expansion. All techniques of truncating the virtual space such as the B0 approximation can be applied. This open-shell inc3-db-B0 approach is combined with the CCSD and CCSD(T) methods and applied to the computations of a singlet-triplet gap and an electron detachment process. Our approach exhibits an accuracy better than 0.6 kcal/mol or 0.3 eV compared with the standard implementation, while it saves a large amount of the computational time and can be efficiently parallelized.
Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M; Vargas, Rubicelia; Garza, Jorge
2015-07-21
In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.
Directory of Open Access Journals (Sweden)
D. Simpson
2012-02-01
Full Text Available A new organic aerosol (OA module has been implemented into the EMEP chemical transport model. Four different volatility basis set (VBS schemes have been tested in long-term simulations for Europe, covering the six years 2002–2007. Different assumptions regarding partitioning of primary OA (POA and aging of POA and secondary OA (SOA, have been explored. Model results are compared to filter measurements, AMS-data and source-apportionment studies, as well as to other model studies. The present study indicates that many different sources contribute significantly to OA in Europe. Fossil POA and oxidised POA, biogenic and anthropogenic SOA (BSOA and ASOA, residential burning of biomass fuels and wildfire emissions may all contribute more than 10% each over substantial parts of Europe. Simple VBS based OA models can give reasonably good results for summer OA but more observational studies are needed to constrain the VBS parameterisations and to help improve emission inventories. The volatility distribution of primary emissions is an important issue for further work. This study shows smaller contributions from BSOA to OA in Europe than earlier work, but relatively greater ASOA. BVOC emissions are highly uncertain and need further validation. We can not reproduce winter levels of OA in Europe, and there are many indications that the present emission inventories substantially underestimate emissions from residential wood burning in large parts of Europe.
Rodriguez-Bautista, Mariano; Díaz-García, Cecilia; Navarrete-López, Alejandra M.; Vargas, Rubicelia; Garza, Jorge
2015-07-01
In this report, we use a new basis set for Hartree-Fock calculations related to many-electron atoms confined by soft walls. One- and two-electron integrals were programmed in a code based in parallel programming techniques. The results obtained with this proposal for hydrogen and helium atoms were contrasted with other proposals to study just one and two electron confined atoms, where we have reproduced or improved the results previously reported. Usually, an atom enclosed by hard walls has been used as a model to study confinement effects on orbital energies, the main conclusion reached by this model is that orbital energies always go up when the confinement radius is reduced. However, such an observation is not necessarily valid for atoms confined by penetrable walls. The main reason behind this result is that for atoms with large polarizability, like beryllium or potassium, external orbitals are delocalized when the confinement is imposed and consequently, the internal orbitals behave as if they were in an ionized atom. Naturally, the shell structure of these atoms is modified drastically when they are confined. The delocalization was an argument proposed for atoms confined by hard walls, but it was never verified. In this work, the confinement imposed by soft walls allows to analyze the delocalization concept in many-electron atoms.
Monari, Antonio; Bendazzoli, Gian Luigi; Evangelisti, Stefano; Angeli, Celestino; Ben Amor, Nadia; Borini, Stefano; Maynau, Daniel; Rossi, Elda
2007-03-01
The dispersion interactions of the Ne2 dimer were studied using both the long-range perturbative and supramolecular approaches: for the long-range approach, full CI or string-truncated CI methods were used, while for the supramolecular treatments, the energy curves were computed by using configuration interaction with single and double excitation (CISD), coupled cluster with single and double excitation, and coupled-cluster with single and double (and perturbative) triple excitations. From the interatomic potential-energy curves obtained by the supramolecular approach, the C6 and C8 dispersion coefficients were computed via an interpolation scheme, and they were compared with the corresponding values obtained within the long-range perturbative treatment. We found that the lack of size consistency of the CISD approach makes this method completely useless to compute dispersion coefficients even when the effect of the basis-set superposition error on the dimer curves is considered. The largest full-CI space we were able to use contains more than 1 billion symmetry-adapted Slater determinants, and it is, to our knowledge, the largest calculation of second-order properties ever done at the full-CI level so far. Finally, a new data format and libraries (Q5Cost) have been used in order to interface different codes used in the present study.
Jeloaica, Leonard
2006-01-01
This work attempts to bring a new light on the understanding of some critical aspects of the physicochemical processes that control Alumina, Zirconia and Hafnia ALD growth, yet not sufficiently understood. These materials are addressed as potentially best candidates to replace gate dielectric SiO2 in the near future electronic applications. Most accurate ab initio correlated methods, like couple-cluster CCSD(T) and CISD(T), with different basis sets functions, as well as the available experim...
Martin, Jan M. L.
The quartic force fields of a number of small polyatomic molecules (specifically, rm H _2O, NH_2, NH_3, CH_4, BH_3, BeH_2, H_2CO, N_2O, CO_2, CS_2, OCS, H_2S, FNO, ClNO, and H_2CS) have been computed ab initio using large basis sets and augmented coupled cluster methods. It has been established throughout that harmonic and fundamental frequencies can consistently be reproduced to within about 10 cm^{ -1} of experimental using spdf basis sets, except in such inherently problematic cases as the umbrella motion in NH_3; such problems are solved by recomputing the harmonic frequencies with an spdf g basis set. Coupled cluster frequencies using small basis sets of spd quality agree surprisingly well with experiment (mean absolute error of 26 cm^ {-1}), but bond distances are generally seriously overestimated. Using spdf basis sets, they are consistently overestimated by 0.002 and 0.006-7 A for single and multiple bonds, respectively; for spdf g basis sets this drops to 0.001 and 0.003-4 A, respectively. Geometries and harmonic frequencies for highly polar fluorine compounds such as HF and FNO are qualitatively wrong unless special anion functions are added to the fluorine basis set. Anharmonicity, rovibrational coupling, and centrifugal distortion constants are consistently predicted well; the anharmonic portions of the computed force fields are probably more reliable than their experimental counterparts in many cases. Remaining errors in the computed geometries and harmonic frequencies are shown to be almost entirely due to a combination of core correlation and residual deficiencies in the electron correlation treatment. A 3-term correction for remaining basis set incompleteness to computed total atomization energies is proposed by the author, and is shown to result in mean absolute errors of as little as 0.5 kcal/mol for spdf g basis sets. Example applications on rm HCO^+, HOC^+, B_2C, BCN, and BNC testify to the predictive power of the methods used in this work.
Ab Initio Potential Energy Surface and Internal Torsional-Wagging States of Hydroxylamine
Makarewicz; Kreglewski; Senent
1997-11-01
The two-dimensional potential energy surface describing the interaction of the large-amplitude torsional and wagging motions in hydroxylamine has been determined from ab initio calculations. This surface has been sampled by a large set of grid points from a two-dimensional configuration space spanned by the torsional and wagging coordinates. At each grid point, the geometry optimization has been performed using the second-order Moller-Plesset perturbation theory with the basis set 6-311 + G(2d, p). At the optimized geometry, the single-point calculation of the electronic energy has been carried out using a larger basis set 6-311 + G(3df, 2p). This method was verified to yield the results comparable to those obtained by a direct optimization of the geometry with the basis set 6-311 + G(3df, 2p) which had been used by A. Chung-Phillips and K. A. Jebber (1995. J. Chem. Phys. 102, 7080-7087) to calculate the energies of only three points in the potential energy surface of hydroxylamine. The trans and cis local minima have been found on the determined potential energy surface. The localization features of the torsional-wagging states have been studied by solving the two-dimensional Schrodinger equation for the coupled torsional and wagging motions. Copyright 1997 Academic Press. Copyright 1997Academic Press
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A. P. Tsimpidi
2010-01-01
Full Text Available New primary and secondary organic aerosol modules have been added to PMCAMx, a three dimensional chemical transport model (CTM, for use with the SAPRC99 chemistry mechanism based on recent smog chamber studies. The new modelling framework is based on the volatility basis-set approach: both primary and secondary organic components are assumed to be semivolatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. This new framework with the use of the new volatility basis parameters for low-NO_{x} and high-NO_{x} conditions tends to predict 4–6 times higher anthropogenic SOA concentrations than those predicted with the older generation of models. The resulting PMCAMx-2008 was applied in Mexico City Metropolitan Area (MCMA for approximately a week during April 2003 during a period of very low regional biomass burning impact. The emission inventory, which uses as a starting point the MCMA 2004 official inventory, is modified and the primary organic aerosol (POA emissions are distributed by volatility based on dilution experiments. The predicted organic aerosol (OA concentrations peak in the center of Mexico City, reaching values above 40 μg m^{−3}. The model predictions are compared with the results of the Positive Matrix Factorization (PMF analysis of the Aerosol Mass Spectrometry (AMS observations. The model reproduces both Hydrocarbon-like Organic Aerosol (HOA and Oxygenated Organic Aerosol (OOA concentrations and diurnal profiles. The small OA underprediction during the rush-hour periods and overprediction in the afternoon suggest potential improvements to the description of fresh primary organic emissions and the formation of the oxygenated organic aerosols, respectively, although they may also be due to errors in the simulation of dispersion and vertical mixing. However, the AMS OOA data are not specific enough to prove that the model reproduces the organic aerosol
Tyuterev, Vladimir G.; Kochanov, Roman V.; Tashkun, Sergey A.
2017-02-01
Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16O3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to Δ V = 6. A particular challenge was a correct description of the B-type bands (even Δ V3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μ m range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm-1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.
Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A
2017-02-14
Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of (16)O3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μm range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm(-1) is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
1989-01-01
Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.
Tsimpidi, A. P.; Karydis, V. A.; Pandis, S. N.; Zavala, M.; Lei, W.; Molina, L. T.
2007-12-01
Anthropogenic air pollution is an increasingly serious problem for public health, agriculture, and global climate. Organic material (OM) contributes ~ 20-50% to the total fine aerosol mass at continental mid-latitudes. Although OM accounts for a large fraction of PM2.5 concentration worldwide, the contributions of primary and secondary organic aerosol have been difficult to quantify. In this study, new primary and secondary organic aerosol modules were added to PMCAMx, a three dimensional chemical transport model (Gaydos et al., 2007), for use with the SAPRC99 chemistry mechanism (Carter, 2000; ENVIRON, 2006) based on recent smog chamber studies (Robinson et al., 2007). The new modeling framework is based on the volatility basis-set approach (Lane et al., 2007): both primary and secondary organic components are assumed to be semivolatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. The emission inventory, which uses as starting point the MCMA 2004 official inventory (CAM, 2006), is modified and the primary organic aerosol (POA) emissions are distributed by volatility based on dilution experiments (Robinson et al., 2007). Sensitivity tests where POA is considered as nonvolatile and POA and SOA as chemically reactive are also described. In all cases PMCAMx is applied in the Mexico City Metropolitan Area during March 2006. The modeling domain covers a 180x180x6 km region in the MCMA with 3x3 km grid resolution. The model predictions are compared with Aerodyne's Aerosol Mass Spectrometry (AMS) observations from the MILAGRO Campaign. References Robinson, A. L.; Donahue, N. M.; Shrivastava, M. K.; Weitkamp, E. A.; Sage, A. M.; Grieshop, A. P.; Lane, T. E.; Pandis, S. N.; Pierce, J. R., 2007. Rethinking organic aerosols: semivolatile emissions and photochemical aging. Science 315, 1259-1262. Gaydos, T. M.; Pinder, R. W.; Koo, B.; Fahey, K. M.; Pandis, S. N., 2007. Development and application of a three- dimensional aerosol
Yoshida, Tatsusada; Hayashi, Takahisa; Mashima, Akira; Chuman, Hiroshi
2015-10-01
One of the most challenging problems in computer-aided drug discovery is the accurate prediction of the binding energy between a ligand and a protein. For accurate estimation of net binding energy ΔEbind in the framework of the Hartree-Fock (HF) theory, it is necessary to estimate two additional energy terms; the dispersion interaction energy (Edisp) and the basis set superposition error (BSSE). We previously reported a simple and efficient dispersion correction, Edisp, to the Hartree-Fock theory (HF-Dtq). In the present study, an approximation procedure for estimating BSSE proposed by Kruse and Grimme, a geometrical counterpoise correction (gCP), was incorporated into HF-Dtq (HF-Dtq-gCP). The relative weights of the Edisp (Dtq) and BSSE (gCP) terms were determined to reproduce ΔEbind calculated with CCSD(T)/CBS or /aug-cc-pVTZ (HF-Dtq-gCP (scaled)). The performance of HF-Dtq-gCP (scaled) was compared with that of B3LYP-D3(BJ)-bCP (dispersion corrected B3LYP with the Boys and Bernadi counterpoise correction (bCP)), by taking ΔEbind (CCSD(T)-bCP) of small non-covalent complexes as 'a golden standard'. As a critical test, HF-Dtq-gCP (scaled)/6-31G(d) and B3LYP-D3(BJ)-bCP/6-31G(d) were applied to the complex model for HIV-1 protease and its potent inhibitor, KNI-10033. The present results demonstrate that HF-Dtq-gCP (scaled) is a useful and powerful remedy for accurately and promptly predicting ΔEbind between a ligand and a protein, albeit it is a simple correction procedure.
Ramírez-Solís, A; Zicovich-Wilson, C M; Hernández-Lamoneda, R; Ochoa-Calle, A J
2017-01-25
The question of the non-magnetic (NM) vs. antiferromagnetic (AF) nature of the ε phase of solid oxygen is a matter of great interest and continuing debate. In particular, it has been proposed that the ε phase is actually composed of two phases, a low-pressure AF ε1 phase and a higher pressure NM ε0 phase [Crespo et al., Proc. Natl. Acad. Sci. U. S. A., 2014, 111, 10427]. We address this problem through periodic spin-restricted and spin-polarized Kohn-Sham density functional theory calculations at pressures from 10 to 50 GPa using calibrated GGA and hybrid exchange-correlation functionals with Gaussian atomic basis sets. The two possible configurations for the antiferromagnetic (AF1 and AF2) coupling of the 0 ≤ S ≤ 1 O2 molecules in the (O2)4 unit cell were studied. Full enthalpy-driven geometry optimizations of the (O2)4 unit cells were done to study the pressure evolution of the enthalpy difference between the non-magnetic and both antiferromagnetic structures. We also address the evolution of structural parameters and the spin-per-molecule vs. pressure. We find that the spin-less solution becomes more stable than both AF structures above 50 GPa and, crucially, the spin-less solution yields lattice parameters in much better agreement with experimental data at all pressures than the AF structures. The optimized AF2 broken-symmetry structures lead to large errors of the a and b lattice parameters when compared with experiments. The results for the NM model are in much better agreement with the experimental data than those found for both AF models and are consistent with a completely non-magnetic (O2)4 unit cell for the low-pressure regime of the ε phase.
Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH
Energy Technology Data Exchange (ETDEWEB)
Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy; Crawford, T Daniel; Windus, Theresa L.; Hase, William L.
2006-09-20
Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.
Hellmann, Robert; Jäger, Benjamin; Bich, Eckard
2017-07-01
A new ab initio interatomic potential energy curve for two ground-state xenon atoms is presented. It is based on supermolecular calculations at the coupled-cluster level with single, double, and perturbative triple excitations [CCSD(T)] employing basis sets up to sextuple-zeta quality, which were developed as part of this work. In addition, corrections were determined for higher coupled-cluster levels up to CCSDTQ as well as for scalar and spin-orbit relativistic effects at the CCSD(T) level. A physically motivated analytical function was fitted to the calculated interaction energies and used to compute the vibrational spectrum of the dimer, the second virial coefficient, and the dilute gas transport properties. The agreement with the best available experimental data for the investigated properties is excellent; the new potential function is superior not only to previous ab initio potentials but also to the most popular empirical ones.
Emergence of rotational bands in ab initio no-core configuration interaction calculations
Caprio, M A; Vary, J P; Smith, R
2015-01-01
Rotational bands have been observed to emerge in ab initio no-core configuration interaction (NCCI) calculations for p-shell nuclei, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. We investigate the ab initio emergence of nuclear rotation in the Be isotopes, focusing on 9Be for illustration, and make use of basis extrapolation methods to obtain ab initio predictions of rotational band parameters for comparison with experiment. We find robust signatures for rotational motion, which reproduce both qualitative and quantitative features of the experimentally observed bands.
An ab initio quantum chemical investigation of the structure and stability of ozone-water complexes
Energy Technology Data Exchange (ETDEWEB)
Kumar, Pradeep [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Sathyamurthy, N., E-mail: nsath@iitk.ac.in [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli 140306 (India)
2013-03-29
Highlights: ► Eclipse geometry most stable for the 1:1 ozone-water complex. ► Cyclic structure most stable for the 1:2 complex. ► Shift in the vertical electronic excitation energy of ozone due to hydration. - Abstract: Ab initio quantum chemical calculations have been carried out to investigate the structure and stability of 1:1 and 1:2 ozone-water complexes. All the geometries have been optimized at the CCSD level of theory using aug-cc-pVDZ and aug-cc-pVTZ basis sets. The importance of correlation-consistent basis sets in deciding the nature of critical points on these complexes is emphasized. An analysis based on the dipole moment of the complexes and the charge distribution on atoms follows. The effect of ozone molecule on the structure and properties of water dimer is also investigated. Values of the vertical electronic excitation energy and the corresponding transition dipole moment have been calculated for the ozone-water complexes using the multi-reference-configuration-interaction method and the aug-cc-pVTZ basis set. The calculated shift in vibrational frequencies due to complex formation is compared with the earlier reported experimental and theoretical values.
Spin-orbit decomposition of ab initio wavefunctions
Johnson, Calvin W
2014-01-01
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, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulting wavefunctions 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 fifty years and six orders of magnitude in basis dimensions. I suggest $L$-$S$ may be a useful tool for analyzing \\textit{ab initio} wavefunctions of light nuclei, for example in the case of rotational bands.
Spin-orbit decomposition of ab initio nuclear wave functions
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.
Baranowska-Łączkowska, Angelika; Bartkowiak, Wojciech; Góra, Robert W; Pawłowski, Filip; Zaleśny, Robert
2013-04-05
Static longitudinal electric dipole (hyper)polarizabilities are calculated for six medium-sized π-conjugated organic molecules using recently developed LPol-n basis set family to assess their performance. Dunning's correlation-consistent basis sets of triple-ζ quality combined with MP2 method and supported by CCSD(T)/aug-cc-pVDZ results are used to obtain the reference values of analyzed properties. The same reference is used to analyze (hyper)polarizabilities predicted by selected exchange-correlation functionals, particularly those asymptotically corrected.
Directory of Open Access Journals (Sweden)
Prasad Yedlapalli
2010-01-01
Full Text Available Structure II clathrate hydrates of pure hydrogen and binary hydrates of THF+H2 are studied using ab initio calculations to determine the stable occupancies of small cavities. Ab initio calculations are carried out for a double cavity consisting of one dodecahedron (small cavity and one hexakaidecahedron (large cavity. These two cavities are attached to each other as in sII hydrates to form a double cavity. One or two H2 molecules are placed in the small cavity and one THF (or 4H2 molecules molecule is placed in the large cavity. We have determined the binding energies of the double cavities at the MP2 level using various basis sets (3-21G, 3-21G(2p, 3-21++G(2p, 6-31G, 6-31G(2p, and 6-31++G(2p. Different basis sets yield different stable occupancies of the small cavity. The results from the highest basis set (6-31++G(2p with zero point energy corrections indicate that the single occupancy is slightly more favorable than the double occupancy in both the cases of pure H2 hydrates and THF + H2 double hydrates.
Kalugina, Yulia N; Lokshtanov, Sergei E; Cherepanov, Victor N; Vigasin, Andrey A
2016-02-07
We present new three-dimensional potential energy surface (PES) and dipole moment surfaces (DMSs) for the CH4-Ar van der Waals system. Ab initio calculations of the PES and DMS were carried out using the closed-shell single- and double-excitation coupled cluster approach with non-iterative perturbative treatment of triple excitations. The augmented correlation-consistent aug-cc-pVXZ (X = D,T,Q) basis sets were employed, and the energies obtained were then extrapolated to the complete basis set limit. The dipole moment surface was obtained using aug-cc-pVTZ basis set augmented with mid-bond functions for better description of exchange interactions. The second mixed virial coefficient was calculated and compared to available experimental data. The equilibrium constant for true dimer formation was calculated using classical partition function based on the knowledge of ab initio PES. Temperature variations of the zeroth spectral moment of the rototranslational collision-induced band as well as its true dimer constituent were traced with the use of the Boltzmann-weighted squared induced dipole properly integrated over respective phase space domains. Height profiles for N2-N2, N2-H2, CH4-N2, (CH4)2, and CH4-Ar true bound dimers in Titan's atmosphere were calculated with the use of reliable ab initio PESs.
Study of Nuclear Clustering from an Ab Initio Perspective
Kravvaris, Konstantinos; Volya, Alexander
2017-08-01
We put forward a new ab initio approach that seamlessly bridges the structure, clustering, and reactions aspects of the nuclear quantum many-body problem. The configuration interaction technique combined with the resonating group method based on a harmonic oscillator basis allows us to treat the reaction and multiclustering dynamics in a translationally invariant way and preserve the Pauli principle. Our presentation includes studies of Be,108 and an exploration of 3 α clustering in 12C.
Ab initio calculation of tight-binding parameters
Energy Technology Data Exchange (ETDEWEB)
McMahan, A.K.; Klepeis, J.E.
1997-12-01
We calculate ab initio values of tight-binding parameters for the f- electron metal Ce and various phases of Si, from local-density functional one-electron Hamiltonian and overlap matrix elements. Our approach allows us to unambiguously test the validity of the common minimal basis and two-center approximations as well as to determine the degree of transferability of both nonorthogonal and orthogonal hopping parameters in the cases considered.
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.
Thermodynamic assessment of the Ho–Te system supported by ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Ghamri, H.; Belgacem-Bouzida, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Djaballah, Y., E-mail: ydjaballah@yahoo.fr [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Hidoussi, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria)
2013-03-05
Highlights: ► We calculated enthalpies of formation of the HoTe and Ho{sub 2}Te{sub 5} compounds by using ab initio method. ► We modeled the Gibbs energy of the HoTe intermediate phase for the first time. ► The thermodynamic parameters of the all phases existing in the system were determined. ► The complete phase diagram of the system (Ho–Te) is calculated. -- Abstract: The phase diagram of the Ho–Te binary system has been assessed by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data of the phase equilibria and enthalpies of formation from ab initio electronic-structure calculations within the framework of density-functional theory. Reasonable models were constructed for all the phases of the system. The liquid phase was described as the substitutional solution model with excess energy expressed by Redlich–Kister polynomial. The compounds Ho{sub 2}Te{sub 5} and HoTe{sub 3} were expressed as stoichiometric phases. The (HoTe) phase was modeled by two-sublattices; (Ho,Va){sub 1}(Te){sub 1}. A consistent set of thermodynamic parameters has been derived, and calculated phase diagram was compared with the experimental data. A good agreement between the calculated results and experimental data was obtained.
Duffy, Daniel J.; Quenneville, Jason; Baumbaugh, T. M.; Kitchener, S. A.; McCormick, R. K.; Dormady, C. N.; Croce, T. A.; Navabi, A.; Stidham, Howard D.; Hsu, Shaw L.; Guirgis, Gamil A.; Deng, Shiping; Durig, James R.
2004-02-01
Ab initio calculations are reported for three of four possible conformers of 1,3-dichloropropane. The fourth conformer, with C s symmetry, has a predicted enthalpy difference of more than 1500 cm -1 from the most stable conformer from each calculation regardless of the basis set used, so there is little chance of observing it. Thus, there is no evidence in the infrared or Raman spectrum of the presence of a fourth conformer. The order of stability given by the ab initio calculations is C 2(GG)>C 1(AG)>C 2v(AA)>C s(GG'), where A indicates the anti form for one of the CH 2Cl groups and G indicates the gauche conformation for the other CH 2Cl group relative to the plane of the carbon atoms. Almost every band observed can be confidently assigned to one or another of the conformers. Many observed bands proved to be of a composite nature, with several nearly coincident vibrations of different conformers contributing to the band contour. Nonetheless, a complete assignment of fundamentals is possible for the most stable C 2 conformer, and 5 of the fundamentals of the C 2v conformer and 13 those of the C 1 conformer can be confidently assigned.
Operator evolution for ab initio nuclear theory
Schuster, Micah D; Johnson, Calvin W; Jurgenson, Eric D; Navratil, Petr
2014-01-01
The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally-invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square-radius and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range and find at short ranges an increased contribution from such ind...
Molecular orbital ab initio and density functional theoretical study on reaction between PH2 and NO
Institute of Scientific and Technical Information of China (English)
HU; Zhengfa(胡正发); WANG; Zhenya(王振亚); LI; Haiyang(李海洋); ZHOU; Shikang(周士康)
2002-01-01
The theoretical study of reaction between PH2 and NO on the ground state potential energy surface is reported by using molecular orbital ab initio calculation and density function theory (DFT). Equilibrium structural parameters, harmonic vibrational frequencies, total energies and zero point energies of all species during reaction are computed by HF, MP2 (full) and B3LYP theory levels with the medium basis set 6-31G*. Theoretical results indicate that intermediate IM1(H2PNO) is firstly formed by overcoming a small energy barrier TS1, and then two four-membered ring transient states TS2 and TS5, with energy barriers 103.3 and 102.6 kJ/mol respectively,then H-migration and isomerization are completed and the products PN and H2O are formed. The reaction is exothermic one with -189.6 k J/mol released.
Makhov, Dmitry V; Saita, Kenichiro; Martinez, Todd J; Shalashilin, Dmitrii V
2015-02-07
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 isotropic 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.
A-dependence of the Spectra of the F Isotopes from ab initio Calculations
Barrett, Bruce R.; Dikmen, Erdal; Maris, Pieter; Vary, James P.; Shirokov, Andrey M.
2016-03-01
Using a succession of Okubo-Lee-Suzuki transformations within the No Core Shell Model (NCSM) formalism, we derive an ab initio, non-perturbative procedure for calculating the input for standard shell-model (SSM) calculations within one major shell. We have used this approach for calculating the spectra of the F isotopes from A=18 to A=25, so as to study the A-dependence of the results. In particular, we are interested in seeing if the theoretical input is weak enough, so that a single set of two-body effective interactions can be used for all of the F isotopes investigated. We will present results from SSM calculations based on input obtained with the JISP16 nucleon-nucleon interaction in an initial 4 ℏΩ NCSM basis space. This work supported in part by TUBITAK-BIDEB, the US DOE, the US NSF, NERSC, and the Russian Ministry of Education and Science.
Non-adiabatic collisions in H+ + O2 system: An initio study
Indian Academy of Sciences (India)
A Saieswari; Sanjay Kumar
2007-09-01
An ab initio study on the low-lying potential energy surfaces of H+ + O2 system for different orientations () of H+ have been undertaken employing the multi-reference configuration interaction (MRCI) method and Dunning's -VTZ basis set to examine their role in influencing the collision dynamics. Nonadiabatic interactions have been analysed for the 2 × 2 case in two dimensions for = 0°, 45° and 90°, and the corresponding diabatic potential energy surfaces have been obtained using the diabatic wavefunctions and their CI coefficients. The characteristics of the collision dynamics have been analysed in terms of vibrational coupling matrix elements for both inelastic and charge transfer processes in the restricted geometries. The strengths of coupling matrix elements reflect the vibrational excitation patterns observed in the state-to-state beam experiments.
Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide
Energy Technology Data Exchange (ETDEWEB)
Crusius, Johann-Philipp, E-mail: johann-philipp.crusius@uni-rostock.de; Hassel, Egon [Lehrstuhl für Technische Thermodynamik, Universität Rostock, 18059 Rostock (Germany); Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard [Institut für Chemie, Universität Rostock, 18059 Rostock (Germany)
2015-06-28
We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N{sub 2}O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N{sub 2}O–N{sub 2}O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N{sub 2}O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.
Ab initio modeling of radiation damage in MgF{sub 2} crystals
Energy Technology Data Exchange (ETDEWEB)
Abuova, F.U. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Kotomin, E.A., E-mail: kotomin@latnet.lv [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia); Lisitsyn, V.M. [Tomsk Polytechnical University, Tomsk 634003 (Russian Federation); Akilbekov, A.T. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Piskunov, S. [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia)
2014-05-01
MgF{sub 2} with a rutile structure is important radiation-resistant material with numerous applications due to its transparency from vacuum ultraviolet to infrared range of photon energies. We present and discuss the results of calculations for basic radiation defects in this crystal. The study is based on the large scale ab initio DFT calculations using hybrid B3PW exchange–correlation functional and atomic basis set. We analyzed the electronic structure, atomic displacements, charge density distribution as well as defect formation energies using large supercells. We compared properties of close and well separated F−H (Frenkel) defect pairs as well as individual defects. We simulated also formation and energetic preference of inert F{sub 2} interstitial molecules as sinks of mobile interstitial fluorine atoms which is relevant for material radiation stability. We discussed also diffusion of the primary electronic defects—F centers.
Ab initio MO calculation of force constants and dipole derivatives for formamide
Sugawara, Yoko; Hamada, Yoshiaki; Hirakawa, Akiko Y.; Tsuboi, Masamichi; Kato, Shigeki; Morokuma, Keiji
1980-08-01
Ab initio SCF MO calculations have been carried out for the equilibrium geometry, vibrational frequencies, force constants, dipole moment and its derivatives of formamide. The energy gradient method was employed and the 4-31G basis set was used. For in-plane vibrations: (1) Calculated normal frequencies were 10-20% greater than the observed fundamental frequencies. (2) Isotope shifts (- d0, - d1, - d2, and - d3 species) were well reproduced. (3) The calculated dipole moment derivatives showed a good correspondence with the infrared intensity pattern. (4) The NH 2 rocking—OCN bending cross term, which should be zero in the Urey—Bradley force field, came out to be as large as -0.18 mdyne A. For out-of-plane vibrations, especially for the NH 2 wagging, it was found to be essential to include polarization functions for N, C and O atoms.
An ab initio potential energy surface and vibrational energy levels of HXeBr
Institute of Scientific and Technical Information of China (English)
Zheng Guo Huang; En Cui Yang; Dai Qian Xie
2008-01-01
A three-dimensional global potential energy surface for the electronic ground state of HXeBr molecule is constructed from morethan 4200 ab initio points. These points are generated using an internally contracted multi-reference configuration interactionmethod with the Davidson correction (icMRCI + Q) and large basis sets. The stabilities and dissociation barriers are identified fromthe potential energy surfaces. The three-body dissociation channel is found to be the dominate dissociation channel for HXeBr.Based on the obtained potentials, low-lying vibrational energy levels of HXeBr calculated using the Lanczos algorithm is found tobe in good agreement with the available experimental band origins.2008 Zheng Guo Huang. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.
Tight-binding model for carbon nanotubes from ab initio calculations.
Correa, J D; da Silva, Antônio J R; Pacheco, M
2010-07-14
Here we present a parametrized tight-binding (TB) model to calculate the band structure of single-wall carbon nanotubes (SWNTs). On the basis of ab initio calculations we fit the band structure of nanotubes of different radii with results obtained with an orthogonal TB model to third neighbors, which includes the effects of orbital hybridization by means of a reduced set of parameters. The functional form for the dependence of these parameters on the radius of the tubes can be used to interpolate appropriate TB parameters for different SWNTs and to study the effects of curvature on their electronic properties. Additionally, we have shown that the model gives an appropriate description of the optical spectra of SWNTs, which can be useful for a proper assignation of SWNTs' specific chirality from optical absorption experiments.
An Ab-Initio Calculation of Raman Spectra of Binary Sodium Silicates
Institute of Scientific and Technical Information of China (English)
尤静林; 蒋国昌; 侯怀宇; 陈辉; 吴永全; 徐匡迪
2004-01-01
Raman spectra of binary sodium silicates are calculated by self-consistent field (SCF) molecular orbital ab initio calculation of the quantum chemical method with several poly silicon-oxygen tetrahedral model clusters when both the basis sets of 6-31 G and 6-31 G(d) are applied. The symmetric stretching vibrational frequency of non-bridging oxygen in a high frequency range and its Raman optical activity and scattering cross section are deduced and analysed. The correlation between this vibrational Raman shift and its microscopic environment of the silicon-oxygen tetrahedron is found based on interior stress of configuration, which depends on the connecting topology of adjacent silicon-oxygen tetrahedra (SiOT). A newly established empirical stress index of tetrahedron is introduced to elucidate the above relationship.
Directory of Open Access Journals (Sweden)
Karl-Heinz Böhm
2014-04-01
Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.
Quiney, HM; Glushkov, VN; Wilson, S
2002-01-01
Using basis sets of distributed s-type Gaussian functions with positions and exponents optimized so as to support Hartree-Fock total energies with an accuracy approaching the sub-muHartree level, Dirac-Hartree-Fock-Coulomb calculations are reported for the ground states of the H-2, LiH, and BH molec
Abe, Akihiro; Furuya, Hidemine; Ichimura, Noriko; Kawauchi, Susumu
1997-02-01
The gas-phase NMR analysis of 5-methoxy-1,3-dioxanes was carried out. The conformational energies estimated from the observed coupling constant data were compared with the results of ab initio MO calculations using d95 + (2df,p) basis set at the MP2 level. While the energy difference between the axial-out and equatorial-out forms was in a reasonable agreement, the 1,5 interaction energy between the methoxy methyl and the ring oxygens was not in accord.
Ab initio study of the low-lying electronic states of the CaO molecule
Energy Technology Data Exchange (ETDEWEB)
Khalil, Hossain; Brites, Vincent; Quere, Frederic Le [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France); Leonard, Celine, E-mail: celine.leonard@univ-paris-est.fr [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France)
2011-07-28
Graphical abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1{Pi}}, b{sup 3}{Sigma}{sup +} and A{sup 1}{Sigma}{sup +}, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: {yields} The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. {yields} Large active space, core-valence correlation and configuration interaction are required. {yields} The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. {yields} These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1}{Pi}, b{sup 3}{Sigma}{sup +} and A{sup 1
Ab initio molecular dynamics using hybrid density functionals
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.
Thermochemical data for CVD modeling from ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Ho, P. [Sandia National Labs., Albuquerque, NM (United States); Melius, C.F. [Sandia National Labs., Livermore, CA (United States)
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.
Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha
2011-11-01
Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.
Gao, Hongwei; Wei, Xiujuan; Liu, Xuting; Yan, Tingxia
2010-03-25
Comparisons of various density functional theory (DFT) methods at different basis sets in predicting the molecular structures and (13)C NMR spectra for [Pt(en)(CBDCA-O, O')], an analogue of the antitumor drug carboplatin, are reported. DFT methods including B3LYP, B3PW91, mPW1PW91, PBE1PBE, BPV86, PBEPBE, and LSDA are examined. Different basis sets including LANL2DZ, SDD, LANL2MB, CEP-4G, CEP-31G, and CEP-121G are also considered. It is remarkable that the LSDA/SDD level is clearly superior to all of the remaining density functional methods in predicting the structure of [Pt(en)(CBDCA-O, O')]. The results also indicate that the B3LYP/SDD level is the best to predict (13)C NMR spectra for [Pt(en)(CBDCA-O, O')] among all DFT methods.
Efficient computation of GW energy level corrections for molecules described in a plane wave basis
Rousseau, Bruno; Laflamme Janssen, Jonathan; Côté, Michel
2013-03-01
An efficient computational approach is presented to compute the ionisation energy and quasiparticle band gap at the level of the GW approximation when the Hilbert space is described in terms of plane waves. The method relies on ab initio calculations as a starting point. Then, the use of the Sternheimer equation eliminates slowly convergent sums on conduction states. Further, the Lanczos method is used to efficiently extract the most important eigenstates of the dielectric operator. This approach avoids the explicit computation of matrix elements of the dielectric operator in the plane wave basis, a crippling bottleneck of the brute force approach. The method is initially applied to organic molecules of current interest in the field of organic photovoltaics. Given the completeness of the plane wave basis, systematic convergence studies can be conducted. Furthermore, the method can readily be extended to describe polymers, which are also of interest for photovoltaic applications, but remain a significant computational challenge for methods based on localized basis sets.
Sherrill, C David; Takatani, Tait; Hohenstein, Edward G
2009-09-24
Large, correlation-consistent basis sets have been used to very closely approximate the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] complete basis set potential energy curves of several prototype nonbonded complexes, the sandwich, T-shaped, and parallel-displaced benzene dimers, the methane-benzene complex, the H2S-benzene complex, and the methane dimer. These benchmark potential energy curves are used to assess the performance of several methods for nonbonded interactions, including various spin-component-scaled second-order perturbation theory (SCS-MP2) methods, the spin-component-scaled coupled-cluster singles and doubles method (SCS-CCSD), density functional theory empirically corrected for dispersion (DFT-D), and the meta-generalized-gradient approximation functionals M05-2X and M06-2X. These approaches generally provide good results for the test set, with the SCS methods being somewhat more robust. M05-2X underbinds for the test cases considered, while the performances of DFT-D and M06-2X are similar. Density fitting, dual basis, and local correlation approximations all introduce only small errors in the interaction energies but can speed up the computations significantly, particulary when used in combination.
Directory of Open Access Journals (Sweden)
Johanna eEgetemeir
2011-09-01
Full Text Available Many everyday life situations require two or more individuals to execute actions together. Assessing brain activation during naturalistic tasks to uncover relevant processes underlying such real-life joint action situations has remained a methodological challenge. In the present study, we introduce a novel joint action paradigm that enables the assessment of brain activation during real-life joint action tasks using functional near-infrared spectroscopy (fNIRS. We monitored brain activation of participants who coordinated complex actions with a partner sitting opposite them. Participants performed table-setting tasks, either alone (solo action or in cooperation with a partner (joint action, or they observed the partner performing the task (action observation. Comparing joint action and solo action revealed stronger activation (higher [oxy-Hb]-concentration during joint action in a number of areas. Among these were areas in the inferior parietal lobule (IPL that additionally showed an overlap of activation during action observation and solo action. Areas with such a close link between action observation and action execution have been associated with action simulation processes. The magnitude of activation in these IPL areas also varied according to joint action type and its respective demand on action simulation. The results validate fNIRS as an imaging technique for exploring the functional correlates of interindividual action coordination in real-life settings and suggest that coordinating actions in real-life situations requires simulating the actions of the partner.
Tsuzuki, Seiji; Honda, Kazumasa; Uchimaru, Tadafumi; Mikami, Masuhiro
2006-03-01
The MP2 (the second-order Møller-Plesset calculation) and CCSD(T) (coupled cluster calculation with single and double substitutions with noniterative triple excitations) interaction energies of all-trans n-alkane dimers were calculated using Dunning's [J. Chem. Phys. 90, 1007 (1989)] correlation consistent basis sets. The estimated MP2 interaction energies of methane, ethane, and propane dimers at the basis set limit [EMP2(limit)] by the method of Helgaker et al. [J. Chem. Phys. 106, 9639 (1997)] from the MP2/aug-cc-pVXZ (X =D and T) level interaction energies are very close to those estimated from the MP2/aug-cc-pVXZ (X =T and Q) level interaction energies. The estimated EMP2(limit) values of n-butane to n-heptane dimers from the MP2/cc-pVXZ (X =D and T) level interaction energies are very close to those from the MP2/aug-cc-pVXZ (X =D and T) ones. The EMP2(limit) values estimated by Feller's [J. Chem. Phys. 96, 6104 (1992)] method from the MP2/cc-pVXZ (X =D, T, and Q) level interaction energies are close to those estimated by the method of Helgaker et al. from the MP2/cc-pVXZ (X =T and Q) ones. The estimated EMP2(limit) values by the method of Helgaker et al. using the aug-cc-pVXZ (X =D and T) are close to these values. The estimated EMP2(limit) of the methane, ethane, propane, n-butane, n-pentane, n-hexane, n-heptane, n-octane, n-nonane, and n-decane dimers by the method of Helgaker et al. are -0.48, -1.35, -2.08, -2.97, -3.92, -4.91, -5.96, -6.68, -7.75, and -8.75kcal /mol, respectively. Effects of electron correlation beyond MP2 are not large. The estimated CCSD(T) interaction energies of the methane, ethane, propane, and n-butane dimers at the basis set limit by the method of Helgaker et al. (-0.41, -1.22, -1.87, and -2.74kcal/mol, respectively) from the CCSD(T )/cc-pVXZ (X =D and T) level interaction energies are close to the EMP2(limit) obtained using the same basis sets. The estimated EMP2(limit) values of the ten dimers were fitted to the form m0+m1X (X
Spin-orbit decomposition of ab initio wavefunctions
Johnson, Calvin W.
2014-01-01
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, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulti...
Reduced dimensionality spin-orbit dynamics of CH3 + HCl ⇌ CH4 + Cl on ab initio surfaces.
Remmert, Sarah M; Banks, Simon T; Harvey, Jeremy N; Orr-Ewing, Andrew J; Clary, David C
2011-05-28
A reduced dimensionality quantum scattering method is extended to the study of spin-orbit nonadiabatic transitions in the CH(3) + HCl ⇌ CH(4) + Cl((2)P(J)) reaction. Three two-dimensional potential energy surfaces are developed by fitting a 29 parameter double-Morse function to CCSD(T)/IB//MP2/cc-pV(T+d)Z-dk ab initio data; interaction between surfaces is described by geometry-dependent spin-orbit coupling functions fit to MCSCF/cc-pV(T+d)Z-dk ab initio data. Spectator modes are treated adiabatically via inclusion of curvilinear projected frequencies. The total scattering wave function is expanded in a vibronic basis set and close-coupled equations are solved via R-matrix propagation. Ground state thermal rate constants for forward and reverse reactions agree well with experiment. Multi-surface reaction probabilities, integral cross sections, and initial-state selected branching ratios all highlight the importance of vibrational energy in mediating nonadiabatic transition. Electronically excited state dynamics are seen to play a small but significant role as consistent with experimental conclusions.
Gao, Wei; Feng, Huajie; Xuan, Xiaopeng; Chen, Liuping
2012-10-01
An assessment study is presented about energy decomposition analysis (EDA) in combination with DFT including revised dispersion correction (DFT-D3) with Slater-type orbital (STO) basis set. There has been little knowledge about the performance of the EDA + DFT-D3 concerning STOs. In this assessment such an approach was applied to calculate noncovalent interaction energies and their corresponding components. Complexes in S22 set were used to evaluate the performance of EDA in conjunction with four representative types of GGA-functionals of DFT-D3 (BP86-D3, BLYP-D3, PBE-D3 and SSB-D3) with three STO basis sets ranging in complexity from DZP, TZ2P to QZ4P. The results showed that the approach of EDA + BLYP-D3/TZ2P has a better performance not only in terms of calculating noncovalent interaction energy quantitatively but also in analyzing corresponding energy components qualitatively. This approach (EDA + BLYP-D3/TZ2P) was thus applied further to two representative large-system complexes including porphine dimers and fullerene aggregates to gain a better insight into binding characteristics.
Rogers, J. D.; Hillman, J. J.
1982-01-01
Ab initio infrared intensities and dipole moment derivatives expressed in atomic polar tensor form are calculated using the 4-31 and 6-31G(double asterisk) basis sets for the isoelectronic HCN, HNC, CO, HCO(+), and HOC(+) series of molecules. The calculated atomic polar tensors are analyzed in terms of the charge-charge flux-overlap model, which is found to be useful in explaining some of the trends observed in the dipole moment derivatives for this series of molecules. A detailed examination of the dipole moment derivatives for the structural isomers indicates some of the ways in which experimental atomic polar tensors for one isomer should be modified to predict infrared intensities for the other isomer. The absolute intensities calculated for the HCO(+) and HOC(+) ions are believed to be accurate to within a factor of 2 and thus should be useful in astrophysical applications.
Kaur, Rajwant
2016-01-01
Rate coefficient for state-to-state rotational transitions in H+ collision with CS has been obtained using accurate quantum dynamical close-coupling calculations to interpret microwave astronomical observations. Accurate three dimensional ab initio potential energy surfaces have been computed for the ground state and low-lying excited states of H+ - CS system using internally contracted MRCI method and aug-cc-pVQZ basis sets. Rotational excitation and deexcitation integral cross sections are computed at low and ultra low collision energies, respectively. Resonances have been observed at very low energies typically below 50 cm-1. Among all the transitions, Deltaj=+1 and Deltaj=-1 are found to be predominant for excitation and deexcitation, respectively. Deexcitation cross section in the ultracold region is found to obey Wigner's threshold law. The magnitude of state-to-state excitation rate obtained is maximum for j'=1 in the temperature range 2-240 K while minimum for deexcitation in ultracold region. The rot...
Phonon spectra of elpasolites Cs2NaRF6 (R=Y,Yb): Ab initio calculations
Chernyshev, Vladimir; Petrov, Vladislav; Nikiforov, Anatoliy; Zakiryanov, Dmitriy
2015-12-01
The influence of hydrostatic pressure on structure and dynamics of a crystal lattice of elpasolites Cs2NaYbF6 and Cs2NaYF6 (S.G. 225) within ab initio approach is investigated. Frequencies and irreducible representations (irreps) of phonon modes are determined. Elastic constants are calculated. The calculations are carried out within MO LCAO approach using DFT method with hybrid functionalities of B3LYP and PBE0 in CRYSTAL09 periodic code. For the description of rare earth ion the pseudopotential replacing internal orbitals including 4f orbitals was used. External 5s and 5p orbitals defining chemical bond were described by valence basis sets.
Phonon spectra of elpasolites Cs{sub 2}NaRF{sub 6} (R=Y,Yb): Ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Chernyshev, Vladimir, E-mail: Vladimir.Chernyshev@urfu.ru; Petrov, Vladislav; Nikiforov, Anatoliy; Zakiryanov, Dmitriy [Ural Federal University, Ekaterinburg (Russian Federation)
2015-12-07
The influence of hydrostatic pressure on structure and dynamics of a crystal lattice of elpasolites Cs{sub 2}NaYbF{sub 6} and Cs{sub 2}NaYF{sub 6} (S.G. 225) within ab initio approach is investigated. Frequencies and irreducible representations (irreps) of phonon modes are determined. Elastic constants are calculated. The calculations are carried out within MO LCAO approach using DFT method with hybrid functionalities of B3LYP and PBE0 in CRYSTAL09 periodic code. For the description of rare earth ion the pseudopotential replacing internal orbitals including 4f orbitals was used. External 5s and 5p orbitals defining chemical bond were described by valence basis sets.
Ab initio study of the diatomic fluorides FeF, CoF, NiF, and CuF.
Koukounas, Constantine; Mavridis, Aristides
2008-11-06
The late-3d transition-metal diatomic fluorides MF = FeF, CoF, NiF, and CuF have been studied using variational multireference (MRCI) and coupled-cluster [RCCSD(T)] methods, combined with large to very large basis sets. We examined a total of 35 (2S+1)|Lambda| states, constructing as well 29 full potential energy curves through the MRCI method. All examined states are ionic, diabatically correlating to M(+)+F(-)((1)S). Notwithstanding the "eccentric" character of the 3d transition metals and the difficulties to accurately be described with all-electron ab initio methods, our results are, in general, in very good agreement with available experimental numbers.
Shayesteh, Alireza; Alavi, S. Fatemeh; Rahman, Moloud; Gharib-Nezhad, Ehsan
2017-01-01
Ab initio potential energy curves have been calculated for the X2Σ+, A2Π, B2Σ+, 12Δ, E2Π and D2Σ+ states of CaH using the multi-reference configuration interaction method with large active space and basis sets. Transition dipole moments were calculated at Ca-H distances from 2.0 a0 to 14.0 a0, and excited state lifetimes were obtained. Our theoretical transition dipole moments can be combined with the available experimental data on the X2Σ+, A2Π and B2Σ+ states to calculate Einstein A coefficients for all rovibronic transitions of CaH appearing in solar and stellar spectra.
Smeyers; Villa; Senent
1998-10-01
The infrared band structure for the methyl torsion and amine hydrogen symmetric wagging in methylamine is calculated by ab initio procedures. The influence of the amine hydrogen symmetric bending on the wagging spectrum is considered explicitly. For this purpose, the potential energy surfaces and kinetic parameters were determined at the RHF/MP2 level with the 6-311G++(3df, 3dp) basis set. The numerical results were fitted to symmetry adapted functional forms. The Schrödinger equations for the nuclear motions were solved by expanding the solutions into products of trigonometric functions. The band frequencies and intensities were calculated from the energy levels, the vibrational functions, and the electric dipole moment variations. The calculated spectra were compared with the available experimental data. It was found that the torsional splittings and frequencies are relatively well reproduced, whereas the wagging and bending frequencies are slightly too high. Copyright 1998 Academic Press.
Spassova, Milena; Enchev, Venelin
2004-03-01
An ab initio HF and MP2 study of the static (hyper)polarizabilities of 2,4-substituted imidazoles and thiazoles is presented. The comparison of the two types of five-membered heterocycles suggests, that the exocyclic heteroatoms have much more influence upon the calculated hyperpolarizabilities, than the ring heteroatoms. It has been found, that adding diffuse functions to the 6-31G** basis set and inclusion of the electron correlation result in drastic changes in the second hyperpolarizability. The changes are more pronounced for the structures with larger number of sulfur atoms. A HF/6-31G** investigation of a push-pull system, in which thiorhodanine has been chosen as acceptor fragment shows an enhancement of the molecular polarizabilities with respect to the corresponding typical donor-acceptor NH 2/NO 2 polyene.
An ab initio potential energy surface and vibrational states of MgH2(1(1)A').
Li, Hui; Xie, Daiqian; Guo, Hua
2004-09-01
A three-dimensional global potential energy surface for the ground electronic state of MgH(2) is constructed from more than 3000 ab initio points calculated using the internally contracted multireference configuration interaction method with the Davidson correction at the complete basis set limit. Low-lying vibrational energy levels of MgH(2) and MgD(2) are calculated using the Lanczos algorithm, and found to be in good agreement with known experimental band origins. The majority of the vibrational energy levels up to 8000 cm(-1) are assigned with normal mode quantum numbers. However, our results indicate a gradual transition from a normal mode regime for the stretching vibrations at low energies to a local mode regime near 7400 cm(-1), as evidenced by a decreasing energy gap between the (n(1),0,0) and (n(1)-1,0,1) vibrational states and bifurcation of the corresponding wave functions.
Energy Technology Data Exchange (ETDEWEB)
Pham Van, Tat [Faculty of Science and Technology, Hoa Sen University (Viet Nam); Deiters, Ulrich K. [Institute of Physical Chemistry, University of Cologne, Luxemburger Str. 116, D-50939 Köln (Germany)
2015-08-18
Highlights: • We construct the angular orientations of dimers H{sub 2}−H{sub 2} and H{sub 2}−O{sub 2}. • We calculate the ab initio intermolecular interaction energies for all built orientations. • Extrapolating the interaction energies to the complete basis set limit aug-cc-pV23Z. • We develop two 5-site ab initio intermolecular potentials of dimers H{sub 2}−H{sub 2}, H{sub 2}−O{sub 2}. • Calculating the virial coefficients of dimer H{sub 2}−H{sub 2} and H{sub 2}−O{sub 2}. - Abstract: The intermolecular interaction potentials of the dimers H{sub 2}−H{sub 2} and H{sub 2}−O{sub 2} were calculated from quantum mechanics, using coupled-cluster theory CCSD(T) and correlation-consistent basis sets aug-cc-pVmZ (m = 2, 3); the results were extrapolated to the basis set limit aug-cc-pV23Z. The interaction energies were corrected for the basis set superposition error with the counterpoise scheme. For comparison also Møller–Plesset perturbation theory (at levels 2–4) with the basis sets aug-cc-pVTZ were considered, but the results proved inferior. The quantum mechanical results were used to construct analytical pair potential functions. From these functions the second virial coefficients of hydrogen and the cross virial coefficients of the hydrogen–oxygen system were obtained by integration; in both cases corrections for quantum effects were included. The results agree well with experimental data, if available, or with empirical correlations.
The keto-enol equilibrium in substituted acetaldehydes: focal-point analysis and ab initio limit
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).
Energy Technology Data Exchange (ETDEWEB)
Harris, Travis V.; Morokuma, Keiji, E-mail: morokuma@fukui.kyoto-u.ac.jp [Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103 (Japan); Kurashige, Yuki; Yanai, Takeshi [Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585 (Japan)
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.
Orlando, Roberto; Lacivita, Valentina; Bast, Radovan; Ruud, Kenneth
2010-06-01
The computational scheme for the evaluation of the second-order electric susceptibility tensor in periodic systems, recently implemented in the CRYSTAL code within the coupled perturbed Hartree-Fock (HF) scheme, has been extended to local-density, gradient-corrected, and hybrid density functionals (coupled-perturbed Kohn-Sham) and applied to a set of cubic and hexagonal semiconductors. The method is based on the use of local basis sets and analytical calculation of derivatives. The high-frequency dielectric tensor (ɛ∞) and second-harmonic generation susceptibility (d) have been calculated with hybrid functionals (PBE0 and B3LYP) and the HF approximation. Results are compared with the values of ɛ∞ and d obtained from previous plane-wave local density approximation or generalized gradient approximation calculations and from experiment. The agreement is in general good, although comparison with experiment is affected by a certain degree of uncertainty implicit in the experimental techniques.
Orlando, Roberto; Lacivita, Valentina; Bast, Radovan; Ruud, Kenneth
2010-06-28
The computational scheme for the evaluation of the second-order electric susceptibility tensor in periodic systems, recently implemented in the CRYSTAL code within the coupled perturbed Hartree-Fock (HF) scheme, has been extended to local-density, gradient-corrected, and hybrid density functionals (coupled-perturbed Kohn-Sham) and applied to a set of cubic and hexagonal semiconductors. The method is based on the use of local basis sets and analytical calculation of derivatives. The high-frequency dielectric tensor (epsilon(infinity)) and second-harmonic generation susceptibility (d) have been calculated with hybrid functionals (PBE0 and B3LYP) and the HF approximation. Results are compared with the values of epsilon(infinity) and d obtained from previous plane-wave local density approximation or generalized gradient approximation calculations and from experiment. The agreement is in general good, although comparison with experiment is affected by a certain degree of uncertainty implicit in the experimental techniques.
An ab initio study on single electron transfer between ClO2 and phenol
Institute of Scientific and Technical Information of China (English)
崔崇威; 黄君礼
2004-01-01
The SET mechanism between chlorine dioxide (ClO2 ) and phenol was studied by using ab initio method at 4-31G* level. Geometries of the reactants, intermediate and products of the reaction were optimized and the single point energy calculations of the species were performed. The relative structure data of the reactants, intermediate and products are given. The SET mechanism between ClO2 and phenol was confirmed by ab initio calculations. The reaction is exothermic about 200. 88 k J/mol.
Explicitly correlated atomic orbital basis second order Møller-Plesset theory.
Hollman, David S; Wilke, Jeremiah J; Schaefer, Henry F
2013-02-14
The scope of problems treatable by ab initio wavefunction methods has expanded greatly through the application of local approximations. In particular, atomic orbital (AO) based wavefunction methods have emerged as powerful techniques for exploiting sparsity and have been applied to biomolecules as large as 1707 atoms [S. A. Maurer, D. S. Lambrecht, D. Flaig, and C. Ochsenfeld, J. Chem. Phys. 136, 144107 (2012)]. Correlated wavefunction methods, however, converge notoriously slowly to the basis set limit and, excepting the use of large basis sets, will suffer from a severe basis set incompleteness error (BSIE). The use of larger basis sets is prohibitively expensive for AO basis methods since, for example, second-order Møller-Plesset perturbation theory (MP2) scales linearly with the number of atoms, but still scales as O(N(5)) in the number of functions per atom. Explicitly correlated F12 methods have been shown to drastically reduce BSIE for even modestly sized basis sets. In this work, we therefore explore an atomic orbital based formulation of explicitly correlated MP2-F12 theory. We present working equations for the new method, which produce results identical to the widely used molecular orbital (MO) version of MP2-F12 without resorting to a delocalized MO basis. We conclude with a discussion of several possible approaches to a priori screening of contraction terms in our method and the prospects for a linear scaling implementation of AO-MP2-F12. The discussion includes concrete examples involving noble gas dimers and linear alkane chains.
Maschio, L.; Ferrabone, M.; Meyer, A.; Garza, J.; Dovesi, R.
2011-01-01
The performance of five different density functionals (LDA, PBE, PBESOL, B3LYP and PBE0) in describing the infrared spectrum of a crystalline periodic system with a large unit cell (spessartine, 80 atoms in the primitive cell) is studied by using the periodic ab initio CRYSTAL09 code and an all electron basis set. The transverse (TO) and longitudinal (LO) optical branches of the 17 IR active modes are evaluated together with the oscillator strengths and the high frequency dielectric tensor ɛ∞ . These ingredients permit to compute the dielectric function ɛ (ν) , and then the reflectance spectrum R (ν) , which is compared with experiment.
Energy Technology Data Exchange (ETDEWEB)
Keegan, Ronan M. [STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Bibby, Jaclyn; Thomas, Jens [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Xu, Dong [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037 (United States); Zhang, Yang [University of Michigan, Ann Arbor, MI 48109 (United States); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom); STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom)
2015-02-01
Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.
Ab initio potential energy surface and bound states for the Kr-OCS complex.
Feng, Eryin; Sun, Chunyan; Yu, Chunhua; Shao, Xi; Huang, Wuying
2011-09-28
The first ab initio potential energy surface of the Kr-OCS complex is developed using the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)]. The mixed basis sets, aug-cc-pVTZ for the O, C, and S atom, and aug-cc-pVQZ-PP for the Kr atom, with an additional (3s3p2d1f) set of midbond functions are used. A potential model is represented by an analytical function whose parameters are fitted numerically to the single point energies computed at 228 configurations. The potential has a T-shaped global minimum and a local linear minimum. The global minimum occurs at R = 7.146 a(0), θ = 105.0° with energy of -270.73 cm(-1). Bound state energies up to J = 9 are calculated for three isotopomers (82)Kr-OCS, (84)Kr-OCS, and (86)Kr-OCS. Analysis of the vibrational wavefunctions and energies suggests the complex can exist in two isomeric forms: T-shaped and quasi-linear. The calculated transition frequencies and spectroscopic constants of the three isotopomers are in good agreement with the experimental values.
Chung, Daniel J H
2016-01-01
We reformulate gauge theories in analogy with the vierbein formalism of general relativity. More specifically, we reformulate gauge theories such that their gauge dynamical degrees of freedom are local fields that transform linearly under the dual representation of the charged matter field. These local fields, which naively have the interpretation of non-local operators similar to Wilson lines, satisfy constraint equations. A set of basis tensor fields are used to solve these constraint equations, and their field theory is constructed. A new local symmetry in terms of the basis tensor fields is used to make this field theory local and maintain a Hamiltonian that is bounded from below. The field theory of the basis tensor fields is what we call the basis tensor gauge theory.
New ab initio based pair potential for accurate simulation of phase transitions in ZnO
Wang, Shuaiwei; Fan, Zhaochuan; Koster, Rik S.; Fang, Changming; Van Huis, Marijn A.; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; Vlugt, Thijs J H
2014-01-01
A set of interatomic pair potentials is developed for ZnO based on the partially charged rigid ion model (PCRIM). The derivation of the potentials combines lattice inversion, empirical fitting, and ab initio energy surface fitting. We show that, despite the low number of parameters in this model (8)
Iwano, Sakae; Kawashima, Yoshiyuki; Hirota, Eizi
2016-06-01
We have systematically investigated the van der Waals complexes consisting of the one from each of the two groups: (Rg, CO, N_2 or CO_2) and (dimethyl ether, dimethyl sulfide, ethylene oxide or ethylene sulfide), by using Fourier transform microwave spectroscopy supplemented by ab initio MO calculations, in order to understand the dynamical behavior of van der Waals complexes and to obtain information on the potential function to internal motions in complexes. Two examples of the N_2 complex were investigated: N_2-DME (dimethyl ether), for which we reported a preliminary result and N_2-EO (ethylene oxide). In the present study we focused attention to the N_2-ES (ethylene sulfide) complex. We have detected two sets of the {b}-type transitions for the 15N_2-ES in ortho and para states, and have analyzed them by using the asymmetric-rotor program of {A}-reduction. In contrast with the N_2-EO, for which each of the ortho and para states were found split into a strong/weak pair, only some transitions of the 15N_2-ES were accompanied by two or three components. The observed spectra of the 14N_2-ES were complicated because of hyperfine splittings due to the nuclear quadrupole coupling of the two nitrogen atoms. We concluded that the N_2 moiety was located in the plane perpendicular to the C-S-C plane and bisecting the CSC angle of the ES. Two isomers were expected to exist for 15NN-ES, one with 15N in the inner and the other in the outer position, and in fact two sets of the spectra were detected. We have carried out ab initio molecular orbital calculations at the level of MP2 with basis sets 6-311++G(d, p), aug-cc-pVDZ, and aug-cc-pVTZ, to complement the information on the intracomplex motions obtained from the observed rotational spectra. Y. Kawashima, A. Sato, Y. Orita, and E. Hirota, J. Phys. Chem. A, 2012 116, 1224 Y. Kawashima, Y. Tatamitani, Y. Morita, and E. Hirota, 61st International Symposium on Molecular Spectroscopy, TE10 (2006) Y. Kawashima and E. Hirota, J
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.
Lee, Edmond P F; Dyke, John M; Mok, Daniel K W; Chau, Foo-tim
2008-05-15
A variety of density functional theory and ab initio methods, including B3LYP, B98, BP86, CASSCF, CASSCF/RS2, CASSCF/MRCI, BD, BD(T), and CCSD(T), with ECP basis sets of up to the quintuple-zeta quality for Y, have been employed to study the X(2)B2 state of YO2 and the X(1)A1 state of YO2(-). Providing that the Y 4s(2)4p(6) outer-core electrons are included in the correlation treatment, the RCCSD(T) method gives the most consistent results and is concluded to be the most reliable and practical computational method for YO2 and YO2(-). In addition, RCCSD(T) potential energy functions (PEFs) of the X(2)B2 state of YO2 and the X(1)A1 state of YO2(-) were computed, employing the ECP28MDF_aug-cc-pwCVTZ and aug-cc-pVTZ basis sets for Y and O, respectively. Franck-Condon factors, which include allowance for Duschinsky rotation and anharmonicity, were calculated using the computed RCCSD(T) PEFs and were used to simulate the first photodetachment band of YO2(-). The simulated spectrum matches very well with the corresponding experimental 355 nm photodetachment spectrum of Wu, H.; Wang, L.-S. J. Phys. Chem. A 1998, 102, 9129, confirming the reliability of the RCCSD(T) PEFs used. Further calculations on low-lying electronic states of YO2 gave T(e)'s and T(vert)'s of the A(2)A1, B(2)B1, and C(2)A2 states of YO2, as well as EAs and VDEs to these states from the X(1)A1 state of YO2(-). On the basis of the ab initio VDEs obtained in the present study, previous assignments of the second and third photodetachment bands of YO2(-) have been revised.
The role of metals in amyloid aggregation - Experiments and ab initio simulations
Minicozzi, V.; Morante, S.; Rossi, G. C.; Stellato, F.; Christian, N.; Jansen, K.
With a combination of modern spectroscopic techniques and numerical first principle simulations it is possible to investigate the physico-chemical basis of the beta-amyloid aggregation phenomenon, which is suspected to be at the basis of the development of the Alzheimer disease. On the experimental side, in fact, X-ray absorption spectroscopy can be successfully used to determine the atomic structure around the metal binding site in samples where beta-amyloid peptides are complexed with either Cu2+ or Zn2+ ions. Exploiting spectroscopic information obtained on a selected set of fragments of the natural Abeta-peptide, the residues that along the sequence are coordinated to the metal are identified. Although copper data can be consistently interpreted assuming that oligopeptides encompassing the minimal 1-16 amino acidic sequence display a metal coordination mode which involves three Histidines (His6, His13, and His14), in complexes with zinc a four Histidines coordination mode is seen to be preferred. Lacking a fourth Histidine in the Abeta1-16 fragment, this geometrical arrangement hints to a Zn2+ promoted inter-peptide aggregation mode. On the theoretical side, first principle ab initio molecular dynamics simulations of the Car-Parrinello type, which have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid-state physics and structural biophysics, have been employed in an effort to give a microscopic basis and find a phenomenological interpretation of the body of available experimental data on Abeta-peptides-metal complexes. Using medium size PC-clusters as well as larger parallel platforms, it is possible to deal with systems comprising 300-500 atoms and 1,000-2,000 electrons for simulation times as long as 2-3 ps. We present structural results that nicely compare with NMR and XAS data.
Campos, Cesar T; Jorge, Francisco E; Alves, Júlia M A
2012-09-01
Recently, segmented all-electron contracted double, triple, quadruple, quintuple, and sextuple zeta valence plus polarization function (XZP, X = D, T, Q, 5, and 6) basis sets for the elements from H to Ar were constructed for use in conjunction with nonrelativistic and Douglas-Kroll-Hess Hamiltonians. In this work, in order to obtain a better description of some molecular properties, the XZP sets for the second-row elements were augmented with high-exponent d "inner polarization functions," which were optimized in the molecular environment at the second-order Møller-Plesset level. At the coupled cluster level of theory, the inclusion of tight d functions for these elements was found to be essential to improve the agreement between theoretical and experimental zero-point vibrational energies (ZPVEs) and atomization energies. For all of the molecules studied, the ZPVE errors were always smaller than 0.5 %. The atomization energies were also improved by applying corrections due to core/valence correlation and atomic spin-orbit effects. This led to estimates for the atomization energies of various compounds in the gaseous phase. The largest error (1.2 kcal mol(-1)) was found for SiH(4).
Institute of Scientific and Technical Information of China (English)
虞忠衡; 彭晓琦; 郭彦伸; 宣正乾
2001-01-01
高度定域的、对称的、键轨道基组的建立是一个多步的计算程序：(1)以定域片断轨道[Фk，Фi，φj]为基，对分子作有条件的RHF运算，算得FUL和DSI°态的片断分子轨道[Ф0l，Ф0n，Ф0m]和[Фl，Фn，Фm].在基组[Фk，Фi，φj]中，Фi∈双占据和空σ片断分子轨道(FMOs)组，φi∈πFMO组，Фk∈单占据σFMO组，它们都精确地定域在各自的片断内；(2)利用Ф0l与Фl间的重叠积分值(Sll>O.5)，可以从DSI°态中，自动地选出Ns个对称的、由单占据轨道线性组合而成的分子轨道Ф0l=∑akФk(k=1，2，…，Ns).接着，用Ф0l取代FUL态中同类的、非对称轨道组Фl=∑aldФk(k=1，2，…，Ns)；(3)以上述新的轨道组[Ф0l，Фn，Фm]为基(其中，Ф0l∈DSI0态，它们离域于整个分子；双占据及空σFMO组Фn和πFMO组Фm属于FUL态)，按FUL态的条件，再次对分子作有条件的RHF运算，从中得到一组对称的、闭壳层正则FMOs，而且每一个FMO均有正确的电子占据数；(4)利用Perkin原理，将第3步所得的正则FMO组定域成一个对称的键轨道基组[Фl′，Фn′Фm′].在这个基组中，π体系Фm′与σ构架Фn′是彻底分离的，而且这两个轨道组始终精确地定域在各自的片断内.%A procedure for constructing a highly localized and symmetrical bond orbital basis set with the πsystems separated off from the σ frameworks has been developed. It is a four- step procedure: ( 1 )over the opened-shell localized fragment molecular orbital (FMO) basis set [φk, φi, φj] where φi ∈ doubly occ. And vacant σFMOs, φj ∈ πFMOs, and φk ∈ singly occ. FMOs, the conditional RHF computations provide each of the FUL and DSI° electronic states of a molecule, such as norbornadiene with a set of the closed-shell FMOs;(2) the symmetrical MOs, φ0l′= ∑ akl′ φk ( k = 1,2,…, Ns) which have delocalized over the whole molecule, in the DSI° substitutes for the
An ab initio HCN/HNC rotational-vibrational line list and opacity function for astronomy
Harris, Gregory John
-vibrational basis set and the parameters of the basis functions. Rotational and vibrational energy levels and dipole transition strengths are calculated with various surfaces and are compared with existing experimental and theoretical values. The new PES and DMS are then used to calculate an extensive HCN/HNC linelist containing energy levels, line frequencies and transition dipoles. From this linelist, room and stellar temperature HCN and HNC spectra are computed and compared with both lab and stellar spectra. Finally, a HCN and HNC opacity function is calculated from the linelist.
Finite Elements in Ab Initio Electronic-Structure Calulations
Pask, J. E.; Sterne, P. A.
Over the course of the past two decades, the density functional theory (DFT) (see e.g., [1]) of Hohenberg, Kohn, and Sham has proven to be an accurate and reliable basis for the understanding and prediction of a wide range of materials properties from first principles (ab initio), with no experimental input or empirical parameters. However, the solution of the Kohn-Sham equations of DFT is a formidable task and this has limited the range of physical systems which can be investigated by such rigorous, quantum mechanical means. In order to extend the interpretive and predictive power of such quantum mechanical theories further into the domain of "real materials", involving nonstoichiometric deviations, defects, grain boundaries, surfaces, interfaces, and the like; robust and efficient methods for the solution of the associated quantum mechanical equations are critical. The finite-element (FE) method (see e.g., [2]) is a general method for the solution of partial differential and integral equations which has found wide application in diverse fields ranging from particle physics to civil engineering. Here, we discuss its application to large-scale ab initio electronic-structure calculations.
Li, Hui; Le Roy, Robert J
2007-07-19
A three-dimensional potential energy surface for the ground electronic state of MgH2 has been constructed from 9030 symmetry-unique ab initio points calculated using the icMRCI+Q method with aug-cc-pVnZ basis sets for n=3, 4, and 5, with core-electron correlation calculated at the MR-ACPF level of theory using cc-pCVnZ basis sets, with both calculations being extrapolated to the complete basis set limit. Calculated spectroscopic constants of MgH2 and MgD2 are in excellent agreement with recent experimental results: for four bands of MgH2 and one band of MgD2 the root-mean-square (rms) band origin discrepancies were only 0.44 and 0.06 cm(-1), respectively, and the rms relative discrepancies in the inertial rotational constants (B[v]) were only 0.0196% and 0.0058%, respectively. Spectroscopic constants for MgHD were predicted using the same potential surface.
Molecular tailoring approach: a route for ab initio treatment of large clusters.
Sahu, Nityananda; Gadre, Shridhar R
2014-09-16
system is broken down into two or more subsystems that can be readily treated computationally. Finally, the properties of the large system are obtained by patching the corresponding properties of all the subsystems. Due to these approximations, the resulting MTA-based energies carry some error in comparison with calculations based on the full system. An approach for correcting these errors has been attempted by grafting the error at a lower basis set onto a higher basis set. Furthermore, investigating the growth patterns and nucleation processes in clusters is necessary for understanding the structural transitions and the phenomena of magic numbers in cluster chemistry. Therefore, systematic building-up or the introduction of stochastics for generating molecular assemblies is the most crucial step for studying large clusters. In this Account, we discuss the working principle of MTA for probing molecular clusters at ab initio level followed by a brief summary of an automated and electrostatics-guided algorithm for building molecular assemblies. The molecular aggregates presented here as test cases are generated based on either an electrostatic criterion or the basin hopping method. At MP2 level computation, the errors in MTA-based grafted energies are typically reduced to a submillihartree level, reflecting the potential of finding accurate energies of molecular clusters much more quickly. In summary, MTA provides a platform for effectively studying large molecular clusters at ab initio level of theory using minimal computer hardware.
Nasrabad, A E; Laghaei, R; Deiters, U K
2004-10-01
Gibbs ensemble Monte Carlo simulations were used to test the ability of intermolecular pair potentials derived ab initio from quantum mechanical principles, enhanced by Axilrod-Teller triple-dipole interactions, to predict the vapor-liquid phase equilibria of pure neon, pure argon, and the binary mixtures neon-argon and argon-krypton. The interaction potentials for Ne-Ne, Ar-Ar, Kr-Kr, and Ne-Ar were taken from literature; for Ar-Kr a different potential has been developed. In all cases the quantum mechanical calculations had been carried out with the coupled-cluster approach [CCSD(T) level of theory] and with correlation consistent basis sets; furthermore an extrapolation scheme had been applied to obtain the basis set limit of the interaction energies. The ab initio pair potentials as well as the thermodynamic data based on them are found to be in excellent agreement with experimental data; the only exception is neon. It is shown, however, that in this case the deviations can be quantitatively explained by quantum effects. The interaction potentials that have been developed permit quantitative predictions of high-pressure phase equilibria of noble-gas mixtures.
Ab initio Studies on Intermolecular Interaction of Formamide and Hydroxyacetonitrile Dimers
Institute of Scientific and Technical Information of China (English)
JU Xue-hai; XIE Lun-jia; XIA Qi-ying; XIAO He-ming
2004-01-01
The structures, the binding energies and the thermodynamic properties of formamide and hydroxyacetonitrile(HAN) dimers have been studied by means of the self-consistent ab initio Hartree-Fock and the second-order Mφller-Plesset correlation energy correction methods. The counterpoise procedure was used to check the basis set superposition error(BSSE) of the binding energies. There exist cyclic structures in a formamide dimer(Ⅰ), a HAN dimer(Ⅱ) and their heterodimer(Ⅲ). The corrected binding energies for dimers Ⅰ, Ⅱ and Ⅲ are respectively -45.53, -45.83 and -43.89 kJ/mol at the MP2/aug-cc-p VDZ//HF/aug-cc-p VDZ level. The change of the Gibbs free energies(ΔG) in the process of Ⅰ+Ⅱ→2Ⅲ was predicted to be -2.74 kJ/mol at 298.15 K. Dimer Ⅲ can be spontaneously produced in the mixture of formamide and HAN, which is in agreement with the experimental fact that most cyanohydrins are capable of interacting with dipeptide cyclo-His-Phe(CHP).
Ab initio calculation of the crystalline structure and IR spectrum of polymers: nylon 6 polymorphs.
Quarti, Claudio; Milani, Alberto; Civalleri, Bartolomeo; Orlando, Roberto; Castiglioni, Chiara
2012-07-19
State-of-the-art computational methods in solid-state chemistry were applied to predict the structural and spectroscopic properties of the α and γ crystalline polymorphs of nylon 6. Density functional theory calculations augmented with an empirical dispersion correction (DFT-D) were used for the optimization of the two different crystal structures and of the isolated chains, characterized by a different regular conformation and described as one-dimensional infinite chains. The structural parameters of both crystalline polymorphs were correctly predicted, and new insight into the interplay of conformational effects, hydrogen bonding, and van der Waals interactions in affecting the properties of the crystal structures of polyamides was obtained. The calculated infrared spectra were compared to experimental data; based on computed vibrational eigenvectors, assignment of the infrared absorptions of the two nylon 6 polymorphs was carried out and critically analyzed in light of previous investigations. On the basis of a comparison of the computed and experimental IR spectra, a set of marker bands was identified and proposed as a tool for detecting and quantifying the presence of a given polymorph in a real sample: several marker bands employed in the past were confirmed, whereas some of the previous assignments are criticized. In addition, some new marker bands are proposed. The results obtained demonstrate that accurate computational techniques are now affordable for polymers characterization, opening the way to several applications of ab initio modeling to the study of many families of polymeric materials.
Synthesis, FTIR, FT-Raman, UV-visible, ab initio and DFT studies on benzohydrazide.
Arjunan, V; Rani, T; Mythili, C V; Mohan, S
2011-08-01
A systematic vibrational spectroscopic assignment and analysis of benzohydrazide (BH) has been carried out by using FTIR and FT-Raman spectral data. The vibrational analysis were aided by electronic structure calculations--ab initio (RHF) and hybrid density functional methods (B3LYP and B3PW91) performed with 6-31G(d,p) and 6-311++G(d,p) basis sets. Molecular equilibrium geometries, electronic energies, IR intensities, harmonic vibrational frequencies, depolarization ratios and Raman activities have been computed. Potential energy distribution (PED) and normal mode analysis have also been performed. The assignments proposed based on the experimental IR and Raman spectra have been reviewed and complete assignment of the observed spectra have been proposed. UV-visible spectrum of the compound was also recorded and the electronic properties, such as HOMO and LUMO energies and λ(max) were determined by time-dependent DFT (TD-DFT) method. The geometrical, thermodynamical parameters and absorption wavelengths were compared with the experimental data. The interactions of carbonyl and hydrazide groups on the benzene ring skeletal modes were investigated. Copyright © 2011 Elsevier B.V. All rights reserved.
Directory of Open Access Journals (Sweden)
A. Bagheri Gh
2010-08-01
Full Text Available The electrochemical oxidation of dopamine and 3,4-dihydroxymethamphetamine (HHMA has been studied in the presence of GSH and cysteine as a nucleophile. In order to determine the optimized geometries, energies, dipole moments, atomic charges, thermochemical analysis and other properties, we performed quantum chemical ab initio and density functional calculations at B3LYP level with 6-31G* basis set. The structural and vibrational properties of 5-S-glutathionyldopamine, 5-S-cysteinyldopamine and 5-S-N-acetylcysteinyldopamine are studied. The chemical shifts of anisotropy and Δδ are calculated. The gauge-invariant atomic orbital (GIAO method was employed to calculate isotropic atomic shielding of compounds. These calculations yield molecular geometries in good agreement with available experimental data. The bond lengths, bond angles, dipole moment, electron affinity, ionization potential, electronegativy, absolute hardness, highest occupied molecular orbital (HOMO and the energy of the lowest unoccupied molecular orbital (LUMO of the studied compounds were calculated in gas phase and water. NMR analysis of dopamine-o-quinone-glutathione conjugate revealed that the addition of glutathione was at C-5 to form glutathionyl-dopamine.
A fully ab initio quartic force field of spectroscopic quality for $SO_3$
Martin, J M L
1999-01-01
The quartic force field of SO$_3$ was computed fully ab initio using coupled cluster (CCSD(T)) methods and basis sets of up to $spdfgh$ quality. The effect of inner-shell correlation was taken into account. The addition of tight $d$ functions is found to be essential for accurate geometries and harmonic frequencies. The equilibrium geometry and vibrational fundamentals are reproduced to within 0.0003 Å and (on average) 1.15 cm^{-1}, respectively. We recommend the following revised values for the harmonic frequencies: $\\omega_1 = 1082.7, \\omega_2 = 502.6, \\omega_3 = 1415.4, \\omega_4 = 534.0 cm^{-1}$. In addition, we have shown that the addition of inner polarization functions to second-row elements is highly desirable even with more approximate methods like B3LYP, and greatly improves the quality of computed geometries and harmonic frequencies of second-row compounds at negligible extra computational cost. For larger such molecules, the B3LYP/VTZ+1 level of theory should be a very good compromise between accu...
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.
Optimized energy landscape exploration using the ab initio based activation-relaxation technique
Machado-Charry, Eduardo; Béland, Laurent Karim; Caliste, Damien; Genovese, Luigi; Deutsch, Thierry; Mousseau, Normand; Pochet, Pascal
2011-07-01
Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C20 clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.
Ab Initio study of the diffusion mechanisms of gallium in a silicon matrix
Levasseur-Smith, K.; Mousseau, N.
2008-07-01
We present the results of a study into the diffusion mechanisms of Ga defects in crystalline Si using ab initio techniques. Five stable neutral configurations for single and multi-atom defects are identified by density-functional theory (DFT) calculations within the local density approximation and using a localized basis set as implemented in the SIESTA package. Formation energy (E_F) calculations on these stable structures show the most likely neutral single-atom defect to be the Ga substitutional, with an EF of 0.7 eV in good agreement with previous work. Charge state studies show the Ga tetrahedral interstitial defect to be in a +1 state for most doping conditions. They also indicate the possibility for a gallium substitutional-tetrahedral interstitial complex to act as a deactivating center for the Ga dopants except in n-doped regime, where the complex adopts a -1 charge state. Migration pathway calculations using SIESTA coupled with the activation relaxation technique (ART nouveau) allow us to determine possible migration paths from the stable configurations found, under various charge states. In general, diffusion barriers decrease as the charge state becomes more negative, suggesting that the presence of Si self-interstitials can enhance diffusion through the kicking out of substitutional Si and by adding negative charge carriers to the system. An overall picture of a possible Ga diffusion and complex formation mechanism is presented based on these results.
Ab initio study on the mechanism of reaction HNCO+NH2
Institute of Scientific and Technical Information of China (English)
冀永强; 雷鸣; 冯文林; 徐振峰
2002-01-01
Ab initio UMP2 and UQCISD(T) calculations, with 6-311G** basis sets, were performed for the titled reactions. The results show that the reactions have two product channels: NH2+ HNCO→NH3+NCO (1) and NH2+HNCO-N2H3+CO (2), where reaction (1) is a hydrogen abstraction reaction via an H-bonded complex (HBC), lowering the energy by 32.48 kJ/mol relative to reactants. The calculated QCISD(T)//MP2(full) energy barrier is 29.04 kJ/mol, which is in excellent accordance with the experimental value of 29.09 kJ/mol. In the range of reaction temperature 2300-2700 K, transition theory rate constant for reaction (1) is 1.68 × 1011- 3.29 × 1011 mL · mol-1· s-1, which is close to the experimental one of 5.0 ×1011 mL× mol-1· s-1 or less. However, reaction (2) is a stepwise reaction proceeding via two orientation modes, cis and trans, and the energy barriers for the rate-control step at our best calculations are 92.79 kJ/mol (for cis-mode) and 147.43 kJ/mol (for trans-mode), respectively, which is much higher than
Kritayakornupong, Chinapong; Vchirawongkwin, Viwat; Rode, Bernd M
2010-06-01
An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree-Fock level in conjunction with Dunning double-zeta plus polarization function basis sets. The simulation predicts an average H-Cl bond distance of 1.28 A, which is in good agreement with the experimental value. The H(HCl)...O(w) and Cl(HCl)...H(w) distances of 1.84 and 3.51 A were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure-making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively. Copyright 2009 Wiley Periodicals, Inc.
Ab initio ro-vibronic spectroscopy of SiCCl (X{sup ~2}Π)
Energy Technology Data Exchange (ETDEWEB)
Brites, Vincent [Université d’Evry Val d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE CNRS UMR 8587, Boulevard F. Mitterrand, 91025 Evry Cedex (France); Mitrushchenkov, Alexander O.; Léonard, Céline, E-mail: celine.leonard@u-pem.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France); Peterson, Kirk A. [Department of Chemistry, Washington State University, Pullman, Washington 99164 (United States)
2014-07-21
The full dimensional potential energy surfaces of the {sup 2}A{sup ′} and {sup 2}A{sup ′′} electronic components of X{sup ~2}Π SiCCl have been computed using the explicitly correlated coupled cluster method, UCCSD(T)-F12b, combined with a composite approach taking into account basis set incompleteness, core-valence correlation, scalar relativity, and higher order excitations. The spin-orbit and dipole moment surfaces have also been computed ab initio. The ro-vibronic energy levels and absorption spectrum at 5 K have been determined from variational calculations. The influence of each correction on the fundamental frequencies is discussed. An assignment is proposed for bands observed in the LIF experiment of Smith et al. [J. Chem. Phys. 117, 6446 (2002)]. The overall agreement between the experimental and calculated ro-vibronic levels is better than 7 cm{sup −1} which is comparable with the 10–20 cm{sup −1} resolution of the emission spectrum.
Optimized energy landscape exploration using the ab initio based activation-relaxation technique.
Machado-Charry, Eduardo; Béland, Laurent Karim; Caliste, Damien; Genovese, Luigi; Deutsch, Thierry; Mousseau, Normand; Pochet, Pascal
2011-07-21
Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C(20) clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.
Williamson, Rodney Lowell
Total geometry optimizations are reported for Cr(CO)_6, HMn(CO)_5 , Fe(CO)_5, Ni(CO) _4, Cr(C_6H _6)_2, Fe(C_5H _5)_2, Ni(C_4 H_4)_2, Cr(NO) _4, (C_5H _5)Mn(CO)_3, and (C _6H_6)Cr(CO) _3. A variety of basis sets were examined, and, based on the results, a relatively compact and accurate basis set is proposed. Addition of electron correlation at the perfect pairing GVB level reduced the average difference in the metal-cyclopentadienyl bond length of 0.08 A. Optimization of the geometry of TiCl_4 and TiCl_3CH_3 at the self-consistent-field (SCF) level results in Ti-Cl bond lengths longer than the experimental values, even when d- and f-type polarization functions are added to the basis set. The bond lengths remain too long even as the Hartree-Fock limit is approached because the SCF level of theory over-estimates the noble-gas-like Cl cdotsCl repulsions, which hinder close Ti -Cl approach. The Ti-C-H angle of TiCl_3 CH_3 is calculated to be close to tetrahedral geometry with little flattening of the hydrogen atoms, which apparently was observed in the electron diffraction. These same calculations do predict the anomalously low methyl-rocking frequency for the titanium complex in agreement with the experimental IR. The large positive geminal hydrogen coupling constant observed in the NMR experiment is due primarily to the sigma -donor and pi-acceptor character of the TiCl_3 moiety and not to any flattening of the methyl group. The structure and bonding of (Cr(Cp)(CO) _2) _2 was examined by optimizing the geometry of the dimer, fragment moiety, and analogous stable monomers. The optimized structure of Cr(Cp)(CO)_2N has a "piano stool" geometry with a fragment moiety geometry nearly identical to the geometry of the fragment moiety in the dimer. Examination of x-ray and theoretical geometries of monomers with the fragment moiety bonded to single ligand show that the geometry of the fragment moiety is insensitive to the ligands bonded to it. Van der Waals calculations
Durig, J. R.; Zhu, X.; Shen, S.
2001-08-01
Variable temperature (-55 to -150°C) studies of the infrared spectra (3500-400 cm -1) of 1-chloropropane (CH 3CH 2CH 2Cl) and 1-bromopropane (CH 3CH 2CH 2Br) dissolved in liquid krypton and xenon, respectively, have been recorded. Utilizing two conformer pairs in krypton solution for chloride and three conformer pairs in xenon solution for bromide, enthalpy differences of 52±3 cm -1 (0.62±0.06 kJ/mol) and 72±7 cm -1 (0.86±0.08 kJ/mol) were obtained for the chloride and bromide, respectively, with the gauche form being the more stable conformer for both molecules. From these data, it is estimated that 28 and 26% of trans form are present at ambient temperature for the chloride and bromide, respectively. The conformation stabilities, harmonic force constants, fundamental frequencies, infrared intensities and Raman activities have been obtained from RHF/6-31G(d) and/or MP2/6-31G(d) ab initio calculations for both halopropanes and these quantities have been compared to the experimental values when appropriate. The optimized geometries have also been obtained with several different ab initio basis sets with full electron correlation by the perturbation method up to MP2/6-311+G(2d,2p). The r0 structural parameters of both halopropanes have been obtained by combining the ab initio data with the previously reported microwave rotational constants for both conformers. The quantities are compared to the corresponding results for some similar molecules.
Energy Technology Data Exchange (ETDEWEB)
Morgado, Claudio A.; Jurecka, Petr; Svozil, Daniel; Hobza, Pavel; Sponer, Jiri
2009-06-09
We have carried out reference quantum-chemical calculations for about 100 geometries of the uracil dimer in stacked conformations. The calculations have been specifically aimed at geometries with unoptimized distances between the monomers including geometries with mutually tilted monomers. Such geometries are characterized by a delicate balance between local steric clashes and local unstacking and had until now not been investigated using reference quantummechanics (QM) methods. Nonparallel stacking geometries often occur in nucleic acids and are of decisive importance, for example, for local conformational variations in B-DNA. Errors in the shortrange repulsion region would have a major impact on potential energy scans which were often used in the past to investigate local geometry variations in DNA. An incorrect description of such geometries may also partially affect molecular dynamics (MD) simulations in applications when quantitative accuracy is required. The reference QM calculations have been carried out using the MP2 method extrapolated to the complete basis-set limit and corrected for higher-order electron-correlation contributions using CCSD(T) calculations with a medium-sized basis set. These reference calculations have been used as benchmark data to test the performance of the DFT-D, SCS(MI)-MP2, and DFTSAPT QM methods and of the AMBER molecular-mechanics (MM) force field. The QM methods show close to quantitative agreement with the reference data, albeit the DFT-D method tends to modestly exaggerate the repulsion of steric clashes. The force field in general also provides a good description of base stacking for the systems studied here. However, for geometries with close interatomic contacts and clashes, the repulsion effects are rather severely exaggerated. The discrepancy reported here should not affect the overall stability of MD simulations and qualitative applications of the force field. However, it may affect the description of subtle
Ab initio valence calculations in chemistry
Cook, D B
1974-01-01
Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge
DEFF Research Database (Denmark)
Gorelik, Tatiana E; van de Streek, Jacco; Kilbinger, Andreas F M
2012-01-01
Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal stru...
Optical and other material properties of SiO2 from ab initio studies
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.
Rizzo, Antonio; Rikken, G L J A; Mathevet, R
2016-01-21
We present a systematic ab initio study of enantio-selective magnetic-field-induced second harmonic generation (MFISHG) on a set of chiral systems ((l)-alanine, (l)-arginine and (l)-cysteine; 3,4-dehydro-(l)-proline; (S)-α-phellandrene; (R,S)- and (S,S)-cystine disulphide; N-(4-nitrophenyl)-(S)-prolinol, N-(4-(2-nitrovinyl)-phenyl)-(S)-prolinol, N-(4-tricyanovinyl-phenyl)-(S)-prolinol, (R)-BINOL, (S)-BINAM and 6-(M)-helicene). The needed electronic frequency dependent cubic response calculations are performed within a density functional theory (DFT) approach. A study of the dependence of the property on the choice of electron correlation, on one-electron basis set extension and on the choice of magnetic gauge origin is carried out on a prototype system (twisted oxygen peroxide). The magnetic gauge dependence analysis is extended also to the molecules of the set. An attempt to analyze the structure-property relationships is also made, based on the results obtained for biphenyl (in a frozen twisted conformation), for prolinol and for some of their derivatives. The strength of the effect is discussed, in order to establish its measurability with a proposed experimental setup.
Institute of Scientific and Technical Information of China (English)
Zhang Jin-Ping; Cheng Xin-Lu; Zhang Hong; Yang Xiang-Dong
2011-01-01
Three low-lying electronic states (X1∑+, a3∑+, and A1Ⅱ) of NO+ ion are studied using the complete active space self-consistent-field (CASSCF) method followed by highly accurate valence internally contracted multi-reference configuration interaction (MRCI) approach in combination of the correlation-consistent sextuple basis set augmented with diffuse functions, aug-cc-pV6Z. The potential energy curves (PECs) of the NO+(X1∑+, a3∑+, A1Ⅱ) are calculated. Based on the PECs, the spectroscopic parameters Re, De, ωe, ωeXe, αe, Be, and D0 are reproduced, which are in excellent agreement with the available measurements. By numerically solving the radial Schr(o)dinger equation of nuclear motion using the Numerov method, the first 20 vibrational levels, inertial rotation and centrifugal distortion constants of NO+(X1∑+, a3∑+, A1Ⅱ) ion are derived when the rotational quantum number J is equal to zero (J = 0)for the first time, which accord well with the available measurements. Finally, the analytical potential energy functions of these states are fitted, which are used to accurately derive the first 20 classical turning points when J = 0. These results are compared in detail with those of previous investigations reported in the literature.
Roper, Ian P E; Besley, Nicholas A
2016-03-21
The simulation of X-ray emission spectra of transition metal complexes with time-dependent density functional theory (TDDFT) is investigated. X-ray emission spectra can be computed within TDDFT in conjunction with the Tamm-Dancoff approximation by using a reference determinant with a vacancy in the relevant core orbital, and these calculations can be performed using the frozen orbital approximation or with the relaxation of the orbitals of the intermediate core-ionised state included. Both standard exchange-correlation functionals and functionals specifically designed for X-ray emission spectroscopy are studied, and it is shown that the computed spectral band profiles are sensitive to the exchange-correlation functional used. The computed intensities of the spectral bands can be rationalised by considering the metal p orbital character of the valence molecular orbitals. To compute X-ray emission spectra with the correct energy scale allowing a direct comparison with experiment requires the relaxation of the core-ionised state to be included and the use of specifically designed functionals with increased amounts of Hartree-Fock exchange in conjunction with high quality basis sets. A range-corrected functional with increased Hartree-Fock exchange in the short range provides transition energies close to experiment and spectral band profiles that have a similar accuracy to those from standard functionals.
Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.; Zakir'yanov, D. O.
2015-06-01
The effect of hydrostatic compression on the lattice structure and dynamics of elpasolites Cs2NaYbF6 and Cs2NaYF6 (sp. gr. 225) has been investigated ab initio. The frequencies and types of fundamental oscillations are determined, and elastic constants are calculated. The computation is performed within the molecular orbitals-linear combinations of atomic orbitals (MO LCAO) approach using the density functional theory (DFT) method with hybrid functionals B3LYP and PBE0 in the CRYSTAL09 program. The rare-earth ion was described by representing the inner (in particular, 4 f) orbitals in the form of a pseudopotential. The outer 5 s and 5 p orbitals, which determine chemical bonding, were described using valence basis sets.
Lattice dynamics of Cs2NaYbF6 and Cs2NaYF6 elpasolites: Ab initio calculation
Chernyshev, V. A.; Petrov, V. P.; Nikiforov, A. E.; Zakir'yanov, D. O.
2015-06-01
The ab initio calculations of the crystal structure and the phonon spectrum of Cs2NaYbF6 and Cs2NaYF6 crystals with the elpasolite structure have been performed. The frequencies and types of fundamental vibrations have been determined. The calculations have been performed in the framework of the density functional theory using the molecular orbital method with hybrid functionals in the CRYSTAL09 program developed for the simulation of periodic structures. The outer 5 s and 5 p shells of the rare-earth ion have been described in Gaussian-type basis sets. The influence of inner shells, including 4 f electron shells, on the outer shells has been described using the pseudopotential. It has been shown that this approach allows the description of the phonon spectrum with the inclusion of the splitting of the longitudinal and transverse optical modes.
Ucun, Fatih; Sağlam, Adnan; Güçlü, Vesile
2007-06-01
The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine and theobromine) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis set level. The calculations were utilized to the CS symmetries of the molecules. The obtained vibrational frequencies and optimised geometric parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.
Yanov, Ilya; Kholod, Yana; Simeon, Tomekia; Kaczmarek, Anna; Leszczynski, Jerzy
The results of an ab initio quantum chemical study of the Sc3N@C80 endohedral complex are reported. The Hartree-Fock (HF) and B3LYP levels of theory were employed in conjunction with STO-3G and 6-31G(d) basis sets to determine the geometry and properties of the local minima conformations of Sc3N cluster inside the C80 cage. Weak bonding between the Sc3N and C80 molecule and a number of very close geometry and nearly identical by energy local minima structures can explain the large mobility of the endohedral cluster, but complicate determination of the global minimum structure. The effect of the endohedral cluster on the vibrational spectrum of Sc3N@C80 is revealed. Based on the theoretical infrared (IR) spectra, the experimental method to distinguish local minima structures of Sc3N@C80 is proposed.
Directory of Open Access Journals (Sweden)
Yahmin Yahmin
2010-06-01
Full Text Available The structure and binding energies of 12-crown-4 and benzo-12-crown-4 complexes with Li+, Na+, K+, Zn2+, Cd2+, and Hg2+were investigated with ab initio calculations using Hartree-Fock approximation and second-order perturbation theory. The basis set used in this study is lanl2mb. The structure optimization of cation-crown ether complexes was evaluated at HF/lanl2mb level of theory and interaction energy of the corresponding complexes was calculated at MP2/lanl2mb level of theory (MP2/lanl2mb//HF/lanl2mb. Interactions of the crown ethers and the cations were discussed in term of the structure parameter of crown ether. The binding energies of the complexes show that all complex formed from transition metal cations is more stable than the complexes formed from alkali metal cations. Keywords: 12-crown-4, benzo-12-crown-4, alkali metals, transition metals
KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.
2014-01-01
We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421
Łodyga, Wiesław; Makarewicz, Jan
2012-05-01
Geometries, anharmonic vibrations, and torsion-wagging (TW) multiplets of hydrazine and its deuterated species are studied using high-level ab initio methods employing the second-order Møller-Plesset perturbation theory (MP2) as well as the coupled cluster singles and doubles model including connected triple corrections, CCSD(T), in conjunction with extended basis sets containing diffuse and core functions. To describe the splitting patterns caused by tunneling in TW states, the 3D potential energy surface (PES) for the large-amplitude TW modes is constructed. Stationary points in the 3D PES, including equivalent local minima and saddle points are characterized. Using this 3D PES, a flexible Hamiltonian is built numerically and then employed to solve the vibrational problem for TW coupled motion. The calculated ground state rav structure is expected to be more reliable than the experimental one that has been determined using a simplified structural model. The calculated fundamental frequencies allowed resolution of the assignment problems discussed earlier in the literature. The determined energy barriers, including the contributions from the small-amplitude vibrations, to the tunneling of the symmetric and antisymmetric wagging mode of 1997 cm-1 and 3454 cm-1, respectively, are in reasonable agreement with the empirical estimates of 2072 cm-1 and 3312 cm-1, respectively [W. Łodyga et al. J. Mol. Spectrosc. 183, 374 (1997), 10.1006/jmsp.1997.7271]. However, the empirical torsion barrier of 934 cm-1 appears to be overestimated. The ab initio calculations yield two torsion barriers: cis and trans of 744 cm-1 and 2706 cm-1, respectively. The multiplets of the excited torsion states are predicted from the refined 3D PES.
Sawant, Dattatray K.; Klaassen, Joshua J.; Durig, James R.
2013-06-01
The infrared and Raman spectra (3200 to 50 cm^{-1}) of the gas, liquid or solution, and solid have been recorded of isocyanocyclopentane, _{c}-C_{5}H_{9}NC. FT-microwave studies have also been carried out and 23 transitions were recorded for the envelope-axial (Ax) conformer. Variable temperature (-55 to -100°C) studies of the infrared spectra (3200 to 400 cm^{-1}) dissolved in liquid xenon have been carried out. From these data, both the Ax and envelope-equatorial (Eq) conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 102 ± 10 cm^{-1} (1.21 ± 0.03 kJ mol^{-1}) with the Ax conformer the more stable form. The percentage of the Eq conformer is estimated to be 38 ± 1% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been made for the observed bands for both conformers with initial predictions by MP2(full)/6-31G(d) ab initio calculations to obtain harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The heavy atom distances (Å): C≡N = 1.176 ; C_{α}-N≡C= 1.432; C_{α}-C_{β},C_{β}' = 1.534; C_{β}-C_{γ}, C_{γ}' = 1.542; C_{γ}-C_{γ}' = 1.554 and angles (°:angleC_{α}-N≡C = 177.8; angleC_{β}C_{α}-N≡C = 110.4; angleC_{β}C_{α}C_{β}'= 102.9; angleC_{α}C_{β}C_{γ} = 103.6; angleC_{β}C_{γ}C_{γ}' = 105.9. The results are discussed and compared to the corresponding properties of some related molecules.
Energy Technology Data Exchange (ETDEWEB)
Yaghlane, Saida Ben [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications – LSAMA, Université de Tunis, Tunis (Tunisia); Cotton, C. Eric; Francisco, Joseph S., E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr [Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 49707 (United States); Linguerri, Roberto; Hochlaf, Majdi, E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr [Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 bd Descartes, 77454 Marne-la-Vallée (France)
2013-11-07
Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.
Ab initio charge-carrier mobility model for amorphous molecular semiconductors
Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.
2016-05-01
Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.
The ab-initio density matrix renormalization group in practice.
Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic
2015-01-21
The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.
Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon
Drumm, Daniel W.; Budi, Akin; Per, Manolo C.; Russo, Salvy P.; L Hollenberg, Lloyd C.
2013-02-01
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%.
McKemmish, Laura K; Tennyson, Jonathan
2016-01-01
Accurate knowledge of the rovibronic near-infrared and visible spectra of vanadium monoxide (VO) is very important for studies of cool stellar and hot planetary atmospheres. Here, the required ab initio dipole moment and spin-orbit coupling curves for VO are produced. This data forms the basis of a new VO line list considering 13 different electronic states and containing over 277 million transitions. Open shell transition, metal diatomics are challenging species to model through ab initio quantum mechanics due to the large number of low-lying electronic states, significant spin-orbit coupling and strong static and dynamic electron correlation. Multi-reference configuration interaction methodologies using orbitals from a complete active space self-consistent-field (CASSCF) calculation are the standard technique for these systems. We use different state-specific or minimal-state CASSCF orbitals for each electronic state to maximise the calculation accuracy. The off-diagonal dipole moment controls the intensity...
Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon.
Drumm, Daniel W; Budi, Akin; Per, Manolo C; Russo, Salvy P; L Hollenberg, Lloyd C
2013-02-27
: 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%.
Reciprocity Theorems for Ab Initio Force Calculations
Wei, C; Mele, E J; Rappe, A M; Lewis, Steven P.; Rappe, Andrew M.
1996-01-01
We present a method for calculating ab initio interatomic forces which scales quadratically with the size of the system and provides a physically transparent representation of the force in terms of the spatial variation of the electronic charge density. The method is based on a reciprocity theorem for evaluating an effective potential acting on a charged ion in the core of each atom. We illustrate the method with calculations for diatomic molecules.
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 accelerat...
Ab initio Bogoliubov coupled cluster theory
Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas
2014-09-01
Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.
Ab initio modeling of decomposition in iron based alloys
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.
Miliordos, Evangelos; Xantheas, Sotiris S
2015-06-21
We report MP2 and Coupled Cluster Singles, Doubles, and perturbative Triples [CCSD(T)] binding energies with basis sets up to pentuple zeta quality for the (H2O)m=2-6,8 water clusters. Our best CCSD(T)/Complete Basis Set (CBS) estimates are -4.99 ± 0.04 kcal/mol (dimer), -15.8 ± 0.1 kcal/mol (trimer), -27.4 ± 0.1 kcal/mol (tetramer), -35.9 ± 0.3 kcal/mol (pentamer), -46.2 ± 0.3 kcal/mol (prism hexamer), -45.9 ± 0.3 kcal/mol (cage hexamer), -45.4 ± 0.3 kcal/mol (book hexamer), -44.3 ± 0.3 kcal/mol (ring hexamer), -73.0 ± 0.5 kcal/mol (D2d octamer), and -72.9 ± 0.5 kcal/mol (S4 octamer). We have found that the percentage of both the uncorrected (De) and basis set superposition error-corrected (De (CP)) binding energies recovered with respect to the CBS limit falls into a narrow range on either sides of the CBS limit for each basis set for all clusters. In addition, this range decreases upon increasing the basis set. Relatively accurate estimates (within set) or the "12, 12" (for the AVTZ, AVQZ, and AV5Z sets) mixing ratio between De and De (CP). These mixing rations are determined via a least-mean-squares approach from a dataset that encompasses clusters of various sizes. Based on those findings, we propose an accurate and efficient computational protocol that can be presently used to estimate accurate binding energies of water clusters containing up to 30 molecules (for CCSD(T)) and up to 100 molecules (for MP2).
Johnson, Clive; Moore, Elaine A; Mortimer, Michael
2005-05-01
Periodic ab initio HF calculations using the CRYSTAL code have been used to calculate (23)Na NMR quadrupole parameters for a wide range of crystalline sodium compounds including Na(3)OCl. An approach is developed that can be used routinely as an alternative to point-charge modelling schemes for the assignment of distinct lines in (23)Na NMR spectra to specific crystallographic sodium sites. The calculations are based on standard 3-21 G and 6-21 G molecular basis sets and in each case the same modified basis set for sodium is used for all compounds. The general approach is extendable to other quadrupolar nuclei. For the 3-21 G calculations a 1:1 linear correlation between experimental and calculated values of C(Q)((23)Na) is obtained. The 6-21 G calculations, including the addition of d-polarisation functions, give better accuracy in the calculation of eta((23)Na). The sensitivity of eta((23)Na) to hydrogen atom location is shown to be useful in testing the reported hydrogen-bonded structure of Na(2)HPO(4).
Energy Technology Data Exchange (ETDEWEB)
Ganster, P
2004-10-15
A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)
Nori-Shargh, Davood; Mousavi, Seiedeh Negar; Kayi, Hakan
2014-05-01
Complete basis set CBS-4, hybrid-density functional theory (hybrid-DFT: B3LYP/6-311+G**) based methods and natural bond orbital (NBO) interpretations have been used to examine the contributions of the hyperconjugative, electrostatic, and steric effects on the conformational behaviors of trans-2,3-dihalo-1,4-diselenane [halo = F (1), Cl (2), Br (3)] and trans-2,5-dihalo-1,4-diselenane [halo = F (4), Cl (5), Br (6)]. Both levels of theory showed that the axial conformation stability, compared to its corresponding equatorial conformation, decreases from compounds 1 → 3 and 4 → 6. Based on the results obtained from the NBO analysis, there are significant anomeric effects for compounds 1-6. The anomeric effect associated with the electron delocalization is in favor of the axial conformation and increases from compounds 1 → 3 and 4 → 6. On the other hand, dipole moment differences between the axial and equatorial conformations [Δ(μ(eq)-μ(ax)] decrease from compounds 1 → 3. Although Δ(μ(eq)-μ(ax)) parameter decreases from compound 1 to compound 3, the dipole moment values of the axial conformations are smaller than those of their corresponding equatorial conformations. Therefore, the anomeric effect associated with the electron delocalizations (for halogen-C-Se segments) and the electrostatic model associated with the dipole-dipole interactions fail to account for the increase of the equatorial conformations stability on going from compound 1 to compound 3. Since there is no dipole moment for the axial and equatorial conformations of compounds 4-6, consequently, the conformational preferences in compounds 1-6 is in general dictated by the steric hindrance factor associated with the 1,3-syn-axial repulsions. Importantly, the CBS-4 results show that the entropy difference (∆S) between the equatorial axial conformations increases from compounds 1 → 3 and 4 → 6. This fact can be explained by the anomeric effect associated
Baima, Jacopo; Ferrabone, Matteo; Orlando, Roberto; Erba, Alessandro; Dovesi, Roberto
2016-02-01
The phonon dispersion and thermodynamic properties of pyrope ({Mg}_3{Al}_2{Si}_3{O}_{12}) and grossular ({Ca}_3{Al}_2{Si}_3{O}_{12} ) have been computed by using an ab initio quantum mechanical approach, an all-electron variational Gaussian-type basis set and the B3LYP hybrid functional, as implemented in the Crystal program. Dispersion effects in the phonon bands have been simulated by using supercells of increasing size, containing 80, 160, 320, 640, 1280 and 2160 atoms, corresponding to 1, 2, 4, 8, 16 and 27 {k} points in the first Brillouin zone. Phonon band structures, density of states and corresponding inelastic neutron scattering spectra are reported. Full convergence of the various thermodynamic properties, in particular entropy ( S) and specific heat at constant volume (CV), with the number of {k} points is achieved with 27 {k} points. The very regular behavior of the S( T) and CV(T) curves as a function of the number of {k} points, determined by high numerical stability of the code, permits extrapolation to an infinite number of {k} points. The limiting value differs from the 27-{k} case by only 0.40 % at 100 K for S (the difference decreasing to 0.11 % at 1000 K) and by 0.29 % (0.05 % at 1000 K) for CV. The agreement with the experimental data is rather satisfactory. We also address the problem of the relative entropy of pyrope and grossular, a still debated question. Our lattice dynamical calculations correctly describe the larger entropy of pyrope than grossular by taking into account merely vibrational contributions and without invoking "static disorder" of the Mg ions in dodecahedral sites. However, as the computed entropy difference is found to be larger than the experimental one by a factor of 2-3, present calculations cannot exclude possible thermally induced structural changes, which could lead to further conformational contributions to the entropy.
Grid-based methods for biochemical ab initio quantum chemical applications
Energy Technology Data Exchange (ETDEWEB)
Colvin, M.E.; Nelson, J.S.; Mori, E. [and others
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.
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
Vadali, Ramkumar V; Shi, Yan; Kumar, Sameer; Kale, Laxmikant V; Tuckerman, Mark E; Martyna, Glenn J
2004-12-01
Many systems of great importance in material science, chemistry, solid-state physics, and biophysics require forces generated from an electronic structure calculation, as opposed to an empirically derived force law to describe their properties adequately. The use of such forces as input to Newton's equations of motion forms the basis of the ab initio molecular dynamics method, which is able to treat the dynamics of chemical bond-breaking and -forming events. However, a very large number of electronic structure calculations must be performed to compute an ab initio molecular dynamics trajectory, making the efficiency as well as the accuracy of the electronic structure representation critical issues. One efficient and accurate electronic structure method is the generalized gradient approximation to the Kohn-Sham density functional theory implemented using a plane-wave basis set and atomic pseudopotentials. The marriage of the gradient-corrected density functional approach with molecular dynamics, as pioneered by Car and Parrinello (R. Car and M. Parrinello, Phys Rev Lett 1985, 55, 2471), has been demonstrated to be capable of elucidating the atomic scale structure and dynamics underlying many complex systems at finite temperature. However, despite the relative efficiency of this approach, it has not been possible to obtain parallel scaling of the technique beyond several hundred processors on moderately sized systems using standard approaches. Consequently, the time scales that can be accessed and the degree of phase space sampling are severely limited. To take advantage of next generation computer platforms with thousands of processors such as IBM's BlueGene, a novel scalable parallelization strategy for Car-Parrinello molecular dynamics is developed using the concept of processor virtualization as embodied by the Charm++ parallel programming system. Charm++ allows the diverse elements of a Car-Parrinello molecular dynamics calculation to be interleaved with low
Sylvetsky, Nitai; Peterson, Kirk A.; Karton, Amir; Martin, Jan M. L.
2016-06-01
In the context of high-accuracy computational thermochemistry, the valence coupled cluster with all singles and doubles (CCSD) correlation component of molecular atomization energies presents the most severe basis set convergence problem, followed by the (T) component. In the present paper, we make a detailed comparison, for an expanded version of the W4-11 thermochemistry benchmark, between, on the one hand, orbital-based CCSD/AV{5,6}Z + d and CCSD/ACV{5,6}Z extrapolation, and on the other hand CCSD-F12b calculations with cc-pVQZ-F12 and cc-pV5Z-F12 basis sets. This latter basis set, now available for H-He, B-Ne, and Al-Ar, is shown to be very close to the basis set limit. Apparent differences (which can reach 0.35 kcal/mol for systems like CCl4) between orbital-based and CCSD-F12b basis set limits disappear if basis sets with additional radial flexibility, such as ACV{5,6}Z, are used for the orbital calculation. Counterpoise calculations reveal that, while total atomization energies with V5Z-F12 basis sets are nearly free of BSSE, orbital calculations have significant BSSE even with AV(6 + d)Z basis sets, leading to non-negligible differences between raw and counterpoise-corrected extrapolated limits. This latter problem is greatly reduced by switching to ACV{5,6}Z core-valence basis sets, or simply adding an additional zeta to just the valence orbitals. Previous reports that all-electron approaches like HEAT (high-accuracy extrapolated ab-initio thermochemistry) lead to different CCSD(T) limits than "valence limit + CV correction" approaches like Feller-Peterson-Dixon and Weizmann-4 (W4) theory can be rationalized in terms of the greater radial flexibility of core-valence basis sets. For (T) corrections, conventional CCSD(T)/AV{Q,5}Z + d calculations are found to be superior to scaled or extrapolated CCSD(T)-F12b calculations of similar cost. For a W4-F12 protocol, we recommend obtaining the Hartree-Fock and valence CCSD components from CCSD-F12b/cc-pV{Q,5}Z-F12
Erba, Alessandro; Navarrete-López, Alejandra M; Lacivita, Valentina; D'Arco, Philippe; Zicovich-Wilson, Claudio M
2015-01-28
The evolution under pressures up to 65 GPa of structural, elastic and vibrational properties of the katoite hydrogarnet, Ca3Al2(OH)12, is investigated with an ab initio simulation performed at the B3LYP level of theory, by using all-electron basis sets with the Crystal periodic program. The high-symmetry Ia3d phase of katoite, stable under ambient conditions, is shown to be destabilized, as pressure increases, by interactions involving hydrogen atoms and their neighbors which weaken the hydrogen bonding network of the structure. The corresponding thermodynamical instability is revealed by anomalous deviations from regularity of its elastic constants and by numerous imaginary phonon frequencies, up to 50 GPa. Interestingly, as pressure is further increased above 50 GPa, the Ia3d structure is shown to become stable again (all positive phonon frequencies and regular elastic constants). However, present calculations suggest that, above about 15 GPa and up to at least 65 GPa, a phase of I4[combining macron]3d symmetry (a non-centrosymmetric subgroup of Ia3d) becomes more stable than the Ia3d one, being characterized by strengthened hydrogen bonds. At low-pressures (between about 5 GPa and 15 GPa), both phases show some instabilities (more so for I4[combining macron]3d than for Ia3d), thus suggesting either the existence of a third phase or a possible phase transition of second order.
Moin, Syed Tarique; Lim, Len Herald V; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M
2011-04-18
An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 Å, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.
Institute of Scientific and Technical Information of China (English)
2008-01-01
Ionic dissociation of chlorosulfonic acid (HSO3Cl) in the molecular clusters HSO3Cl-(H2O)n (n = 1-4) and HSO3Cl-NH3-(H2O)n (n = 0-3) was investigated by density functional theory and ab initio molecular orbital theory. The equilibrium structures, binding energies, and thermodynamic properties, such as relative enthalpy and relative Gibbs free energy, and were calculated using the hybrid density func- tional (B3LYP) method and the second order M?ller-Plesset approximation (MP2) method with the 6-311++G** basis set. Chlorosulfonic acid was found to require a minimum of three water molecules for ionization to occur and at least one water molecule to protonate ammonia. The corresponding clusters with fewer water molecules were found to be strongly hydrogen-bonded. The related properties and acid strength of chlorosulfonic acid were discussed and compared to the acid strengths of perchloric acid and sulfuric acid in the context of clusters with ammonia and water. The relative stabilities of these clusters were also investigated.
Energy Technology Data Exchange (ETDEWEB)
Scholes, G.D.; Fleming, G.R. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley National Lab., CA (United States). Physical Biosciences Div.; Gould, I.R. [Imperial Coll. of Science, Technology and Medicine, London (United Kingdom). Dept. of Chemistry; Cogdell, R.J. [Univ. of Glasgow (United Kingdom). Div. of Biochemistry and Molecular Biology
1999-04-01
The results of ab initio molecular orbital calculations of excited states and electronic couplings (for energy transfer) between the B800 and B850 bacteriochlorophyll a (Bchl) chromophores in the peripheral light-harvesting complex (LH2) of the purple photosynthetic bacterium Rhodopseudomonas acidophila are reported. Electronic couplings are estimated from supermolecule calculations of Bchl dimers using the Ci-singles methodology and 3-21G{sup *} or 6-31G{sup *} basis sets. A scheme for dissecting the coupling into contributions from the Coulombic coupling and the short-range coupling (i.e., dependent on interchromophore orbital overlap) is reported. B850 couplings are calculated to be [total (Coulombic + short)]: intrapolypeptide dimer 320 (265 + 55) cm{sup {minus}1} and interpolypeptide dimer 255 (195 + 60) cm{sup {minus}1} at the CIS/6-31G{sup *} level. These results differ significantly from those estimated using the point dipole approximation. The effect of including Mg ligands (His residues) and H-bonding residues (Trp and Tyr) is also investigated. The consequences for superradiance and energy transfer dynamics and mechanism are discussed.
Ford, Thomas A.
2014-09-01
The molecular structures, vibrational spectra and atomic charges of the alicyclic ethers containing from two to five carbon atoms have been determined by means of ab initio calculations, at the level of second order Møller-Plesset perturbation theory and using Dunning's augmented correlation-consistent polarized valence triple-zeta basis set. Two isomers of the oxetane, tetrahydrofuran and tetrahydropyran molecules have been identified and their relative energies determined. Structural properties, such as the COC bond angles and the CH bond lengths, are found to increase steadily with increasing ring size and with decreasing ionization energy. The mean CH2 stretching and bending wavenumbers exhibit the reverse behaviour, while the mean wavenumbers of the CH2 wagging and twisting modes follow the same trend as the structural features. The ring mode wavenumbers vary in a less regular way. The charges of the oxygen, α-carbon and axial and equatorial α- and β-hydrogen atoms also do not show systematic dependences on ring size or ionization energy. The trends in the values of these properties have been rationalized.
Ab initio calculation of the potential bubble nucleus 34Si
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
2001-01-01
The adsorption of H And S2- species on Pd (100) has been studied with ab initio, density-functional calculations and electrochemical methods. A cluster of five Pd atoms with a frozen geometry described the surface. The computational calculations were performed through the GAUSSIAN94 program, and the basis functions adapted to a pseudo-potential obtained by using the Generator Coordinate Method adapted to the this program. Using the cyclic voltammetry technique through a Model 283 Potentiostat...
Energy Technology Data Exchange (ETDEWEB)
Razee, S.S.A.; Staunton, J.B. [Department of Physics, University of Warwick, Coventry (United Kingdom); Ginatempo, B.; Bruno, E. [Dipartimento di Fisica and Unita INFM, Universita di Messina, Messina (Italy); Pinski, F.J. [Department of Physics, University of Cincinnati, OH (United States)
2001-09-24
A theory is presented for describing the effects of annealing magnetic alloys in magnetic fields. It has an ab initio spin-polarized relativistic Korringa-Kohn-Rostoker coherent potential approximation (KKR-CPA) electronic structure basis and uses the framework of concentration waves. Alloys which would otherwise be soft magnets are found experimentally to develop directional chemical order and significant uniaxial anisotropy when annealed in magnetic fields. Our approach is able to provide a quantitative description of these effects together with the underlying electronic mechanisms. We describe applications to the soft magnetic alloys permalloy and FeCo. (author)
Pham, Thi Nu; Ono, Shota; Ohno, Kaoru
2016-04-01
Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.
Exploring proton transfer in 1,2,3-triazole-triazolium dimer with ab initio method
Energy Technology Data Exchange (ETDEWEB)
Li, Ailin; Yan, Tianying; Shen, Panwen [Department of Material Chemistry, Institute of New Energy Material Chemistry, Nankai University, Tianjin, 300071 (China)
2011-02-01
Ab initio calculations are utilized to search for transition state structures for proton transfer in the 1,2,3-triazole-triazolium complexes on the basis of optimized dimers. The result suggests six transition state structures for single proton transfer in the complexes, most of which are coplanar. The energy barriers, between different stable and transition states structures with zero point energy (ZPE) corrections, show that proton transfer occurs at room temperature with coplanar configuration that has the lowest energy. The results clearly support that reorientation gives triazole flexibility for proton transfer. (author)
Ramsdellite-structured LiTiO 2: A new phase predicted from ab initio calculations
Koudriachova, M. V.
2008-06-01
A new phase of highly lithiated titania with potential application as an anode in Li-rechargeable batteries is predicted on the basis of ab initio calculations. This phase has a composition LiTiO2 and may be accessed through electrochemical lithiation of ramsdellite-structured TiO2 at the lowest potential reported for titanium dioxide based materials. The potential remains constant over a wide range of Li-concentrations. The new phase is metastable with respect to a tetragonally distorted rock salt structure, which hitherto has been the only known polymorph of LiTiO2.
Klippenstein, Stephen J; Harding, Lawrence B; Ruscic, Branko
2017-09-07
The fidelity of combustion simulations is strongly dependent on the accuracy of the underlying thermochemical properties for the core combustion species that arise as intermediates and products in the chemical conversion of most fuels. High level theoretical evaluations are coupled with a wide-ranging implementation of the Active Thermochemical Tables (ATcT) approach to obtain well-validated high fidelity predictions for the 0 K heat of formation for a large set of core combustion species. In particular, high level ab initio electronic structure based predictions are obtained for a set of 348 C, N, O, and H containing species, which corresponds to essentially all core combustion species with 34 or fewer electrons. The theoretical analyses incorporate various high level corrections to base CCSD(T)/cc-pVnZ analyses (n = T or Q) using H2, CH4, H2O, and NH3 as references. Corrections for the complete-basis-set limit, higher-order excitations, anharmonic zero-point energy, core-valence, relativistic, and diagonal Born-Oppenheimer effects are ordered in decreasing importance. Independent ATcT values are presented for a subset of 150 species. The accuracy of the theoretical predictions is explored through (i) examination of the magnitude of the various corrections, (ii) comparisons with other high level calculations, and (iii) through comparison with the ATcT values. The estimated 2σ uncertainties of the three methods devised here, ANL0, ANL0-F12, and ANL1, are in the range of ±1.0-1.5 kJ/mol for single-reference and moderately multireference species, for which the calculated higher order excitations are 5 kJ/mol or less. In addition to providing valuable references for combustion simulations, the subsequent inclusion of the current theoretical results into the ATcT thermochemical network is expected to significantly improve the thermochemical knowledge base for less-well studied species.
Simeon, Tomekia M.; Yanov, Ilya; Leszczynski, Jerzy
This article presents the results of systematic ab initio quantum chemical study of charged and neutral analogues of fullerene molecules: C59X[XSi, Ge, Sn], C59X- [XB, Al, Ga, In], and C59X+ [XN, P, As, Sb]. Hartree-Fock (HF) and density functional theory (DFT) levels of theory with Stuttgart-Dresden basis set were used to investigate the structure and properties of substituted fullerene molecules. A replacement of fullerene carbon atom with a heteroatom results in a unique chemical site on the fullerene surface, which may be used as a reactive center or to modify the electronic properties. We show the possibility of utilization of substituted fullerenes as atom-like building units. Heteroatom substitution allows the tuning of the physical and chemical properties of original molecule for different material science and nanotechnology applications.
Ab-initio study of magnetic properties and phase transitions in Ga (Mn) N with Monte Carlo approach
Energy Technology Data Exchange (ETDEWEB)
Sbai, Y.; Ait Raiss, A.; Salmani, E. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Bahmad, L., E-mail: Bahmad@fsr.ac.ma [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Benyoussef, A. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco); Hassan II Academy of Science and Technology, Rabat (Morocco)
2015-12-15
On the basis of ab-initio calculations and Monte Carlo simulations the magnetic and electronic properties of Gallium nitride (GaN) doped with the transition metal Manganese (Mn) were studied. The ab initio calculations were done using the AKAI–KKR–CPA method within the Local Density Approximation (LDA) approximation. We doped our Diluted Magnetic Semiconductor (DMS), with different concentrations of magnetic impurities Mn and plotted the density of state (DOS) for each one. Showing a half-metallic behavior and ferromagnetic state especially for Ga{sub 0.95}Mn{sub 0.05}N making this DMS a strong candidate for spintronic applications. Moreover, the magnetization and susceptibility of our system as a function of the temperature has been calculated and give for various system size L to study the size effect. In addition, the transition temperature was deduced from the peak of the susceptibility. The Ab initio results are in good agreement with literature especially for (x=0.05) of Mn which gives the most interesting results. - Highlights: • The AKAI–KKR–CPA method has been applied to study the doped compound GaN:Mn. • The local density approximation (LDA) has been applied. • The ab-initio calculations have been performed. • The density of states (DOS) have been plotted for differents doping concentrations, using Monte Carlo simulations.
Prasath, M.; Muthu, S.; Arun Balaji, R.
2013-09-01
The FT-IR and FT-Raman spectrum of 7-chloro-2-methylamino-5-phenyl-3H-1, 4-benzodiazepine-4-oxide (7CMP4BO) has been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The optimized geometry, Thermodynamic properties, NBO, Molecular Electrostatic Potentials, PES, frequency and intensity of the vibrational bands of 7CMP4BO were obtained by the ab initio HF and density functional theory (DFT), B3LYP/6-31G (d,p) basis set. The molecule orbital contributions were studied by using the total (TDOS), partial (PDOS), and overlap population (OPDOS) density of states. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated molecule have been computed using DFT quantum mechanical calculations. The observed and the calculated frequencies are found to be in good agreement. The experimental spectra also coincide satisfactorily with those of theoretically calculated values.
E2 and SN2 Reactions of X(-) + CH3CH2X (X = F, Cl); an ab Initio and DFT Benchmark Study.
Bento, A Patrícia; Solà, Miquel; Bickelhaupt, F Matthias
2008-06-01
We have computed consistent benchmark potential energy surfaces (PESs) for the anti-E2, syn-E2, and SN2 pathways of X(-) + CH3CH2X with X = F and Cl. This benchmark has been used to evaluate the performance of 31 popular density functionals, covering local-density approximation, generalized gradient approximation (GGA), meta-GGA, and hybrid density-functional theory (DFT). The ab initio benchmark has been obtained by exploring the PESs using a hierarchical series of ab initio methods [up to CCSD(T)] in combination with a hierarchical series of Gaussian-type basis sets (up to aug-cc-pVQZ). Our best CCSD(T) estimates show that the overall barriers for the various pathways increase in the order anti-E2 (X = F) SN2 (X = F) SN2 (X = Cl) ∼ syn-E2 (X = F) SN2 dominates for Cl(-) + CH3CH2Cl, while syn-E2 is in all cases the least favorable pathway. Best overall agreement with our ab initio benchmark is obtained by representatives from each of the three categories of functionals, GGA, meta-GGA, and hybrid DFT, with mean absolute errors in, for example, central barriers of 4.3 (OPBE), 2.2 (M06-L), and 2.0 kcal/mol (M06), respectively. Importantly, the hybrid functional BHandH and the meta-GGA M06-L yield incorrect trends and qualitative features of the PESs (in particular, an erroneous preference for SN2 over the anti-E2 in the case of F(-) + CH3CH2F) even though they are among the best functionals as measured by their small mean absolute errors of 3.3 and 2.2 kcal/mol in reaction barriers. OLYP and B3LYP have somewhat higher mean absolute errors in central barriers (5.6 and 4.8 kcal/mol, respectively), but the error distribution is somewhat more uniform, and as a consequence, the correct trends are reproduced.
On the hierarchical parallelization of ab initio simulations
Ruiz-Barragan, Sergi; Shiga, Motoyuki
2016-01-01
A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.
Discovering chemistry with an ab initio nanoreactor
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 alpha-alpha scattering
Elhatisari, Serdar; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-01-01
Processes involving alpha particles and alpha-like nuclei comprise a major part of stellar nucleosynthesis and hypothesized mechanisms for thermonuclear supernovae. In an effort towards understanding alpha processes from first principles, we describe in this letter the first ab initio calculation of alpha-alpha scattering. We use lattice effective field theory to describe the low-energy interactions of nucleons and apply a technique called the adiabatic projection method to reduce the eight-body system to an effective two-cluster system. We find good agreement between lattice results and experimental phase shifts for S-wave and D-wave scattering. The computational scaling with particle number suggests that alpha processes involving heavier nuclei are also within reach in the near future.
An ab initio study of hydroxylated graphane
Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola
2017-09-01
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.
Giant magnetoresistance An ab-initio description
Binder, J
2000-01-01
A new theoretical concept to study the microscopic origin of Giant Magnetoresistance (GMR) from first principles is presented. The method is based on ab-initio electronic structure calculations within the spin density functional theory using a Screened KORRINGA-KOHNROSTOKER method. Scattering at impurity atoms in the multilayers is described by means of a GREEN's-function method. The scattering potentials are calculated self-consistently. The transport properties are treated quasi-classically solving the BOLTZMANN equation including the electronic structure of the layered system and the anisotropic scattering. The solution of the BOLTZMANN equation is performed iteratively taking into account both scattering out and scattering in terms (vertex corrections). The method is applied to Co/Cu and Fe/Cr multilayers. Trends of scattering cross sections, residual resistivities and GMR ratios are discussed for various transition metal impurities at different positions in the Co/Cu or Fe/Cr multilayers. Furthermore the...
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Dakkouri, Marwan; Grosser, Martin
2002-06-01
monocyanosilacyclobutane (MCYSCB). Searching for reasonable support for the explanation of the structural results of DESCB we performed detailed natural population analysis as well as Mulliken population analysis (MPA) on DESCB and other related molecules. In contrast to the Mulliken charges, the natural atomic charges provided helpful information concerning the bonding properties in DESCB and the corresponding compounds. By varying the size of some basis sets, we could demonstrate the validity of the repeatedly discussed dependency of the Mulliken MPA on the basis set. For the performance of the quantum mechanical calculations we employed the following methods and basis sets: HF/6-31G(d,p), DFT/B3PW91/6-31G(d), DFT/B3PW91/6-311++G(d,p), MP2/6-31G(d,p) and MP2/6-311++G(d,p).
Schnitzler, Elijah G; Jäger, Wolfgang
2014-02-14
The pure rotational, high-resolution spectrum of the benzoic acid-water complex was measured in the range of 4-14 GHz, using a cavity-based molecular beam Fourier-transform microwave spectrometer. In all, 40 a-type transitions and 2 b-type transitions were measured for benzoic acid-water, and 12 a-type transitions were measured for benzoic acid-D2O. The equilibrium geometry of benzoic acid-water was determined with ab initio calculations, at the B3LYP, M06-2X, and MP2 levels of theory, with the 6-311++G(2df,2pd) basis set. The experimental rotational spectrum is most consistent with the B3LYP-predicted geometry. Narrow splittings were observed in the b-type transitions, and possible tunnelling motions were investigated using the B3LYP/6-311++G(d,p) level of theory. Rotation of the water moiety about the lone electron pair hydrogen-bonded to benzoic acid, across a barrier of 7.0 kJ mol(-1), is the most likely cause for the splitting. Wagging of the unbound hydrogen atom of water is barrier-less, and this large amplitude motion results in the absence of c-type transitions. The interaction and spectroscopic dissociation energies calculated using B3LYP and MP2 are in good agreement, but those calculated using M06-2X indicate excess stabilization, possibly due to dispersive interactions being over-estimated. The equilibrium constant of hydration was calculated by statistical thermodynamics, using ab initio results and the experimental rotational constants. This allowed us to estimate the changes in percentage of hydrated benzoic acid with variations in the altitude, region, and season. Using monitoring data from Calgary, Alberta, and the MP2-predicted dissociation energy, a yearly average of 1% of benzoic acid is expected to be present in the form of benzoic acid-water. However, this percentage depends sensitively on the dissociation energy. For example, when using the M06-2X-predicted dissociation energy, we find it increases to 18%.
Gatial, Anton; Herich, Peter; Tarabová, Denisa; Milata, Viktor; Prónayová, Nadežda
2017-07-01
The conformers of push-pull 3-[(2,2-dimethylhydrazinyl)methylene]-pentane-2,4-dione (CH3)2Nsbnd NHsbnd CHdbnd C(COCH3)2 (DMHMP) have been studied experimentally by NMR and vibrational spectroscopy and theoretically by ab initio calculations at MP2 and DFT B3LYP levels in various basis sets. The NMR spectra were obtained in chloroform and dimethylsulfoxide and the IR and Raman spectra of DMHMP as a solid and as a solute in various less and more polar solvents at room temperature have been recorded. DMHMP was prepared as a pure solid and the data from X-ray analysis revealed that DMHMP exists in solid state as EZa conformer with an intramolecular hydrogen bond. The geometries and relative energies of possible conformers of DMHMP were evaluated at the both levels of theory in several basis sets and compared with the data from X-ray analysis. According to the NMR spectra the studied compound exists as a single entity. On the other hand vibrational spectra revealed that in less polar DMHMP solutions the presence of the second less polar ZZa conformer is possible, whereas in more polar solvent only one EZa conformer is observed. The influence of the environment polarity on this conformational equilibrium is discussed with respect to the SCRF solvent effect calculations using IEFPCM model. The observed IR and Raman bands were compared with calculated MP2/cc-pVTZ harmonic vibrational frequencies and assigned on the basis of potential energy distribution.
Exploring the free energy surface using ab initio molecular dynamics
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.
Vrentas, Catherine E; Moayeri, Mahtab; Keefer, Andrea B; Greaney, Allison J; Tremblay, Jacqueline; O'Mard, Danielle; Leppla, Stephen H; Shoemaker, Charles B
2016-10-07
Infection with Bacillus anthracis, the causative agent of anthrax, can lead to persistence of lethal secreted toxins in the bloodstream, even after antibiotic treatment. VHH single-domain antibodies have been demonstrated to neutralize diverse bacterial toxins both in vitro and in vivo, with protein properties such as small size and high stability that make them attractive therapeutic candidates. Recently, we reported on VHHs with in vivo activity against the protective antigen component of the anthrax toxins. Here, we characterized a new set of 15 VHHs against the anthrax toxins that act by binding to the edema factor (EF) and/or lethal factor (LF) components. Six of these VHHs are cross-reactive against both EF and LF and recognize the N-terminal domain (LFN, EFN) of their target(s) with subnanomolar affinity. The cross-reactive VHHs block binding of EF/LF to the protective antigen C-terminal binding interface, preventing toxin entry into the cell. Another VHH appears to recognize the LF C-terminal domain and exhibits a kinetic effect on substrate cleavage by LF. A subset of the VHHs neutralized against EF and/or LF in murine macrophage assays, and the neutralizing VHHs that were tested improved survival of mice in a spore model of anthrax infection. Finally, a bispecific VNA (VHH-based neutralizing agent) consisting of two linked toxin-neutralizing VHHs, JMN-D10 and JMO-G1, was fully protective against lethal anthrax spore infection in mice as a single dose. This set of VHHs should facilitate development of new therapeutic VNAs and/or diagnostic agents for anthrax. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Ab initio materials physics and microscopic electrodynamics of media
2016-01-01
We argue that the amazing progress of first-principles materials physics necessitates a revision of the Standard Approach to electrodynamics of media. We hence subject this Standard Approach to a thorough critique, which shows both its inherent conceptual problems and its practical inapplicability to modern ab initio calculations. We then go on to show that the common practice in ab initio materials physics has overcome these difficulties by taking a different, microscopic approach to electro...
The importance of basis states: an example using the Hydrogen basis
Forestell, Lindsay
2015-01-01
We use a simple system, the electron configuration in a Hydrogen-like atom, to demonstrate the importance of using a complete basis set to provide a proper quantum mechanical description. We first start with what might be considered a successful strategy --- to diagonalize a truncated Hamiltonian matrix, written in a basis consisting of Hydrogen ($Z=1$) basis states. This fails to provide the correct answer, and we then demonstrate that the continuum basis states provided the rest of the true wave function, for the bound ground states. This work then shows, in a relatively simple system, the need to utilize a complete basis set, consisting of both bound and continuum states.
Ab initio calculations in the symplectic no-core configuration interaction framework
McCoy, Anna; Caprio, Mark; Dytrych, Tomas
2016-09-01
A major challenge in quantitatively predicting nuclear structure directly from realistic nucleon-nucleon interactions, i.e., ab initio, arises due to an explosion in the dimension of the traditional Slater determinant basis as the number of nucleons and included shells increases. The need for including highly excited configurations arises, in large part, because the kinetic energy induces strong coupling across shells. However, the kinetic energy conserves symplectic symmetry. By combining this symplectic symmetry with the no-core configuration interaction (NCCI) framework, we reduce the size of basis necessary to obtain accurate results for p-shell nuclei. Supported by the US DOE under Grants DE-AC05-06OR23100 and DE-FG02-95ER-40934, and the Czech Science Foundation under Grant No. 16-16772S.
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Energy Technology Data Exchange (ETDEWEB)
Dytrych, T. [Academy of Sciences of the Czech Republic (ASCR), Prague (Czech Republic); Louisiana State Univ., Baton Rouge, LA (United States); Maris, Pieter [Iowa State Univ., Ames, IA (United States); Launey, K. D. [Louisiana State Univ., Baton Rouge, LA (United States); Draayer, J. P. [Louisiana State Univ., Baton Rouge, LA (United States); Vary, James [Iowa State Univ., Ames, IA (United States); Langr, D. [Czech Technical Univ., Prague (Czech Republic); Aerospace Research and Test Establishment, Prague (Czech Republic); Saule, E. [Univ. of North Carolina, Charlotte, NC (United States); Caprio, M. A. [Univ. of Notre Dame, IN (United States); Catalyurek, U. [The Ohio State Univ., Columbus, OH (United States). Dept. of Electrical and Computer Engineering; Sosonkina, M. [Old Dominion Univ., Norfolk, VA (United States)
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.
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Dytrych, T; Launey, K D; Draayer, J P; Vary, J P; Langr, D; Saule, E; Caprio, M A; Catalyurek, U; Sosonkina, M
2016-01-01
We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and significant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis affords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Dytrych, T.; Maris, P.; Launey, K. D.; Draayer, J. P.; Vary, J. P.; Langr, D.; Saule, E.; Caprio, M. A.; Catalyurek, U.; Sosonkina, M.
2016-10-01
We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU3-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and significant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis affords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.
An accurate potential energy curve for helium based on ab initio calculations
Janzen, A. R.; Aziz, R. A.
1997-07-01
Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.
Interatomic Potentials for NiZr Alloys from Experimental and Ab initio Calculations
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
We applied an approach to the development of many-body interatomic potentials for NiZr alloys, gaining an improved accuracy and reliability. The functional form of the potential is that of the embedded method, but it has been improved as follows. (1) The database used for the development of the potential includes both experimental data and a large set of energies of different structures of the alloys generated by Fab initio calculations. (2) The optimum parametrization of the potential for the given database is obtained by fitting.Using this approach we developed reliable interatomic potentials for Ni and Zr. The potential accurately reproduces basic equilibrium properties of the alloys.
Moore, Keith; Lane, Ian C
2015-01-01
BaH is an attractive molecular candidate for laser cooling to ultracold temperatures and a potential precursor for the production of ultracold gases of hydrogen and deuterium. The theoretical challenge is to simulate the laser cooling cycle as reliably as possible and this paper addresses the generation of highly accurate ab initio potentials for such studies. The performance of various basis sets within the multi-reference configuration-interaction (MRCI) approximation with the Davidson correction (MRCI+Q) is tested and taken to the complete basis set limit. It is shown that the calculated molecular constants using a 46 electron Effective Core-Potential (ECP), the augmented polarized core-valence quintuplet basis set (aug-pCV5Z-PP) but only including three active electrons in the MRCI calculation are in close agreement with the available experimental values. The predicted dissociation energy D$_e$ for the X$^2\\Sigma^+$ state (extrapolated to the complete basis set (CBS) limit) is 16975.14 cm$^{-1}$ (2.099 eV...
Ab initio calculation of the Hoyle state
Epelbaum, Evgeny; Lee, Dean; Meißner, Ulf-G
2011-01-01
The Hoyle state plays a crucial role in the hydrogen 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^{1} 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^{2,3}, 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 properties of the Hoyle state and in agreement with the experimentally observed energy. These lattice simulations provide insight into the structure of this unique state and new clues as to the amount of fine...
Ab initio phase diagram of iridium
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.
Phonocatalysis. An ab initio simulation experiment
Directory of Open Access Journals (Sweden)
Kwangnam Kim
2016-06-01
Full Text Available Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.
Ab initio phonon scattering by dislocations
Wang, Tao; Carrete, Jesús; van Roekeghem, Ambroise; Mingo, Natalio; Madsen, Georg K. H.
2017-06-01
Heat management in thermoelectric and power devices as well as in random access memories poses a grand challenge and can make the difference between a working and an abandoned device design. Despite the prevalence of dislocations in all these technologies, the modeling of their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce an efficient ab initio approach based on Green's functions computed by two-dimensional reciprocal space integration. By combining elasticity theory and density functional theory, we calculate the scattering strength of a 90∘ misfit edge dislocation in Si. Because of the breakdown of the Born approximation, earlier literature models fail, even qualitatively. We find that a dislocation density larger than 109cm-2 is necessary to substantially influence thermal conductivity at room temperature and above. We quantify how much of the reduction of thermal conductivity measured in nanograined samples can be explained by realistic dislocation concentrations.
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
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).
DEFF Research Database (Denmark)
Åstrand, Per-Olof; Ramanujam, P.S.; Hvilsted, Søren
2000-01-01
Electronic excitation energies of 16 azobenzene dyes have been calculated by ab initio methods within the second-order polarization propagator approximation (SOPPA). Good agreement with expriment is found for the lowest singlet and triplet states for both the trans- and cis-azobenzene molecules......, the experimental singlet π → π* transitions are reproduced for a set of azobenzene dyes with different electron donor and acceptor groups and the correct shifts in excitation energy are obtained for the different substituents. It has also been demonstrated that ab initio methods can be used to determine suitable...... candidates for azo components used in materials for data storage....
Kawashima, Yoshiyuki; Iwano, Sakae; Hirota, Eizi
2016-06-01
This paper presents an extension of the preceding talk on the FTMW spectroscopy of N_2-ES (ethylene sulfide), namely the results on N_2-DMS (dimethyl sulfide). We have previously investigated two N_2 complexes: N_2-DME (dimethyl ether), for which we reported a prelimanary result, and N_2-EO (ethylene oxide). We have observed the ground-state rotational spectrum of the N_2-DMS complex, i.e. c-type transitions in the frequency region from 5 to 24 GHz, which we assigned to the normal, 15N_2-DMS, and 15NN-DMS species of the N_2-DMS. We have found both the ortho and para states for the 14N_2-DMS and 15N_2-DMS species. In the case of the 15N_2-DMS, some transitions with Ka = 2 and 3 were observed slightly split by the internal rotation of the two methyl tops of the DMS. The observed spectra of the 15N_2-DMS were analyzed by using the XIAM program. In the case of the para state of the 15N_2-DMS, three rotational and five centrifugal distortion constants with the V3 barrier to the methyl group internal rotation, whereas, in the case of the ortho state of the 15N_2-DMS, two more centrifugal distortion constants, ΦJK and ΦKJ, were needed to reproduce the observed spectra. For the N_2-DMS complex, we concluded that the N_2 moiety was located in a plane perpendicular to the C-S-C plane and bisecting the CSC angle of the DMS. We have carried out ab initio molecular orbital calculations at the level of MP2 with basis sets 6-311++G(d, p), aug-cc-pVDZ, and aug-cc-pVTZ, to complement the information on the intracomplex motions obtained from the observed rotational spectra. We have applied a natural bond orbital (NBO) analysis to the N_2-DMS and N_2-ES to calculate the stabilization energy CT (=Δ Eσσ*), which was closely correlated with the binding energy EB, as found for other related complexes. Y. Kawashima, Y. Tatamitani, Y. Morita, and E. Hirota, 61st International Symposium on Molecular Spectroscopy, TE10 (2006) Y. Kawashima and E. Hirota, J. Phys. Chem. A 2013 117, 13855
Ab Initio Investigations of the Excited Electronic States of CaOCa
Fawzy, Wafaa M.; Heaven, Michael
2016-06-01
Chemical bonding in alkaline earth hypermetalic oxides is of fundamental interest. Previous Ab initio studies of CaOCa predicted a centrosymmetric linear geometry for both the 1Σg^+ ground state and the low lying triplet 3Σu^+ state. However, there have been no reports concerning the higher energy singlet and triplet states. The present work is focused on characterization of the potential energy surface (PES) of the excited 1Σu^+ state (assuming a centrosymmetric linear geometry) and obtaining predictions for the 1Σu^+←1Σg^+ vibronic transitions. We employed the multireference configuration interaction (MRCISD) method with state-averaged, full-valence complete active space self-consistent field (SA-FV-CASSCF) wavefunctions. In these calculations, the active space consisted of ten valence electrons in twelve orbitals, where all the valence electrons were correlated. Contributions of higher excitation and relativistic effects were taken into account using the Davidson correction and the Douglas-Kroll (DK) Hamiltonian, respectively. The correlation-consistent polarized weighed core-valence quadruple zeta basis set (cc-pwCVQZ-DK) was used for all three atoms. The full level of theory is abbreviated as SA-FV-CASSCF (10,12)-MRCISD-Q/cc-pwCVQZ-DK. The calculations were carried out using the MOLPRO2012 suite of programs. For the centrosymmetric linear geometry in all states, initial investigations of one-dimensional radial cuts provided equilibrium bond distances of 2.034 {Å}, 2.034 {Å}, and 1.999 {Å} for the 1Σg^+ , 3Σu^+ , and 1Σu^+ states, respectively. The vertical excitation frequency of the 1Σu^+←1Σg^+ optical transition was calculated to occur at 14801 wn. These predictions were followed by spectroscopic searches by Heaven et al. Indeed, rotationally resolved vibronic progressions were recorded in the vicinity of the predicted electronic band origin. Calculation of the three-dimensional PES showed that the potential minimum in the 1Σu^+ corresponds
Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S
2014-06-10
We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good
Economic communication model set
Zvereva, Olga M.; Berg, Dmitry B.
2017-06-01
This paper details findings from the research work targeted at economic communications investigation with agent-based models usage. The agent-based model set was engineered to simulate economic communications. Money in the form of internal and external currencies was introduced into the models to support exchanges in communications. Every model, being based on the general concept, has its own peculiarities in algorithm and input data set since it was engineered to solve the specific problem. Several and different origin data sets were used in experiments: theoretic sets were estimated on the basis of static Leontief's equilibrium equation and the real set was constructed on the basis of statistical data. While simulation experiments, communication process was observed in dynamics, and system macroparameters were estimated. This research approved that combination of an agent-based and mathematical model can cause a synergetic effect.
Institute of Scientific and Technical Information of China (English)
Liu Yu-Fang; Sun Jin-Feng; Ma Heng; Zhu Zun-Lue
2007-01-01
The accurate dissociation energy and harmonic frequency for the highly excited 21 Πu state of dimer 7Li2 have been calculated using a symmetry-adapted-cluster configuration-interaction method in complete active space.The calculated results are in excellent agreement with experimental measurements.The potential energy curves at numerous basis sets for this state are obtained over a wide internuclear separation range from about 2.4ao to 37.0ao.And the conclusion is gained that the basis set 6-311++G(d,p) is a most suitable one.The calculated spectroscopic constants De,Re,ωe,ωeχe,αe and Be at 6-311++G(d,p) are 0.9670 eV,0.3125 nm,238.6 cm-1,1.3705cm-1,0.0039 cm-1 and 0.4921 cm-1.respectively.The vibrational levels are calculated by solving the radial Schr(o)dinger equation of nuclear motion.A total of 53 vibrational levels are found and reported for the first time.The classical turning points have been computed.Comparing with the measurements,in which only the first nine vibrational levels have been obtained so far,the present calculations are very encouraging.A careful comparison of the present results of the parameters De and ωe with those obtained from previous theories clearly shows that the present calculations are much closer to the measurements than previous theoretical results,thus representing an improvement on the accuracy of the ab initio calculations of the potentials for this state.
Balabin, Roman M.
2009-10-01
High-level ab initio electronic structure calculations, including extrapolations to the complete basis set (CBS) limit, were performed, and highly precise relative energies of five-member N-heterocycles were determined. Nitrogen-containing heterocycles studied included tautomers of tetrazole (CH2N4) and triazoles (C2H3N3). Valence focal-point analysis of 1H-tetrazole, 2H-tetrazole, 5H-tetrazole, 1H-1,2,3-triazole, 2H-1,2,3-triazole, 1H-1,2,4-triazole, and 4H-1,2,4-triazole and a number of transition state (TS) calculations were performed, using energy values determined by CCSD(T)/aug-cc-pVTZ, MP3/aug-cc-pVQZ, and MP2/aug-cc-pV5Z. An accuracy of 0.10-0.25 kcal mol-1 (35-87 cm-1) was obtained for comparison of tautomer energy differences. Relative CCSD(T)/CBS energies of 2.07, 3.98, and 6.25 kcal mol-1 for 1H-tetrazole, 1H-1,2,3-triazole, and 4H-1,2,4-triazole, respectively, were calculated. Use of electron correlation methods resulted in markedly different convergence behaviors for triazole and tetrazole tautomers. Similarly, differences in convergence were observed for TSs with respect to corresponding minima structures. It was confirmed that the MP2 method predicts an acyclic structure for 5H-tetrazole. The same was not observed for the corresponding TS geometry. Comparison with density functional theory (B3LYP) and model chemistry methods (CBS-4M and CBS-QB3) is reported.
Valdiviés-Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M
2015-09-28
Periodic quantum-chemistry methods as implemented in the CRYSTAL14 code were considered to analyse the interaction of acid clinoptilolite with water. Initially adsorbed molecules hydrolyse the Al-O bonds, giving rise to defective dealuminated materials. A suitable and representative periodic model of the partially disordered hydrated H-zeolite is the primitive cell (18 T sites) of a decahydrated trialuminated structure of HEU topology. The water distribution inside the material cavities was initially investigated. The model considered for further dealumination was the most stable one from those generated through a combined force field Monte Carlo and ab initio optimization strategy. Optimizations and energy estimations were made at the hybrid DFT level of theory (PBE0 functional) with an atomic basis set of VDZP quality. The energetics of the different pathways involved in the dealumination process was addressed by considering the Gibbs free energy with thermal and zero-point corrections through phonon analysis. It arises that hydrated models exhibit protonated water clusters stabilized by different kinds of H-bonds. The first Al extraction is slightly more energetically favourable from T3 than T2 sites, but at the same time the latter is more probable owing to its larger Al population. However, concerning the second dealumination step, it is more favourable removing the Al atom from both remaining sites after a starting abstraction from T2 rather than T3. These facts determine that the most probable overall pathways go through a first Al removal from T2. The agreement with experimental results is discussed.
Energy Technology Data Exchange (ETDEWEB)
Surin, L. A., E-mail: surin@ph1.uni-koeln.de [I. Physikalisches Institut, University of Cologne, Zülpicher St. 77, 50937 Cologne (Germany); Institute of Spectroscopy, Russian Academy of Sciences, Fizicheskaya St. 5, 142190 Troitsk, Moscow (Russian Federation); Tarabukin, I. V.; Panfilov, V. A. [Institute of Spectroscopy, Russian Academy of Sciences, Fizicheskaya St. 5, 142190 Troitsk, Moscow (Russian Federation); Schlemmer, S. [I. Physikalisches Institut, University of Cologne, Zülpicher St. 77, 50937 Cologne (Germany); Kalugina, Y. N. [Department of Optics and Spectroscopy, Tomsk State University, 36 Lenin Ave., 634050 Tomsk (Russian Federation); Faure, A.; Rist, C. [University Grenoble Alpes, IPAG, F-38000 Grenoble (France); CNRS, IPAG, F-38000 Grenoble (France); Avoird, A. van der, E-mail: A.vanderAvoird@theochem.ru.nl [Theoretical Chemistry, Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands)
2015-10-21
The rotational spectrum of the van der Waals complex CH{sub 4}–CO has been measured with the intracavity OROTRON jet spectrometer in the frequency range of 110–145 GHz. Newly observed and assigned transitions belong to the K = 2–1 subband correlating with the rotationless j{sub CH4} = 0 ground state and the K = 2–1 and K = 0–1 subbands correlating with the j{sub CH4} = 2 excited state of free methane. The (approximate) quantum number K is the projection of the total angular momentum J on the intermolecular axis. The new data were analyzed together with the known millimeter-wave and microwave transitions in order to determine the molecular parameters of the CH{sub 4}–CO complex. Accompanying ab initio calculations of the intermolecular potential energy surface (PES) of CH{sub 4}–CO have been carried out at the explicitly correlated coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)-F12a] and an augmented correlation-consistent triple zeta (aVTZ) basis set. The global minimum of the five-dimensional PES corresponds to an approximately T-shaped structure with the CH{sub 4} face closest to the CO subunit and binding energy D{sub e} = 177.82 cm{sup −1}. The bound rovibrational levels of the CH{sub 4}–CO complex were calculated for total angular momentum J = 0–6 on this intermolecular potential surface and compared with the experimental results. The calculated dissociation energies D{sub 0} are 91.32, 94.46, and 104.21 cm{sup −1} for A (j{sub CH4} = 0), F (j{sub CH4} = 1), and E (j{sub CH4} = 2) nuclear spin modifications of CH{sub 4}–CO, respectively.
Roemelt, Michael
2015-07-01
Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.
Energy Technology Data Exchange (ETDEWEB)
Collier, W.B. [Department of Chemistry, Oral Roberts University, Tulsa, Oklahoma 74171 (United States); Magdo, I. [Gedeon Richter Ltd., Molecular Design Unit, P.O. Box 27, H-1475, Budapest (Hungary); Klots, T.D. [Bartlesville Thermodynamic Group, BDM Petroleum Technologies, P.O. Box 2543, Bartlesville, Oklahoma 74005 (United States)
1999-03-01
This paper reports the application of a scaled {ital ab initio} calculated harmonic force field to predict the frequencies, infrared intensities, Raman intensities, and depolarization ratios of benzofuran, benzothiophene, indole, benzothiazole, and benzoxazole. The theoretical calculations were made using the Hartree{endash}Fock HF/3-21G{sup {asterisk}} and HF/6-31G{sup {asterisk}} basis sets and density-functional theory (DFT)B3-LYP/6-31G{sup {asterisk}} levels. The equilibrium calculated force constants are scaled according to the method of Pulay and compared with the experimentally determined frequencies, intensities, and depolarization ratios to assess the accuracy and fit of the theoretical calculation. Methods for quantitative comparison of intensities were developed. The double numerical differentiation algorithm of Komornicki and McIver was analyzed and used to calculate the Raman intensities for the (DFT)B3-LYP/6-31G{sup {asterisk}} model. The (DFT)B3-LYP/6-31G{sup {asterisk}} model is approaching the harmonic limit in the planar and nonplanar refinement of these bicyclics with wave number fits of 5 and 4 cm{sup {minus}1}, respectively. It reduces the need for scale factors and increases their transfer accuracy, largely because the scale factors values cluster near unity. The Komornicki and McIver algorithm is still a viable method for calculating Raman intensity information for methods that do not have analytic routines programmed. The main shortcoming to this method may lie in the tighter self-consistent field (SCF) convergence criterion possibly needed to calculate Raman intensities for the totally symmetric modes of large molecules. The (DFT)B3-LYP/6-31G{sup {asterisk}} model was superior for calculating the planar intensities, but equal to the HF methods for predicting the nonplanar intensities. {copyright} {ital 1999 American Institute of Physics.}
Ab Initio Studies of Stratospheric Ozone Depletion Chemistry
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.
Energy Technology Data Exchange (ETDEWEB)
Orimoto, Yuuichi; Xie, Peng; Liu, Kai [Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Yamamoto, Ryohei [Department of Molecular and Material Sciences, Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Imamura, Akira [Hiroshima Kokusai Gakuin University, 6-20-1 Nakano, Aki-ku, Hiroshima 739-0321 (Japan); Aoki, Yuriko, E-mail: aoki.yuriko.397@m.kyushu-u.ac.jp [Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580 (Japan); Japan Science and Technology Agency, CREST, 4-1-8 Hon-chou, Kawaguchi, Saitama 332-0012 (Japan)
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
Energy Technology Data Exchange (ETDEWEB)
R.J. Garrett
2002-01-14
As part of the internal Integrated Safety Management Assessment verification process, it was determined that there was a lack of documentation that summarizes the safety basis of the current Yucca Mountain Project (YMP) site characterization activities. It was noted that a safety basis would make it possible to establish a technically justifiable graded approach to the implementation of the requirements identified in the Standards/Requirements Identification Document. The Standards/Requirements Identification Documents commit a facility to compliance with specific requirements and, together with the hazard baseline documentation, provide a technical basis for ensuring that the public and workers are protected. This Safety Basis Report has been developed to establish and document the safety basis of the current site characterization activities, establish and document the hazard baseline, and provide the technical basis for identifying structures, systems, and components (SSCs) that perform functions necessary to protect the public, the worker, and the environment from hazards unique to the YMP site characterization activities. This technical basis for identifying SSCs serves as a grading process for the implementation of programs such as Conduct of Operations (DOE Order 5480.19) and the Suspect/Counterfeit Items Program. In addition, this report provides a consolidated summary of the hazards analyses processes developed to support the design, construction, and operation of the YMP site characterization facilities and, therefore, provides a tool for evaluating the safety impacts of changes to the design and operation of the YMP site characterization activities.
MP2, DFT and ab initio calculations on thioxanthone.
Beni, Alireza Salimi; Chermahini, Alireza Najafi; Sharghi, Hashem; Monfared, Setareh Mirzaei
2011-11-01
Density functional theory (DFT), HF and MP2 calculations have been carried out to investigate thioxanthone molecule using the standard 6-31+G(d,p) basis set. The results of MP2 calculations show a butterfly structure for thioxanthone. The calculated results show that the predicted geometry can well reproduce the structural parameters. The predicted vibrational frequencies were assigned and compared with experimental IR spectra. A good harmony between theory and experiment is found. The theoretical electronic absorption spectra have been calculated using CIS method. (13)C and (1)H NMR of the title compound have been calculated by means of B3LYP density functional method with 6-31+G(d,p) basis set. The comparison of the experimental and the theoretical results indicate that density functional B3LYP method is able to provide satisfactory results for predicting NMR properties. Copyright © 2011 Elsevier B.V. All rights reserved.
smyRNA: a novel Ab initio ncRNA gene finder.
Directory of Open Access Journals (Sweden)
Raheleh Salari
Full Text Available BACKGROUND: Non-coding RNAs (ncRNAs have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs. METHODOLOGY/PRINCIPAL FINDINGS: We present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences. CONCLUSIONS/SIGNIFICANCE: Our method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown ncRNA families. AVAILABILITY: (http://compbio.cs.sfu.ca/taverna/smyrna.
Strubbe, David A.; Grossman, Jeffrey C.
Classical inter-atomic potentials can be successful at predicting the vibrations of materials at system sizes intractable by quantum methods. However, to predict Raman spectra, electrons must be re-introduced, for example via a bond-polarizability model which attributes the polarizability to cylindrically symmetrical inter-atomic bonds. Parameters in assumed functional forms are fit to experimental spectra, and then a Raman intensity can be computed for each mode. In the case of amorphous silicon, the existing models do not show satisfactory agreement with experimental spectra. To generate a more accurate and transferable bond-polarizability model, we have instead begun with ab initio calculated Raman tensors for a set of a-Si:H structures [DA Strubbe et al., arXiv:1511.01139]. This atomistic data set al.lows us to obtain parameters and functional forms for a general model, without confounding errors from the potentials. This Raman model can be used to study large structural models with relevance for photovoltaics, such as medium- and long-range order in a-Si:H, nanocrystalline Si, amorphous/crystalline interfaces, or a-Si:H nanowires, at sizes that would be inaccessible for ab initio calculations. We analyze the applicability of this approach to other materials systems.
Ab initio calculations of the optical properties of crystalline and liquid InSb
Energy Technology Data Exchange (ETDEWEB)
Sano, Haruyuki, E-mail: h-sano@ishikawa-nct.ac.jp [National Institute of Technology, Ishikawa College, Kitacyujo, Tsubata, Ishikawa 929-0392 (Japan); Mizutani, Goro [School of Materials Science, Japan Advanced Institute of Science and Technology, Tatsunokuchi, Ishikawa 923-1292 (Japan)
2015-11-15
Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.
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.
Authorization basis requirements comparison report
Energy Technology Data Exchange (ETDEWEB)
Brantley, W.M.
1997-08-18
The TWRS Authorization Basis (AB) consists of a set of documents identified by TWRS management with the concurrence of DOE-RL. Upon implementation of the TWRS Basis for Interim Operation (BIO) and Technical Safety Requirements (TSRs), the AB list will be revised to include the BIO and TSRs. Some documents that currently form part of the AB will be removed from the list. This SD identifies each - requirement from those documents, and recommends a disposition for each to ensure that necessary requirements are retained when the AB is revised to incorporate the BIO and TSRs. This SD also identifies documents that will remain part of the AB after the BIO and TSRs are implemented. This document does not change the AB, but provides guidance for the preparation of change documentation.
Probing community nurses' professional basis
DEFF Research Database (Denmark)
Schaarup, Clara; Pape-Haugaard, Louise; Jensen, Merete Hartun
2017-01-01
Complicated and long-lasting wound care of diabetic foot ulcers are moving from specialists in wound care at hospitals towards community nurses without specialist diabetic foot ulcer wound care knowledge. The aim of the study is to elucidate community nurses' professional basis for treating...... diabetic foot ulcers. A situational case study design was adopted in an archetypical Danish community nursing setting. Experience is a crucial component in the community nurses' professional basis for treating diabetic foot ulcers. Peer-to-peer training is the prevailing way to learn about diabetic foot...... ulcer, however, this contributes to the risk of low evidence-based practice. Finally, a frequent behaviour among the community nurses is to consult colleagues before treating the diabetic foot ulcers....
Gas phase ion chemistry of coumarins: ab initio calculations used to ...
African Journals Online (AJOL)
Gas phase ion chemistry of coumarins: ab initio calculations used to justify ... and quadrupole mass spectrometer (qMS) coupled to a gas chromatograph is ... Ab Initio calculations, Electron ionization, Positive chemical ionization, Negative ...
Lan, Tran Nguyen; Kurashige, Yuki; Yanai, Takeshi
2014-05-13
The density matrix renormalization group (DMRG) method is used in conjunction with the complete active space (CAS) procedure, the CAS configuration interaction (CASCI), and the CAS self-consistent field (CASSCF) to evaluate hyperfine coupling constants (HFCCs) for a series of diatomic (2)Σ radicals (BO, CO(+), CN, and AlO) and vinyl (C2H3) radical. The electron correlation effects on the computed HFCC values were systematically investigated using various levels of active space, which were increasingly extended from single valence space to large-size model space entailing double valence and at least single polarization shells. In addition, the core correlation was treated by including the core orbitals in active space. Reasonably accurate results were obtained by the DMRG-CASSCF method involving orbital optimization, while DMRG-CASCI calculations with Hartree-Fock orbitals provided poor agreement of the HFCCs with the experimental values. To achieve further insights into the accuracy of HFCC calculations, the orbital contributions to the total spin density were analyzed at a given nucleus, which is directly related to the FC term and is numerically sensitive to the level of correlation treatment and basis sets. The convergence of calculated HFCCs with an increasing number of renormalized states was also assessed. This work serves as the first study on the performance of the ab initio DMRG method for HFCC prediction.
Directory of Open Access Journals (Sweden)
Veinardi Suendo
2012-07-01
Full Text Available Chlorophyll a is one the most abundant pigment on Earth that responsible for trapping the light energy to perform photosynthesis in green plants. This molecule has been studied for many years from different point of views in both experimental and theoretical interests. In this study, the restricted Hartree-Fock configuration interaction single (RHF/CIS, time-dependent density functional theory (TDDFT and several semi-empirical methods (CNDO/s and ZINDO calculations were carried out to reconstruct the UV-Vis absorption spectra of chlorophyll a. In some extend, the calculation results based on single molecule approach were succeeded to reconstruct the absorption spectra but required to be rescaled to fit the experimental one. In general, the semi-empirical methods provide better energy scaling factor that closer to unity. However, they lack of vertical transition fine features with respect to the spectrum obtained experimentally. Here, the ab initio calculations provide more complete features, especially the TDDFT at high level of basis sets that also has a good accuracy in the transition energies. The contribution of ground states and excited states orbitals in the main vertical transitions is discussed based on delocalization nature of the wavefunctions and the presence of solvent through polarizable continuum model (PCM.
Sridevi, C; Shanthi, G; Velraj, G
2012-04-01
This study represents an integrated approach towards understanding the vibrational, electronic, NMR, reactivity and structural aspects of 2-amino-4H-chromene-3-carbonitrile (ACC). A detailed interpretation of the FT IR, UV and NMR spectra were reported. Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. The electronic properties was also studied and the most prominent transition corresponds to π→π*. The lower frontier orbital energy gap and high dipole moment illustrates the high reactivity of the title molecule. The NMR results indicated that the observed chemical shifts depend not only on the structure of the molecule being studied, but also on the solvent used. ACC exhibited good nonlinear optical activity and was much greater than that of urea. Molecular electrostatic potential (MEP) results predicted that the enaminonitrile fragment of ACC to be the most reactive site for both electrophilic and nucleophilic attack. In addition, the thermodynamic properties of the compound were calculated at different temperatures and corresponding relations between the properties and temperature were also studied. Copyright © 2011 Elsevier B.V. All rights reserved.
Noël, Yves; De La Pierre, Marco; Zicovich-Wilson, Claudio M; Orlando, Roberto; Dovesi, Roberto
2014-07-14
The properties of the (n,n) icosahedral family of carbon fullerenes up to n = 10 (6000 atoms) have been investigated through ab initio quantum-mechanical simulation by using a Gaussian type basis set of double zeta quality with polarization functions (84,000 atomic orbitals for the largest case), the hybrid B3LYP functional and the CRYSTAL14 code featuring generalization of symmetry treatment. The geometry of giant fullerenes shows hybrid features, between a polyhedron and a sphere; as n increases, it approaches the former. Hexagon rings at face centres take a planar, graphene-like configuration; the 12 pentagon rings at vertices impose, however, a severe structural constraint to which hexagon rings at the edges must adapt smoothly, adopting a bent (rather than sharp) transversal profile and an inward longitudinal curvature. The HOMO and LUMO electronic levels, as well as the band gap, are well described using power laws. The gap is predicted to become zero for n ≥ 34 (69,360 atoms). The atomic excess energy with respect to the ideal graphene sheet goes to zero following the log(Nat)/Nat law, which is well described through the continuum elastic theory applied to graphene; the limits for the adopted model are briefly outlined. Compared to larger fullerenes of the series, C60 shows unique features with respect to all the considered properties; C240 presents minor structural and energetic peculiarities, too.
Energy Technology Data Exchange (ETDEWEB)
Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.; Mifflin, Amanda L.; Hess, Wayne P.; Wang, Hongfei; Cramer, Christopher J.; Govind, Niranjan
2016-03-03
Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical iden- tication of hydrocarbons and in vibrational sum-frequency generation (SFG) spec- *troscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a chal- lenge from a theoretical viewpoint. In this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effects in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes chal- lenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show signicant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.
Directory of Open Access Journals (Sweden)
Georges Dive
2004-11-01
Full Text Available Abstract: Vertical ionization energies (IE as a function of the conformation are determined at the quantum chemistry level for eighteen ÃŽÂ±-L-amino acids. Geometry optimization of the neutrals are performed within the Density Functional Theory (DFT framework using the hybrid method B3LYP and the 6-31G**(5d basis set. Few comparisons are made with wave-function-based ab initio correlated methods like MP2, QCISD or CCSD. For each amino acid, several conformations are considered that lie in the range 10-15 kJ/mol by reference to the more stable one. Their IE are calculated using the Outer-Valence-Green's-Functions (OVGF method at the neutrals' geometry. Few comparisons are made with MP2 and QCISD IE. It turns out that the OVGF results are satisfactory but an uncertainty relative to the most stable conformer at the B3LYP level persists. Moreover, the value of the IE can largely depend on the conformation due to the fact that the ionized molecular orbitals (MO can change a lot as a function of the nuclear structure.
Heuvel, Willem Van den; Soncini, Alessandro
2015-01-01
We present an ab initio methodology dedicated to the determination of the electronic structure and magnetic properties of ground and low-lying excited states, i.e., the crystal field levels, in lanthanide(III) complexes. Currently, the most popular and successful ab initio approach is the CASSCF/RASSI-SO method, consisting of the optimization of multiple complete active space self-consistent field (CASSCF) spin eigenfunctions, followed by full diagonalization of the spin--orbit coupling (SOC) Hamiltonian in the basis of the CASSCF spin states featuring spin-dependent orbitals. Based on two simple observations valid for Ln(III) complexes, namely: (i) CASSCF 4f atomic orbitals are expected to change very little when optimized for different multiconfigurational states belonging to the 4f-electronic configuration, (ii) due to strong SOC the total spin is not a good quantum number, we propose here an efficient ab initio strategy which completely avoids any multiconfigurational calculation, by optimizing a unique s...
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.
A Complete Basis Set Model Chemistry for Excited States
2007-11-02
6-311G(2d,d,p) ZPE & Thermal: B3LYP/6-311G(2d,d,p) SCF: UHF/6-311+G(3d2f,2df,2p) CBS( extrap ) - MP2: UHF/6-311+G(3d2f,2df,2p) MP3, MP4(SDQ...0.0000956 0.0000245 Before Extrap 0.0030328 0.0005829 0.0001180 "Approved for public release; distribution unlimited" 22 MP2 CBS Limit The αα second- order
CLOPW: a mixed basis set full potential electronic structure method
Bekker, Hermie Gerhard
1997-01-01
This thesis is about the development of the full potental CLOPW package for electronic structure calculations. Chapter 1 provides the necessary background in the theory of solid state physics. It gives a short overview of the effective one particle model as commonly used in solid state physics. It a
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.
Recent achievements in ab initio modelling of liquid water
Khaliullin, Rustam Z
2013-01-01
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.
Use of ab initio quantum chemical methods in battery technology
Energy Technology Data Exchange (ETDEWEB)
Deiss, E. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)
1997-06-01
Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.
P-V Relation for Mercuric Calcogenides: Ab Initio Method
Directory of Open Access Journals (Sweden)
G. Misra
2011-01-01
Full Text Available Mercuric Calcogenides found many applications in electronic and optical devices as semiconducting materials. An equation of state provides useful information about the relationship between pressure (P, volume (V and temperature (T that helps to understand the behaviour of materials under the effect of high pressure and high temperature. The present paper sheds light on the electronic structure of Mercuric Calcogenides by simulating its electronic properties through ab initio method. This ab initio method is extended to derive the equation of state for Mercuric Calcogenides. The present equation of state has also been tested for the prediction of End Point. The computed results compare well with Quantum statistical data.
Weiss, I.
2007-01-01
The thesis introduces the new concept of dendroidal set. Dendroidal sets are a generalization of simplicial sets that are particularly suited to the study of operads in the context of homotopy theory. The relation between operads and dendroidal sets is established via the dendroidal nerve functor wh
Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki
2007-11-01
Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.
Ji, Pengfei; Zhang, Yuwen
2016-03-01
On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.
Ji, Pengfei
2016-01-01
On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provide a general way that is accessible to other metals in laser heating.
Ab initio study of ferromagnetic La0.5Ba0.5CoO3
Indian Academy of Sciences (India)
Umesh V Waghmare
2003-10-01
We study structure and magnetic properties of La0.5Ba0.5CoO3 (LBCO) using ab initio density functional theory (DFT) method based on pseudopotentials and a plane-wave basis. We find the cubic structure of LBCO is ferromagnetic and lower in energy than the nonmagnetic rhombohedral structure. Through the calculation of -point phonons of LBCO in the cubic structure, we determine its structural instabilities and find that they correspond to the structural phase transition accompanying a para-ferromagnetic transition observed recently.
Energy Technology Data Exchange (ETDEWEB)
Orlando, Roberto, E-mail: roberto.orlando@unito.it; Erba, Alessandro; Dovesi, Roberto [Dipartimento di Chimica, Università di Torino and NIS, Nanostructured Interfaces and Surfaces, Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); De La Pierre, Marco [Dipartimento di Chimica, Università di Torino and NIS, Nanostructured Interfaces and Surfaces, Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); Nanochemistry Research Institute, Department of Chemistry, Curtin University, GPO Box U1987, Perth, WA 6845 (Australia); Zicovich-Wilson, Claudio M. [Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad, 1001, Col. Chamilpa, 62209 Cuernavaca (Morelos) (Mexico)
2014-09-14
Use of symmetry can dramatically reduce the computational cost (running time and memory allocation) of self-consistent-field ab initio calculations for molecular and crystalline systems. Crucial for running time is symmetry exploitation in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices (overlap, Fock, and density) in the Atomic Orbital (AO) basis are avoided and a direct transformation from the packed AO to the symmetry adapted crystalline orbital basis is performed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. Quantitative examples, referring to the implementation in the CRYSTAL code, are given for high symmetry families of compounds such as carbon fullerenes and nanotubes.
Institute of Scientific and Technical Information of China (English)
Shuang-jiang Lv; Pei-yu Zhang; Guo-zhong He
2012-01-01
A new potential energy surface is presented for the triplet state 3A' of the chemical reaction S(3P)+H2 from a set of accurate ab initio data.The single point energies are computed using highly correlated complete active space self-consistent-field and multi-reference configuration interaction wave functions with a basis set of aug-cc-pV5Z.We have fitted the full set of energy values using many-body expansion method with an Aguado-Paniagua function.Based on the new potential energy surface,we carry out the time-dependent wave packet scattering calculations over the collision energy range of 0.8-2.2 eV.Both the centrifugalsudden approximation and Coriolis Coupling cross sections are obtained.In addition,the total reaction probabilities are calculated for the reactant H2 initially in the vibrational states v=0-3 (j=0).It is found that initial vibrational excitation enhances the title reaction.
Tailoring oxygen vacancies at ZnO( 1 1 ¯ 00 ) surface: An ab initio study
Korir, K. K.; Catellani, A.; Cicero, G.
2016-09-01
Oxygen vacancies in ZnO crystals have significant impacts on its properties and applications. On the basis of ab initio results, we describe the oxygen vacancy distribution and diffusion paths away from the ZnO( 1 1 ¯ 00 ) surface, aiming to elucidate thermodynamics and kinetic stability of the vacancies and a possible control mechanism. In view of defect engineering and sensor applications, we propose efficient routes to chemically control the equilibrium concentration of the oxygen vacancies at ZnO surfaces by exposure to specific reactive gases: we show that the oxygen vacancy concentration can be increased using sulfur oxide as post-growth treatment, while under exposure to ozone, no significant amount of oxygen vacancies can be sustained on the surface.
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.
Ab-initio Study of the Diffusion Mechanisms of Gallium in a Silicon Matrix
Levasseur-Smith, Kevin; Mousseau, Normand
2007-03-01
We present the results of a study into the diffusion mechanisms of Ga defects in crystalline Si. The dominant neutral configurations for single and multi-atom defects are established by ab-initio calculations using the density functional theory in the LDA approximation, with a LCAO basis as implemented in the SIESTA package. We find formation energies of 0.7 eV and 2.9 eV, respectively, for the substitutional and tetrahedral interstitial defects, while the diatomic substitutional-tetrahedral complex has a formation energy of 2.2 eV. Subsequent calculations using this same DFT package in conjunction with the activation relaxation technique (ART nouveau) allow us to determine possible diffusion pathways as well as their corresponding saddle points and energy barriers.
Ab-initio simulations of self-diffusion mechanisms in semiconductors
Energy Technology Data Exchange (ETDEWEB)
El-Mellouhi, Fedwa [Departement de physique and Regroupement quebecois sur les materiaux de pointe, Universite de Montreal, C.P. 6128, succ. Centre-ville, Montreal, Que., H3C 3J7 (Canada)], E-mail: f.el.mellouhi@umontreal.ca; Mousseau, Normand [Departement de physique and Regroupement quebecois sur les materiaux de pointe, Universite de Montreal, C.P. 6128, succ. Centre-ville, Montreal, Que., H3C 3J7 (Canada)], E-mail: normand.mousseau@umontreal.ca
2007-12-15
We present an application of SIEST-A-RT that combines the activation relaxation technique, ART nouveau, and the local-basis ab-initio code SIESTA, to study self-defect migration pathways in semiconductors. SIESTA provides reliable descriptions of defect properties in semiconductors directly comparable to experiment as well as, once combined with ART nouveau, a detailed description of their possible migration mechanisms. We use this package to characterize the properties of vacancies in silicon and GaAs, such as relaxation geometries, formation energies at low and high temperature, diffusion mechanisms and migration barriers. We show here that diffusion in bulk semiconductors is a rich and complex phenomenon that depends not only on the geometry of the defect and the surrounding lattice but also on its charge.
Ab-initio simulations of self-diffusion mechanisms in semiconductors
El-Mellouhi, Fedwa; Mousseau, Normand
2007-12-01
We present an application of SIEST-A-RT that combines the activation relaxation technique, ART nouveau, and the local-basis ab-initio code SIESTA, to study self-defect migration pathways in semiconductors. SIESTA provides reliable descriptions of defect properties in semiconductors directly comparable to experiment as well as, once combined with ART nouveau, a detailed description of their possible migration mechanisms. We use this package to characterize the properties of vacancies in silicon and GaAs, such as relaxation geometries, formation energies at low and high temperature, diffusion mechanisms and migration barriers. We show here that diffusion in bulk semiconductors is a rich and complex phenomenon that depends not only on the geometry of the defect and the surrounding lattice but also on its charge.
Ab-initio calculations on two-electron ions in strongly coupled plasma environment
Bhattacharyya, S; Mukherjee, T K
2015-01-01
In this work, the controversy between the interpretations of recent measurements on dense aluminum plasma created with Linac coherent light sources (LCLS) X-ray free electron laser (FEL) and Orion laser has been addressed. In both kind of experiments, helium-like and hydrogen-like spectral lines are used for plasma diagnostics . However, there exist no precise theoretical calculations for He-like ions within dense plasma environment. The strong need for an accurate theoretical estimates for spectral properties of He-like ions in strongly coupled plasma environment leads us to perform ab initio calculations in the framework of Rayleigh-Ritz variation principle in Hylleraas coordinates where ion-sphere potential is used. An approach to resolve the long-drawn problem of numerical instability for evaluating two-electron integrals with extended basis inside a finite domain is presented here. The present values of electron densities corresponding to disappearance of different spectral lines obtained within the fram...
Rafiee, Marjan A; Hadipour, Nasser L; Naderi-manesh, Hossein
2004-03-01
In this paper, ab initio calculated NQR parameters for some quinoline-containing derivatives are presented. The calculations are carried out in a search for the relationships between the charge distribution of these compounds and their ability to interact with haematin. On the basis of NQR parameters, pi-electron density on the nitrogen atom of the quinoline ring plays a dominant role in determining the ability of quinolines to interact with haematin. This point was confirmed with investigation of Fe+3 cation-pi quinoline ring interactions in 2- and 4-aminoquinoline. However, our results do not show any preference for those carbon atoms of the quinoline ring which previous reports have noted. In order to calculate the NQR parameters, the electric field gradient (EFG) should be evaluated at the site of a quadrupolar nucleus in each compound. EFGs are calculated by the Gaussian 98 program using the B3LYP/6-31 G* level of theory.
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.
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.
Ab initio molecular dynamics simulation of laser melting of silicon
Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.
1996-01-01
The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting tr
Resonance and Aromaticity : An Ab Initio Valence Bond Approach
Rashid, Zahid; van Lenthe, Joop H.; Havenith, Remco W. A.
2012-01-01
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 wav
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter
2004-01-01
The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical...
Ab initio study of alanine polypeptide chain twisting
DEFF Research Database (Denmark)
Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.
2006-01-01
chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...
Relaxation of Small Molecules: an ab initio Study
Institute of Scientific and Technical Information of China (English)
CAO Yi-Gang; JIAO Zheng-Kuan; A. Antons; K. Schroeder; S. Blügel2
2002-01-01
Using an ab initio total energy and force method, we have relaxed several group IV and group V elementalclusters, in detail the arsenic and antimony dimers, silicon, phosphorus, arsenic and antimony tetramers. The obtainedbond lengths and cohesive energies are more accurate than other calculating methods, and in excellent agreement withthe experimental results.
Ab initio interatomic potentials and the thermodynamic properties of fluids
Vlasiuk, Maryna; Sadus, Richard J.
2017-07-01
Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.
Bicanonical ab Initio Molecular Dynamics for Open Systems.
Frenzel, Johannes; Meyer, Bernd; Marx, Dominik
2017-08-08
Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.
Ab-Initio Theory of Charge Transport in Organic Crystals
Hannewald, K.; Bobbert, P. A.
2005-06-01
A theory of charge transport in organic crystals is presented. Using a Holstein-Peierls model, an explicit expression for the charge-carrier mobilities as a function of temperature is obtained. Calculating all material parameters from ab initio calculations, the theory is applied to oligo-acene crystals and a brief comparison to experiment is given.
Structural flexibility of DABCO. Ab initio and DFT benchmark study
Nizovtsev, Anton S.; Ryzhikov, Maxim R.; Kozlova, Svetlana G.
2017-01-01
The energy and structural parameters of 1,4-diazabicyclo[2.2.2]octane (DABCO) obtained by various DFT methods are examined versus ab initio and experimental data. The features of twisting potentials of DABCO and closely-related species (1-azabicyclo[2.2.2]octane and bicyclo[2.2.2]octane) are discussed in light of computational schemes applied.
Ground state analytical ab initio intermolecular potential for the Cl{sub 2}-water system
Energy Technology Data Exchange (ETDEWEB)
Hormain, Laureline; Monnerville, Maurice, E-mail: maurice.monnerville@univ-lille1.fr; Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane [Laboratoire de Physique des Lasers Atomes et Molécules, Unité Mixte de Recherche (UMR) 8523, Université Lille I, Bât. P5, 59655 Villeneuve d’Ascq Cedex (France); Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón [Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, México (Mexico)
2015-04-14
The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl{sub 2} molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl{sub 2} − H{sub 2}O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl{sub 2} interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl{sub 2} on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.
Energy Technology Data Exchange (ETDEWEB)
Okajima, Toshiya; Hashikawa, Akane [Saga University, Saga (Japan). Department of Chemistry
1999-08-10
The difference of the reactivity for S{sub N}2 type oxirane ring opening of exo and endo Aflatoxin B{sub 1} (AFB{sub 1}) 8,9-oxide (exo-1 and endo-1, respectively) was analyzed with ab initio molecular orbital theory. All stationary points including transition-state structures were optimized with no geometry constraint at the RHF/3-21G basis set, and energies were evaluate at Becke3LYP/3-21G level based on the RHF/3-21G geometries. The calculation clarified the following three points: (1) the activation energy ({delta}E{sup {ne}}) for endo attacking of NH{sub 3} molecule (the reaction with exo derivatives containing exo-1) is considerably smaller than those for exo attacking (the reaction with endo ones containing endo-1), (2) the reactivity for nucleophilic oxirane ring opening is controlled by the distortion of LUMO{sub C-O} of oxirane ring, which is probably caused by exo/endo relationship between oxirane ring and five-membered dihydrofurano ring (B) with respect to A ring, and (3) the remaining part (inclusing coumarin skeleton) of AFB{sub 1} oxid has little influence on the geometry around the reaction center and the activation energy. (author)
Morita, Masato; Kłos, Jacek; Buchachenko, Alexei A.; Tscherbul, Timur V.
2017-06-01
We use accurate ab initio and quantum scattering calculations to explore the prospects for sympathetic cooling of the heavy molecular radical SrOH (2Σ+) by ultracold Li atoms in a magnetic trap. Our ab initio calculations show that the chemical reaction between spin-polarized Li and SrOH, which occurs on the triplet Li-SrOH potential energy surface (PES), is strongly endothermic and hence energetically forbidden at ultralow temperatures. The chemical reaction Li (2S) +SrOH (2Σ+) →Sr (1S) +LiOH (1Σ+) occurs barrierlessly on the singlet PES and is exothermic by 2505 cm-1. A two-dimensional PES for the triplet electronic state of Li-SrOH is calculated ab initio using the partially spin-restricted coupled cluster method with single, double, and perturbative triple excitations and a large correlation-consistent basis set. The highly anisotropic PES has a deep global minimum in the skewed Li-HOSr geometry with De=4932 cm-1 and saddle points in collinear configurations. Our quantum scattering calculations predict low spin-relaxation rates in fully spin-polarized Li + SrOH collisions with the ratios of elastic to inelastic collision rates well in excess of 100 over a wide range of magnetic fields (1-1000 G) and collision energies (10-5 to 0.1 K), suggesting favorable prospects for sympathetic cooling of SrOH molecules with spin-polarized Li atoms in a magnetic trap. We find that spin relaxation in Li + SrOH collisions occurs via a direct mechanism mediated by the magnetic dipole-dipole interaction between the electron spins of Li and SrOH, and that the indirect (spin-rotation) mechanism is strongly suppressed. The upper limit to the Li + SrOH reaction rate coefficient calculated for the singlet PES using adiabatic capture theory is found to decrease from 4 ×10-10cm3 /s to a limiting value of 3.5 ×10-10cm3 /s with decreasing temperature from 0.1 K to 1 μ K .
Energy Technology Data Exchange (ETDEWEB)
Ventelon, L. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN/SRMP), 91 - Gif-sur-Yvette (France)
2008-07-01
In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)
NestedMICA as an ab initio protein motif discovery tool
Directory of Open Access Journals (Sweden)
Down Thomas A
2008-01-01
Full Text Available Abstract Background Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally developed for finding transcription binding site motifs, to find short protein signals, and compared its performance with another popular protein motif finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven by a Monte Carlo technique called Nested Sampling. It uses multi-class sequence background models to represent different "uninteresting" parts of sequences that do not contain motifs of interest. In order to assess NestedMICA as a protein motif finder, we have tested it on synthetic datasets produced by spiking instances of known motifs into a randomly selected set of protein sequences. NestedMICA was also tested using a biologically-authentic test set, where we evaluated its performance with respect to varying sequence length. Results Generally NestedMICA recovered most of the short (3–9 amino acid long test protein motifs spiked into a test set of sequences at different frequencies. We showed that it can be used to find multiple motifs at the same time, too. In all the assessment experiments we carried out, its overall motif discovery performance was better than that of MEME. Conclusion NestedMICA proved itself to be a robust and sensitive ab initio protein motif finder, even for relatively short motifs that exist in only a small fraction of sequences. Availability NestedMICA is available under the Lesser GPL open-source license from: http://www.sanger.ac.uk/Software/analysis/nmica/