Restricted Hartree-Fock Calculations Research Articles

A Task-Based Approach to Parallel Restricted Hartree-Fock Calculations.

In recent years, parallelism via multithreading has become extremely important to the optimization of high-performance electronic structure theory codes. Such multithreading is generally achieved via OpenMP constructs, using a fork-join threading model to enable thread-level data parallelism within the code. An alternative approach to multithreading is task-based parallelism, which displays multiple benefits relative to fork-join thread parallelism. A novel Restricted Hartree-Fock (RHF) algorithm, utilizing task-based parallelism to achieve optimal performance, was developed and implemented into the JuliaChem electronic structure theory software package. The new RHF algorithm utilizes a unique method of shell quartet batch creation, enabling construction and distribution of fine-grained shell quartet batches in a load-balanced manner using the Julia task construct. These shell quartet batches are then distributed statically across message-passing interface (MPI) ranks and dynamically across threads within an MPI rank, requiring no explicit inter-rank or interthread synchronization to do so. Compared to the hybrid MPI/OpenMP RHF algorithm present in the GAMESS software package, the task-based algorithm demonstrates speedups of up to ∼40% for systems in the S22(3) test set of molecules, with system sizes up to ∼1000 basis functions. The JuliaChem algorithm demonstrates the viability of both the task-based parallelism model and the Julia programming language for construction of performant electronic structure theory codes targeting systems of a size of chemical interest.

Propagation of Holes and Electrons in Metal-Organic Frameworks.

Charge transport in two zinc metal-organic frameworks (MOFs) has been investigated using periodic semiempirical molecular orbital calculations with the AM1* Hamiltonian. Restricted Hartree-Fock calculations underestimate the band gap using Koopmans theorem (ca. 2 eV compared to the experimental value of 2.8 eV). However, it almost doubles when the constraint on the wave function to remain spin-restricted is removed and the energies of the UHF Natural Orbitals are used. Charge-transport simulations using propagation of the electron- or hole-density in imaginary time allow charge-transport paths and mechanisms to be determined. The calculated relative mobilities in the directions of the three crystal axes agree with experimental expectations, but the absolute values are not reliable using the current technique. Hole-mobility along the crystal c-axis (along the metal stacks) is found to be 13 times higher in the zinc MOF with anthracene linker (Zn-ANMOF-74) than in the other directions, whereas the factor is far smaller (1.7) for electron mobility. Directional preferences are far less distinct in the equivalent structure with phenyl linkers (Zn-MOF-74). The imaginary-time simulation technique does not give quantitative mobilities. The simulations reveal a change in mechanism between the different directions: Coherent polaron migration is observed along the stacks but tunneling hops between them.

Glycine nanostructures and domains in beta-glycine: computational modeling and PFM observations

ABSTRACTIn this work computational molecular modeling of β-glycine nanostructures is presented, using various approaches, mostly semi-empirical quantum approximation PM3 type in HyperChem software in restricted Hartree-Fock calculations. The main aims of present studies focus on the molecular modeling for the β-glycine domains and domain walls formation and interaction. Obtained results are presented in visual 3D-models of the glycine domains and domain walls, compared with experimentally observed by PFM domain walls structures. Modeling is arranged with calculated values of physical data (polarization, etc.). Analysis of these new computed and corroborated PFM experimental data for β-glycine domains are presented.

Molecular structure, vibrational spectra, UV–vis, NBO, and NMR analyses on nevirapine using ab initio DFT methods

Nevirapine is an anti-human immunodeficiency virus (HIV) agent that belongs to the class of the non-nucleoside inhibitors of the HIV-1 virus reverse transcriptase. Spectral characteristics of nevirapine have been probed into by methods of Fourier transform infrared (FTIR), FT-Raman, UV-visible, and quantum chemistry. The UV spectrum was measured in methanol. In order to gain some valuable insight into the recorded spectrum, the quantum mechanical calculations were performed for nevirapine using both ZINDO and time-dependent density functional theory at B3LYP/6-31G(d,p) level. The optimized molecular geometry, bond orders, natural bond order analysis, and harmonic vibrational wavenumbers of nevirapine were calculated by restricted Hartree-Fock and density functional B3LYP methods with the 6-31G(d,p) basis set using Gaussian 03 W program. The harmonic vibrational frequencies calculated have been compared with experimental FTIR and FT-Raman spectra. The restricted Hartree-Fock and density functional theory-based nuclear magnetic resonance (NMR) calculation procedure was also performed, and it was used for assigning the 13C and 1H NMR chemical shifts of nevirapine.

Crossed molecular beams study of inelastic non-adiabatic processes in gas phase collisions between sodium ions and ZnBr2 molecules in the 0.10–3.50 keV energy range

Inelastic electronically non-adiabatic reactions between Na(+) ions and neutral ZnBr(2) molecules, both in their electronic ground state, have been studied using crossed beams techniques and measuring the decaying emission radiation of the excited species produced. The fluorescent emission corresponding to Na(3 (2)P) produced by a charge transfer reaction was observed, as well as that corresponding to the decay of Zn(4s 5s (3)S), generated by dissociation of the neutral target molecule, to Zn(4s 4p (3)P). The phosphorescent decaying emission of Zn*(4s 4p (3)P) to the zinc ground state was also observed. For each emission process, the cross section energy dependences have been measured in the 0.10-3.50 keV energy range in the laboratory system. The ground electronic state of the (NaZnBr(2))(+) collision system has been characterized by ab initio chemical structure calculations at the second order Möller-Plesset perturbation level of theory using pseudo-potentials. By performing restricted open shell Hartree-Fock calculations for C(2v) geometries, four singlet and four triplet potential energy surfaces of the system have been calculated and used to interpret qualitatively the observed reactions. A simple two-state dynamical model is presented that allows an estimation of the maximum values for measured cross sections at high collision energies to be made.

Fock-space multi-reference coupled-cluster response with the effect of triples on dipole moment of ClO and SF radicals#

Dipole moment calculations of SF and ClO radicals have been carried out using the recently developed partial triples correction to Fock-space multi-reference coupled cluster method. Theoretical calculation of the doublet SF and ClO radicals is useful due to their importance in atmospheric chemistry. The dipole moments of these radicals are extremely sensitive to correlation effects. A brief insight to the way the triples correction has been implemented is presented. We compare the results obtained from our analytic response treatment with that of restricted open Hartree-Fock (ROHF) calculations. Results are presented for both relaxed and non-relaxed approach in the ROHF method. Results suggest the importance of triples corrections. The effects of orbital relaxation are also analysed from the results.

FTIR, FT-Raman spectra and quantum chemical studies of nebivolol

Fourier transform infrared and Raman spectra of nebivolol have been recorded. The structure, conformational stability, geometry optimisation, and vibrational wave numbers have been investigated. Satisfactory vibrational assignments were made for the stable conformer of the molecule using Restricted Hartree–Fock (RHF) and density functional theory (DFT) calculation (B3LYP) with the 6-31G(d,p) basis set. Comparison of the observed fundamental vibrational wave numbers of the molecule and calculated results by RHF and DFT methods indicates that B3LYP is superior for molecular vibrational problems. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. The RHF and DFT-based NMR calculation procedure was also done. It was used to assign the 13C NMR chemical shift of nebivolol.

Two component calculations of Pt2 with relativistic effective core potential including spin‐orbit operator

AbstractThe Kramers restricted two‐component ab initio calculations were performed for the eight lowest electronic states of Pt2 using the relativistic effective core potential with the spin‐orbit operator at the multireference first‐order configuration interaction level of theory employing two‐component molecular spinors as one‐electron basis. The dominant role of the spin‐orbit effects are mainly accounted for by using two‐component spinors as one‐electron wave function, and the importance of the dynamic and the nondynamic electron correlation effects are shown by employing configuration interaction and coupled cluster methods to obtain reliable spectroscopic data for this molecule. The two‐component molecular spinors were generated from Kramers restricted Hartree–Fock calculations for the average configuration and used in the multireference Kramers restricted configuration interaction method to account for nondynamic correlation effect. Effect of dynamic correlations was investigated with the Kramers restricted coupled‐cluster (KRCC) method. Spectroscopic constants calculated at the KRCC level are in good agreement with the most recent experimental values. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

Assignments of Normally Unoccupied Orbitals to the Temporary Negative Ion States of Several Lanthanide NMR Shift Reagents and Comments on Resonance Involvement in Electron Circular Dichroism

We have measured the total electron scattering cross sections of several NMR shift reagent molecules X(hfc)3, where X = Yb, Er, Eu and Pr, by means of electron transmission spectroscopy (ETS) to determine their vertical attachment energies. A strong low-energy resonance (<1 eV) is observed in all of the compounds except for Yb(hfc)3. We explain this anomaly in terms of the ground-state electron configuration of each molecule. Also, with the aid of restricted open-shell Hartree-Fock (ROHF) calculations on analogous molecules with truncated fluorocarbon chains, we have assigned specific normally unoccupied orbitals to the resonances observed in ETS. To our knowledge, these molecules are the largest for which this procedure has been successfully completed. Nolting et al. (J. Phys. B 1997, 30, 5491) have demonstrated that the above NMR shift reagents exhibit electron circular dichroism (ECD) between 1 and 10 eV. Using our new total cross section data, we comment on the possibility of resonance involvement in the generation of ECD.

Molecules in clusters: The case of planar LiBeBCNOF built from a triangular form LiOB and a linear four-center species FBeCN

Krüger some years ago proposed a cluster LiBeBCNOF, now called periodane. His ground-state isomer proposal has recently been refined by Bera et al. using DFT. Here, we take the approach of molecules in such a cluster as starting point. We first study therefore the triangular molecule LiOB by coupled cluster theory (CCSD) and thereby specify accurately its equilibrium geometry in free space. The second fragment we consider is FBeCN, but treated now by restricted Hartree–Fock (RHF) theory. This four-center species is found to be linear, and the bond lengths are obtained from both RHF and CCSD calculations. Finally, we bring these two entities together and find that while LiOB remains largely intact, FBeCN becomes bent by the interaction with LiOB. Hartree–Fock and CCSD theories then predict precisely the same lowest isomer found by Bera et al. solely on the basis of DFT.

Ab Initio Calculated Structures and Vibrational Spectra of 1,3-Diethoxy-p-tert-butylcalix[4]crown-5-ether Complexed with Potassium Cation

Molecular structures were optimized for the 1,3-diethoxycalix[4]crown-5-ether (2) in the various isomers and their potassium-ion complexes by using B3LYP/6-31+G(d,p)//B1LYP/6-31G(d,p) method after ab initio RHF/ 6-31G calculation. The cone-shaped isomer of 2 with cr-binding mode has shown the strongest binding efficiency among the six different complexes attributed to seven electrostatic interactions between the potassium cation and the oxygen atoms of crown-5-ether and ethoxy groups of the host (2). The vibrational spectra of 2 and its K + -complexes were obtained by restricted Hartree-Fock (RHF) calculations with the 6-31G basis set. The characteristic vibrational frequencies of various C-O-C stretching and bending motions are analyzed.

Structural Characterization of Al10O6iBu16(μ-H)2, a High Aluminum Content Cluster: Further Studies of Methylaluminoxane (MAO) and Related Aluminum Complexes

The first structurally characterized isobutyl-containing aluminoxane compound is presented. The Al10O6iBu16(mu-H)2 (I) cluster is produced from neat octakis-isobutyltetraluminoxane (Al4O2iBu8) at 80 degrees C in 6-8 h followed by slow crystallization. The crystal is triclinic (space group P1) with the molecule lying on an inversion center. This aluminoxane contains both nearly linear, 154(2) degrees, aluminum-bridging hydrides and three-coordinate aluminum sites. Solid-state 27Al magic-angle spinning (MAS) NMR experiments were done at 19.6 and 40 T (833 MHz and 1.703 GHz, 1H) and at 30-35 kHz spinning speeds, leading to the determination of the Cq and eta values for the two four-coordinate Al sites and a lower limit of Cq for the three-coordinate Al site. Geometry-optimized restricted Hartree-Fock calculations at the double-zeta level of an idealized structure (methyl substituted, D2h geometry) yielded Cq and eta in close agreement with experiment; Cq agrees within 3 MHz.

A Solid-State 95Mo NMR and Computational Investigation of Dodecahedral and Square Antiprismatic Octacyanomolybdate(IV) Anions: Is the Point-Charge Approximation an Accurate Probe of Local Symmetry?

Solid-state 95Mo NMR spectroscopy is shown to be an efficient and effective tool for analyzing the diamagnetic octacyanomolybdate(IV) anions, Mo(CN)(8)4-, of approximate dodecahedral, D(2d), and square antiprismatic, D(4d), symmetry. The sensitivity of the Mo magnetic shielding (sigma) and electric field gradient (EFG) tensors to small changes in the local structure of these anions allows the approximate D(2d) and D(4d) Mo(CN)(8)4- anions to be readily distinguished. The use of high applied magnetic fields, 11.75, 17.63 and 21.1 T, amplifies the overall sensitivity of the NMR experiment and enables more accurate characterization of the Mo sigma and EFG tensors. Although the magnitudes of the Mo sigma and EFG interactions are comparable for the D(2d) and D(4d) Mo(CN)(8)4- anions, the relative values and orientations of the principal components of the Mo sigma and EFG tensors give rise to 95Mo NMR line shapes that are significantly different at the fields utilized here. Quantum chemical calculations of the Mo sigma and EFG tensors, using zeroth-order regular approximation density functional theory (ZORA DFT) and restricted Hartree-Fock (RHF) methods, have also been carried out and are in good agreement with experiment. The most significant and surprising result from the DFT and RHF calculations is a significant EFG at Mo for an isolated Mo(CN)(8)4- anion possessing an ideal square antiprismatic structure; this is contrary to the point-charge approximation, PCA, which predicts a zero EFG at Mo for this structure.

An ab initio evaluation of the role of p,π interaction: I. Ethylene derivatives

The RHF/6-311G(d) and MP2/6-311G(d) calculations with full geometry optimization were performed for XCH=CH2 molecules (X = F, Cl, Br, CH3, CH2CH3, CH2F, CHO). The py electron density distribution in these molecules and the bonding molecular orbitals formed by the py orbitals of atoms of the planar fragment of these molecule (atomic orbitals whose symmetry axes are perpendicular to this plane) are not determined by the p,π conjugation between the lone electron pair of the heteroatom in substituent X and π electrons of the C=C bond. Changes in the population of the py orbitals of the halogen and carbon atoms in going from X = F to X = Cl and Br are not associated with changes in the extent of this p,π interaction. Taking into account the electon correlation in the MP2 method does not noticeably alter the features of the electron density distribution in these molecules estimated by restricted Hartree-Fock calculations.

알칼리금속 양이온과 착물을 형성한 캘릭스[4]아릴에스터의 진동스펙트럼에 대한 순수양자역학적 연구

infrared(IR) absorption spectra were calculated for the ethyl ester of p-tert-butylcalix[4]arene (1) in the cone conformer and its alkali-metal-ion complex. The vibrational spectra were obtained by restricted Hartree-Fock (RHF) calculations with the 6-31G basis set. The characteristic vibrational frequencies of various C-O and C

The structure of low-index surfaces of β-Ga 2O 3

The physical and electronic structure of the (1 0 0), (0 1 0), (0 0 1) and ( 1 0 1 ¯ ) faces of β-Ga 2O 3 are addressed using ab initio theory. Restricted Hartree–Fock calculations, with large-core Ga and O pseudopotentials, are done to optimize the structure of first the bulk and then of slabs “cut” in the required orientations. The slab unit cells are fully relaxed during optimization, and the displacements of all atoms from the ideally-terminated positions are obtained as functions of depth into the bulk. For the relaxed slabs, single-point density functional theory calculations using the B3LYP functional and all-electron basis sets are performed to obtain surface energies, ionic charges and bond overlap populations. All surfaces exhibit a decrease in surface energy upon relaxation, and the local bonding at the surface is analyzed by comparing nearest-neighbor bond lengths and overlap populations with those in the bulk. The ( 1 0 1 ¯ ) surface, which exhibits a high energy when ideally terminated, undergoes large displacements and changes in bonding during relaxation leading to a substantial lowering of the surface energy. The band structure is also obtained for the lowest-energy surface, which is one of the possible non-polar terminations of the (1 0 0). The results provide insight into the growth and structure of β-Ga 2O 3 nanoribbons.

Electron correlations in two-dimensional small quantum dots

We consider circular and elliptic quantum dots with parabolic external confinement, containing 0--22 electrons and with values of ${r}_{s}$ in the range $0&lt;{r}_{s}&lt;3$. We perform restricted and unrestricted Hartree-Fock calculations, and further take into account electron correlations using second-order perturbation theory. We demonstrate that in many cases correlations qualitatively change the spin structure of the ground state from that obtained under Hartree-Fock and spin-density-functional calculations. In some cases the correlation effects destroy Hund's rule. We also demonstrate that the correlations destroy static spin-density waves observed in Hartree-Fock and spin-density-functional calculations.

Finite jellium models. I. Restricted Hartree–Fock calculations

Restricted Hartree-Fock calculations have been performed on the Fermi configurations of n electrons confined within a cube. The self-consistent-field orbitals have been expanded in a basis of N particle-in-a-box wave functions. The difficult one- and two-electron integrals have been reduced to a small set of canonical integrals that are calculated accurately using quadrature. The total energy and exchange energy per particle converge smoothly toward their limiting values as n increases; the highest occupied molecular orbital-lowest unoccupied molecular orbital gap and Dirac coefficient converge erratically. However, the convergence in all cases is slow.

Globally convergent trust-region methods for self-consistent field electronic structure calculations

As far as more complex systems are being accessible for quantum chemical calculations, the reliability of the algorithms used becomes increasingly important. Trust-region strategies comprise a large family of optimization algorithms that incorporates both robustness and applicability for a great variety of problems. The objective of this work is to provide a basic algorithm and an adequate theoretical framework for the application of globally convergent trust-region methods to electronic structure calculations. Closed shell restricted Hartree-Fock calculations are addressed as finite-dimensional nonlinear programming problems with weighted orthogonality constraints. A Levenberg-Marquardt-like modification of a trust-region algorithm for constrained optimization is developed for solving this problem. It is proved that this algorithm is globally convergent. The subproblems that ensure global convergence are easy-to-compute projections and are dependent only on the structure of the constraints, thus being extendable to other problems. Numerical experiments are presented, which confirm the theoretical predictions. The structure of the algorithm is such that accelerations can be easily associated without affecting the convergence properties.

Structure of the Amodiaquine−FPIX μ Oxo Dimer Solution Complex at Atomic Resolution

Using NMR inversion recovery experiments and XPLOR distance restraint calculations, we recently deduced the structure of ferriprotoporphyrin IX (FPIX) heme mu oxo dimer-antimalarial drug complexes for chloroquine (CQ), quinine (QN), and quinidine (QD) at atomic resolution [A. Leed et al., Biochemistry 2002, 41, 10245-55]. Using similar methods, we now report an unexpected structure for the complex formed between FPIX and the related drug amodiaquine (AQ). The deduced structure is further supported by comparing AQ chemical-shift data to restricted Hartree-Fock calculations. The structure further highlights the critical nature of quinoline drug side-chain composition in stabilizing noncovalent association to FPIX. Heme Fe-AQ proton distances are longer, relative to those of the CQ complex, and the AQ aromatic side chain seems to have a significant role in stabilizing the complex. Relative to the FPIX-CQ complex, a similar 2:1 stoichiometry was determined for the AQ complex, in contrast to a 4:1 stoichiometry previously suggested from calorimetry data. These solution structures add to our rapidly growing understanding of the mechanism of quinoline antimalarial drug action and will help elucidate the mechanism(s) of quinoline antimalarial drug resistance phenomena.