Hartree-Fock Level Research Articles

Towards chemically accurate QM/MM simulations on GPUs

Computational chemistry simulations are extensively used to model natural phenomena. To maintain performance similar to molecular mechanics, but achieve comparable accuracy to quantum mechanical calculations, many researchers are using hybrid QM/MM methods. In this article we evaluate our GPU-accelerated ONIOM implementation by measurements on the crambin and HIV integrase proteins with different size QM model systems. We demonstrate that by using a larger QM region, a better energy accuracy can be achieved at the expense of simulation time. This trade-off is important to consider for the researcher running QM/MM calculations. Furthermore, we show that the ONIOM energy monotonically approaches the pure quantum mechanical energy of the whole system. The experiments are made feasible by utilizing the cutting-edge BrianQC quantum chemistry module for Hartree-Fock level SCF and our GPU-accelerated MMFF94 force field implementation for molecular mechanics calculations.

QSPR Models to Predict Thermodynamic Properties of Cycloalkanes Using Molecular Descriptors and GA-MLR Method.

Aims and Objectives:QSPR models establish relationships between different types of structural information to their observed properties. In the present study the relationship between the molecular de-scriptors and quantum properties of cycloalkanes is represented.Materials and Methods:Genetic Algorithm (GA) and Multiple Linear Regressions (MLR) were successful-ly developed to predict quantum properties of cycloalkanes. A large number of molecular descriptors were calculated with Dragon software and a subset of calculated descriptors was selected with a genetic algorithm as a feature selection technique. The quantum properties consist of the heat capacity (Cv)/ Jmol-1K-1 entropy(S)/ Jmol-1K-1 and thermal energy(Eth)/ kJmol-1 were obtained from quantum-chemistry technique at the Hartree-Fock (HF) level using the ab initio 6-31G* basis sets.Results:The Genetic Algorithm (GA) method was used to select important molecular descriptors and then they were used as inputs for SPSS software package. The predictive powers of the MLR models were dis-cussed using Leave-One-Out (LOO) cross-validation, leave-group (5-fold)-out (LGO) and external predic-tion series. The statistical parameters of the training and test sets for GA–MLR models were calculated.Conclusion:The resulting quantitative GA-MLR models of Cv, S, and Eth were obtained:[r2=0.950, Q2=0.989, r2ext=0.969, MAE(overall,5-flod)=0.6825 Jmol-1K-1], [r2=0.980, Q2=0.947, r2ext=0.943, MAE(overall,5-flod)=0.5891Jmol-1K-1], and [r2=0.980, Q2=0.809, r2ext=0.985, MAE(overall,5-flod)=2.0284 kJmol-1]. The results showed that the predictive ability of the models was satisfactory, and the constitutional, topological indices and ring descriptor could be used to predict the mentioned properties of 103 cycloalkanes.

Characterization of magnetic states of graphene quantum dots of different shapes by application of electric field

In this work, we have demonstrated that the optical properties of magnetic states of graphene quantum dots (GQDs) is significantly influenced by their shape and application of external electric field. Our computations at the restricted Hartree-Fock and unrestricted Hartree-Fock level employing the Pariser-Parr-Pople (PPP) model based Hamiltonian have illustrated that the optical band-gap of the nonmagnetic (NM) state changes much more drastically than the antiferromagnetic (AFM) and ferromagnetic (FM) configurations as the shape of the GQD is altered. Further, the geometric configuration of GQDs and external electric field govern the energetic ordering of their magnetic states and consequently, nature of phase transition exhibited by these quantum dots. In addition, the optical spectra of AFM state of diamond shaped graphene quantum dot exhibits a spin-dependent splitting on application of external electric field while no such splitting is observed for the AFM phase of hexagonal shaped graphene quantum dot. This splitting was attributed to the type of spin-density distribution in GQDs. Further, the electro-absorption (EA) spectra exhibits distinct variations for the different magnetic phases of GQDs. Hence, our results have indicated that EA spectra is an efficient method to characterize the different magnetic states of GQDs of varied shapes.

The role of d-electron metal ions complexation on the nonlinear-optical parameters of new trans-dichloropalladium(II) complex

The UV-Vis spectroscopy and nonlinear-optical properties of new trans-dichloropalladium(II) complex of 7-azaindole have been investigated using computational chemistry and experimental method. Optical properties were executed using UV-Vis spectroscopy in the spectral range (200–800) nm. The TD-DFT/B3LYP functional method with LanL2DZ basis set for palladium atom and 6-311G++(d,p) for remaining atoms were used to extract the electronic absorption spectra. For nonlinear-optical properties calculation, second-order hyperpolarizabilities (γ), we used the time-dependent Hartree-Fock (TDHF) level of theory with LanL2DZ and 6-31G(d,p) functional for appropriate atoms. In this work, we studied the influence of the metal cations complexation on the possibility of modulating NLO properties at the molecular level. The calculated results are in good agreement with the experimental values.

Tannin Basic Building Blocks as Potential Scavengers of Chemical Carcinogens: A Computational Study.

Tannins are natural compounds that have historically been used in the tanning of leather. In the scientific literature, one finds many reports of their possible beneficial health effects, although these are not always unequivocally confirmed. In order to gain a better insight into their proposed anticancer potential, we studied the scavenging capacity of the basic tannin building blocks against various chemical carcinogens of the epoxy type. The reactivity of gallic acid, ellagic acid, and epicathechin was examined using quantum mechanical calculations at the Hartree-Fock level of theory in conjunction with flexible basis sets and implicit solvation models. The monomeric tannin building blocks exhibited significant scavenging potential, with epicatechin presenting the best scavenger, thus encouraging and guiding future experimental studies of their anticarcinogenic properties.

Excitation functions of the Zn(p,xn)Ga reactions

The excitation functions for 64,66,67,68,70Zn(p,n)64,66,67,68,70Ga and 64,66,67,68,70Zn(p,2n)63,65,66,67,69Ga have been calculated for incident proton energies from threshold values to 30 MeV using the statistical model code TALYS-1.6. The (p,n) and (p,2n) cross sections have been calculated using both phenomenological Koning and Delaroche (KD) and semimicroscopic Jeukenne-Lejeune-Mahaux-Bruyeres (JLMB) optical model potentials. The phenomenological back-shifted Fermi gas model (BFM) and microscopic Hartree-Fock (HF) approaches for calculation of level densities have been compared in the present work. The pre-equilibrium process has been treated using exciton model. The sensitivity of cross section data to different models of optical model potential and level density have been investigated. It is found that the (p,n) and (p,2n) cross section calculations with semimicroscopic JLMB optical model potential and microscopic HF level density show agreement with the data. The (p,n) and (p,2n) cross section calculations have been compared with corresponding cross sections from nuclear data library, TENDL-2019. The (p,xn) cross sections obtained will be useful in several applications, particularly, for optimization of production routes for Ga isotopes.

Quantitative modeling for prediction of thermodynamic properties of some pyridine derivatives using molecular descriptors and genetic algorithm‐multiple linear regressions

AbstractPyridines are compounds with a wide range of biological activities and they are the basis of several groups of drugs. In this study, the relationship between molecular descriptors and the thermal energy (Eth kJ/mol), heat capacity (C v J/molK), entropy (S J/mol K), enthalpy of formation (ΔH f kJ/mol), and Gibbs free energy (ΔG kJ/mol) of pyridine derivatives is studied. These properties were calculated at the Hartree–Fock level of theory and 6‐311G* G basis sets by Gaussian 09 software. The chemical structures of 171 pyridine derivatives were drawn by the Gauss View 05 program. The genetic algorithm‐multiple linear regression (GA‐MLR) and backward methods—were used to select the suitable descriptors and also for predicting the thermodynamic properties of pyridine derivatives. The correlations between the molecular descriptors in the best models were discussed by the Pearson coefficient correlation and collinearity statistics. The predictive powers of the GA‐MLR models are studied using leave‐one‐out (LOO) cross‐validation and external test set. The best quantitative structure–property relationship (QSPR) models are obtained based on the statistical parameters, such as R 2, Q 2 LOO, and RMSE values for the data sets. The predictive ability of the GA‐MLR models with two‐three selected molecular descriptors was found to be satisfactory and could be used for modeling and predicting of the mentioned properties of nontested pyridine derivatives.

Functional Extrapolations to Tame Unbound Anions in Density-Functional Theory Calculations.

Standard flavors of density-functional theory (DFT) calculations are known to fail in describing anions, due to large self-interaction errors. The problem may be circumvented using localized basis sets of reduced size, leaving no variational flexibility for the extra electron to delocalize. Alternatively, a recent approach exploiting DFT evaluations of total energies on electronic densities optimized at the Hartree-Fock (HF) level has been reported, showing that the self-interaction-free HF densities are able to lead to an improved description of the additional electron, returning affinities in close agreement with the experiments. Nonetheless, such an approach can fail when the HF densities are too inaccurate. Here, an alternative approach is presented, in which an embedding environment is used to stabilize the anion in a bound configuration. Similar to the HF case, when computing total energies at the DFT level on these corrected densities, electron affinities in very good agreement with experiments can be recovered. The effect of the environment can be evaluated and removed by an extrapolation of the results to the limit of vanishing embedding. Apart from the definition of the domain of the embedding potential, the approach is free from parameters and it can be easily applied to DFT calculations with delocalized basis sets, e.g., plane waves, for which alternative approaches are either not viable or more computationally demanding. The proposed extrapolation strategy can be thus applied also to extended systems, as often studied in condensed-matter physics and materials science, and we illustrate how the embedding environment can be exploited to determine the energy of an adsorbing anion, here a chloride ion on a metal surface, whose charge configuration would be incorrectly predicted by standard density functionals.

X-ray constrained spin-coupled technique: theoretical details and further assessment of the method.

One of the well-established methods of modern quantum crystallography is undoubtedly the X-ray constrained wavefunction (XCW) approach, a technique that enables the determination of wavefunctions which not only minimize the energy of the system under examination, but also reproduce experimental X-ray diffraction data within the limit of the experimental errors. Initially proposed in the framework of the Hartree-Fock method, the strategy has been gradually extended to other techniques of quantum chemistry, but always remaining limited to a single-determinant ansatz for the wavefunction to extract. This limitation has been recently overcome through the development of the novel X-ray constrained spin-coupled (XCSC) approach [Genoni et al. (2018). Chem. Eur. J. 24, 15507-15511] which merges the XCW philosophy with the traditional spin-coupled strategy of valence bond theory. The main advantage of this new technique is the possibility of extracting traditional chemical descriptors (e.g. resonance structure weights) compatible with the experimental diffraction measurements, without the need to introduce information a priori or perform analyses a posteriori. This paper provides a detailed theoretical derivation of the fundamental equations at the basis of the XCSC method and also introduces a further advancement of its original version, mainly consisting in the use of molecular orbitals resulting from XCW calculations at the Hartree-Fock level to describe the inactive electrons in the XCSC computations. Furthermore, extensive test calculations, which have been performed by exploiting high-resolution X-ray diffraction data for salicylic acid and by adopting different basis sets, are presented and discussed. The computational tests have shown that the new technique does not suffer from particular convergence problems. Moreover, all the XCSC calculations provided resonance structure weights, spin-coupled orbitals and global electron densities slightly different from those resulting from the corresponding unconstrained computations. These discrepancies can be ascribed to the capability of the novel strategy to capture the information intrinsically contained in the experimental data used as external constraints.

Hole dynamics in a photovoltaic donor-acceptor couple revealed by simulated time-resolved X-ray absorption spectroscopy.

Theoretical and experimental methodologies that can characterize electronic and nuclear dynamics, and the coupling between the two, are needed to understand photoinduced charge transfer in molecular building blocks used in organic photovoltaics. Ongoing developments in ultrafast pump-probe techniques such as time-resolved X-ray absorption spectroscopy, using an X-ray free electron laser in combination with an ultraviolet femtosecond laser, present desirable probes of coupled electronic and nuclear dynamics. In this work, we investigate the charge transfer dynamics of a donor-acceptor pair, which is widely used as a building block in low bandgap block copolymers for organic photovoltaics. We simulate the dynamics of the benzothiadiazole-thiophene molecule upon photoionization with a vacuum ultraviolet (VUV) pulse and study the potential of probing the subsequent charge dynamics using time-resolved X-ray absorption spectroscopy. The photoinduced dynamics are calculated using on-the-fly nonadiabatic molecular dynamics simulations based on Tully's Fewest Switches Surface Hopping approach. We calculate the X-ray absorption spectrum as a function of time after ionization at the Hartree-Fock level. The changes in the time-resolved X-ray absorption spectrum at the sulfur K-edge reveal the ultrafast charge carrier dynamics in the molecule occurring on a femtosecond time scale. These theoretical findings anticipate that ultrafast time-resolved X-ray absorption spectroscopy using an X-ray probe in combination with a VUV pump offers a new approach to investigate the detailed dynamics of organic photovoltaic materials.

Molecular Electrostatic Potential and Electron Density of Large Systems in Solution Computed with the Fragment Molecular Orbital Method.

A solvent screening model for the molecular electrostatic potential is developed for the fragment molecular orbital method combined with the polarizable continuum model at the Hartree-Fock and density functional theory levels. The accuracy of the generated potentials is established in comparison to calculations without fragmentation. Solvent effects upon the molecular electrostatic potential and electron density of solute are discussed. The method is applied to two proteins: chignolin (PDB: 1UAO ) and ovine prostaglandin H(2) synthase-1 ( 1EQG ).

Analytic evaluation of first-order properties within the mean-field variant of spin-free exact two-component theory.

We present a scheme for the calculation of energies and analytic energy gradients within spin-free exact two-component (SFX2C) theory in its mean-field variant, which we refer to as SFX2C-mf. In the presented scheme, the Foldy-Wouthuysen transformation is carried out after the spin-free four-component Hartree-Fock treatment such that in electron-correlated calculations only the non-mean-field part of the two-electron interactions is handled in an untransformed manner. The formulation of analytic gradients requires some adjustments in comparison with the nonrelativistic case, i.e., the additional solution of the spin-free Dirac Coulomb coupled-perturbed Hartee-Fock equations together with a simplified treatment of orbital relaxation at the SFX2C-mf level. The improved accuracy of SFX2C-mf in comparison with SFX2C-1e is demonstrated in the calculation of energies, dipole moments, and electric-field gradients for the hydrogen halides HX, X = F-At. It is shown that the main contribution to the improvement stems from the elimination of the error at the Hartree-Fock (HF) level; however, the corresponding correlation contribution is also improved such that SFX2C-mf can be considered a suitable scheme for the treatment of heavy-element compounds for which the error of SFX2C-1e is rather substantial.

Inter-Coulombic Decay in Laterally Arranged Quantum Dots Controlled by Polarized Lasers

The inter-Coulombic decay (ICD) process, where one electronically excited species relaxes while the neighboring one is concomitantly ionized, has been recently discovered likewise in atomic, molecular, biological, and nanostructured systems. Any theoretical prediction of it relies strongly on an accurate treatment of the involved resonance and continuum states. Here, we describe laser-induced ICD in quantum dots with electron dynamics at a multiconfiguration time-dependent Hartree–Fock level for the first time for a two-dimensional continuum, such that ICD control with laser polarization is within reach. This explicit electron dynamics is possible through the efficient Multigrid POTFIT tensor decomposition of the Coulomb interaction on a grid. Conclusively, ICD turns out to be much faster in laterally arranged self-assembled or lithographic quantum dots connected to a two-dimensional wetting-layer continuum than in previously investigated dots in nanowires.

Machine learning modeling of Wigner intracule functionals for two electrons in one-dimension.

In principle, many-electron correlation energy can be precisely computed from a reduced Wigner distribution function (W), thanks to a universal functional transformation (F), whose formal existence is akin to that of the exchange-correlation functional in density functional theory. While the exact dependence of F on W is unknown, a few approximate parametric models have been proposed in the past. Here, for a dataset of 923 one-dimensional external potentials with two interacting electrons, we apply machine learning to model F within the kernel Ansatz. We deal with over-fitting of the kernel to a specific region of phase-space by a one-step regularization not depending on any hyperparameters. Reference correlation energies have been computed by performing exact and Hartree-Fock calculations using discrete variable representation. The resulting models require W calculated at the Hartree-Fock level as input while yielding monotonous decay in the predicted correlation energies of new molecules reaching sub-chemical accuracy with training.

Efficient implementation of the analytical second derivatives of hartree-fock and hybrid DFT energies within the framework of the conductor-like polarizable continuum model.

Calculation of vibrational frequencies for solvated systems is essential to study reactions in complex environments. In this paper, we report the implementation of the analytical self-consistent field Hessian at the Hartree-Fock and density functional theory levels in the framework of the conductor-like polarizable continuum model (C-PCM) into the ORCA quantum chemistry suite. The calculated vibrational frequencies agree very well with those computed through numerical differentiation of the analytical gradients. The deviation between both sets of data is smaller than 3 cm-1 for frequencies larger than 200 cm-1 and smaller than 5 cm-1 for the low-frequency regime (100 cm-1 < ω < 200 cm-1 ). The accuracy of the frequencies is not significantly affected by the size of the density functional theory (DFT) integration grid, with a deviation lower than 0.5 cm-1 between data computed with the smallest and that with the largest DFT grid size. The calculation of the analytical Hessian is between 3 and 12 times faster than its numerical counterpart. The C-PCM terms only add an overhead of 10-30% relative to the gas phase calculations. Finally, for acetone, the (B3LYP) values for the frequency shifts obtained in going from the gas phase to liquid acetone are in agreement with experiment. © 2019 Wiley Periodicals, Inc.

Optical orientation with linearly polarized light in transition metal dichalcogenides

We study the optical properties of semiconducting transition metal dichalcogenide monolayers under the influence of strong out-of-plane magnetic fields, using the effective massive Dirac model. We pay attention to the role of spin-orbit coupling effects, doping level and electron-electron interactions, treated at the Hartree-Fock level. We find that optically-induced valley and spin imbalance, commonly attained with circularly polarized light, can also be obtained with linearly polarized light in the doped regime. Additionally, we explore an exchange-driven mechanism to enhance the spin-orbit splitting of the conduction band, in n-doped systems, controlling both the carrier density and the intensity of the applied magnetic field.

Quantum chemistry with Coulomb Sturmians: Construction and convergence of Coulomb Sturmian basis sets at the Hartree-Fock level

The first discussion of basis sets consisting of exponentially decaying Coulomb Sturmian functions for modelling electronic structures is presented. The proposed basis set construction selects Coulomb Sturmian functions using separate upper limits to their principle, angular momentum and magnetic quantum numbers. Their common Coulomb Sturmian exponent is taken as a fourth parameter. The convergence properties of such basis sets are investigated for second and third row atoms at the Hartree-Fock level. Thereby important relations between the values of the basis set parameters and the physical properties of the electronic structure are recognised. For example, an unusually large limit for the angular momentum quantum number in unrestricted Hartree-Fock calculations can be linked to the breaking of spherical symmetry in such cases. Furthermore, a connection between the optimal, i.e. minimum-energy, Coulomb Sturmian exponent and the average Slater exponents values obtained by Clementi and Raimondi (E. Clementi and D. L. Raimondi, J. Chem. Phys. 38, 2686 (1963)) is made. These features of Coulomb Sturmian basis sets emphasise their ability to correctly reproduce the physical features of Hartree-Fock wave functions.

Stabilizing influence of silicon substitution on dibenzene and its isomers

The stabilizing effect of silicon substitution on sixteen different isomers of dibenzene $$(\hbox {C}_{{12}}\hbox {H}_{12})$$ has been investigated using second-order Moller-Plesset perturbation (MP2) theory and the cc-pVDZ basis set. While the most stable isomers of $$\hbox {Si}_{{12}}\hbox {H}_{12 }$$ have only Si–Si bonds, some of the stable isomers have isolated $$\hbox {Si}{=}\hbox {Si}$$ bonds and may be amenable to experimental observation. Vibrational frequencies were calculated for the optimized geometries at the Hartree-Fock level of theory to ensure that they corresponded to true minima on the potential energy landscape. Natural bonding orbital analysis confirms the existence of isolated $$\hbox {Si}{=}\hbox {Si}$$ double bonds in some of the isomers. Dipole moment values were determined to check for the presence of centre of symmetry in certain geometries. Ab initio calculations suggest that silicon analogs of several isomers of unstable dibenzene moiety are stable. While the most stable isomers of $$\hbox {Si}_{{12}}\hbox {H}_{{12}}$$ have all tetrahedral silicon atoms, some of the stable isomers do contain $$\hbox {Si}{=}\hbox {Si}$$ bonds, suggesting that they may be amenable to experimental observation.

Calculations of positron binding and annihilation in polyatomic molecules.

A model-potential approach to calculating positron-molecule binding energies and annihilation rates is developed. Unlike existing ab initio calculations, which have mostly been applied to strongly polar molecules, the present methodology can be applied to both strongly polar and weakly polar or nonpolar systems. The electrostatic potential of the molecule is calculated at the Hartree-Fock level, and a model potential that describes short-range correlations and long-range polarization of the electron cloud by the positron is then added. The Schrödinger equation for a positron moving in this effective potential is solved to obtain the binding energy. The model potential contains a single adjustable parameter for each type of atom present in the molecule. The wave function of the positron bound state may be used to compute the rate of electron-positron annihilation from the bound state. As a first application, we investigate positron binding and annihilation for the hydrogen cyanide molecule. Results for the binding energy are found to be in accord with existing calculations, and we predict the rate of annihilation from the bound state to be Γ = 0.1-0.2 × 109 s-1.

Incorporating Brueckner-Hartree-Fock correlations in energy density functionals

Recently, a microscopically motivated nuclear energy density functional was derived by applying the density matrix expansion to the Hartree-Fock (HF) energy obtained from long-range chiral effective field theory two- and three-nucleon interactions. However, the HF approach cannot account for all many-body correlations. One class of correlations is included by Brueckner-Hartree-Fock (BHF) theory, which gives an improved definition of the one-body HF potential by replacing the interaction by a reaction matrix $G$. In this paper, we find that the difference between the $G$-matrix and the nucleon-nucleon potential $V_{\mathrm{NN}}$ can be well accounted for by a truncated series of contact terms. This is consistent with renormalization group decoupling generating a series of counterterms as short-distance physics is integrated out. The coefficients $C_{n}$ of the power series expansion $\sum C_{n}q^{n}$ for the counterterms are examined for two potentials at different renormalization group resolutions and at a range of densities. The success of this expansion for $G-V_{\mathrm{NN}}$ means we can apply the density matrix expansion at the HF level with low-momentum interactions and density-dependent zero-range interactions to model BHF correlations.