The Effects of Split Valence Basis Sets on Muon Hyperfine Interaction in Guanine Nucleobase and Nucleotide Structures

The DFT cluster method was employed to investigate the electronic structures and muonium hyperfine interactions in guanine nucleobase and nucleotide using three different basis sets. The total energy and Fermi contact values were calculated for muon trapped at carbon '8'. The three basis sets, 6-31G, 6-311G and 6-311G(d,p), were used in tandem with the B3LYP functional. There are significant quantitative differences in the calculated total energy. 6-311G(d,p) produced the lowest total energy as compared to the other basis sets. The lowering of the total energy is due to the increase in the number of basis functions to describe the atomic orbitals, which is consistent with the postulate on basis set completeness. The 6-31G basis set produced the muon Fermi contact value that is the closest to the experimental value. The calculated Fermi contact values for the nucleobase and nucleotide are significantly lowered in going from the double-zeta to the triple-zeta basis set by 5% and 4% respectively. The lowering of the Fermi contact value can be attributed to the extension of the triple-zeta basis set in describing the valence atomic orbitals. The presence of the sugar phosphate group in the nucleotide instead of the methyl group tends to lower the Fermi contact value. Thus, the sugar phosphate group should be taken into consideration when designing a calculation model.

Download Full-text

The application of an optimization technique to the development of universal basis sets

Canadian Journal of Chemistry ◽

10.1139/v92-081 ◽

1992 ◽

Vol 70 (2) ◽

pp. 580-588 ◽

Cited By ~ 29

Author(s):

R. Custodio ◽

J. D. Goddard ◽

M. Giordan ◽

N. H. Morgon

Keyword(s):

Total Energy ◽

Energy Criterion ◽

Basis Set ◽

Basis Sets ◽

Weight Functions ◽

Statistical Criterion ◽

Minimum Total Energy ◽

Discretization Technique ◽

Universal Bases ◽

Molecular Calculations

The Simplex method was used to define atomic and universal meshes using the integral discretization technique for the Griffin–Hill–Wheeler-Hartree–Fock equations. This technique represents a basis set as an exponential set of the form:[Formula: see text]For atoms, the minimum total energy criterion was employed. For the universal basis, three different procedures were tested: (a) defining the universal basis using information on the isolated atoms, (b) determining the universal Ω0(k) through atomic calculations and reoptimizing the ΔΩ(k) for different symmetries employing simultaneously a single atomic calculation as a reference point, and (c) optimizing the universal mesh using a statistical criterion such as the squares of the deviations of the total energy. The meshes obtained by the minimum total energy criterion or the squares of deviations of the total energy for the universal basis are accurate for the total energy but the weight functions are deficient in the valence region. Shifting the optimized Ω0(k) to [Formula: see text], fixing [Formula: see text], and reoptimizing ΔΩ(k) for each symmetry species produces a better description of weight functions at the expense of a less accurate total energy. In general, no significant statistical difference was observed for the various universal bases generated by procedures (a) and (b) or by (c) provided the shift correction was made to the latter. Application of these bases to diatomic molecules (N2, CO, P2, CS) showed that the universal bases are as accurate as those optimized for atomic systems. If the bases are transferred from atoms to molecules, the shift corrections to the weight functions of the atoms are not useful in molecular calculations. The almost equivalent molecular properties and the good total energies show that the best basis for molecular calculations is that optimized by procedure (c). Keywords: universal basis sets, integral discretization technique.

Download Full-text

Quasi-Relativistic Calculation of EPR g-Tensors with Derivatives of the Decoupling Transformation, Gauge-Including Atomic Orbitals, and Magnetic Balance

10.26434/chemrxiv-2021-32gxb ◽

2021 ◽

Author(s):

Yannick J. Franzke ◽

Jason M. Yu

Keyword(s):

Density Functional ◽

Hyperfine Coupling Constant ◽

Basis Set ◽

Basis Sets ◽

Generalized Gradient ◽

Atomic Orbitals ◽

Experimental Findings ◽

The Impact ◽

Derivatives Of ◽

Magnetic Balance

We present an exact two-component (X2C) ansatz for the EPR g-tensor using gauge-including atomic orbitals (GIAOs) and a magnetically balanced basis set expansion. In contrast to previous X2C and "fully" relativistic ansätze for the g-tensor, this implementation results in a gauge-origin invariant formalism. Furthermore, the derivatives of the relativistic decoupling matrix are considered to form the complete analytical derivative of the X2C Hamiltonian. To reduce the associated computational costs, we apply the diagonal local approximation to the unitary decoupling transformation (DLU) and the (multipole-accelerated) resolution of the identity approximation. The X2C ansatz is compared to Douglas-Kroll-Hess theory and the zeroth-order regular approximation for 11 diatomic molecules. The impact of the relativistic Hamiltonian, the basis set, and the density functional approximation is subsequently assessed for a set of 17 transition-metal complexes to complement our previous work on the hyperfine coupling constant [DOI: 10.33774/chemrxiv-2021-wnz1v-v2]. In total, 24 basis sets and 22 density functional approximations are considered. The quasi-relativistic X2C and DLU-X2C Hamiltonians accurately reproduce the results of the parent "fully" relativistic four-component theory when accounting for two-electron picture-change effects with the modified screened nuclear spin-orbit approximation in the respective one-electron integrals and integral derivatives. Generally, the uncontracted Dyall and segmented-contracted Karlsruhe x2c-type basis sets perform well when compared to large even-tempered basis sets. Moreover, (range-separated) hybrid density functional approximations are needed to match the experimental findings. Here, hybrids based on the meta -generalized gradient approximation are not an a priori improvement. Compared to the other computational parameters, the impact of the GIAOs and the magnetic balance on the actual results in standard calculations is less pronounced. Routine calculations of large molecules are possible with widely available and comparably low- cost hardware as demonstrated for [Pt(C6Cl5)4]− with 3360 basis functions and three spin-(1/2) La(II) and Lu(II) compounds. Both approaches based on a common gauge origin and GIAOs using triple- ζ basis sets lead to a good agreement with the experimental findings. The best agreement is found with hybrid functionals such as PBE0 and ωB97X-D.

Download Full-text

Quantum Mechanical Study of YTiO3 to the Investigation of Piezoelectricity

Physics Research International ◽

10.1155/2011/123492 ◽

2011 ◽

Vol 2011 ◽

pp. 1-5

Author(s):

Raimundo Dirceu de Paula Ferreira ◽

Marcos Antonio Barros dos Santos ◽

Maycon da Silva Lobato ◽

Jardel Pinto Barbosa ◽

Marcio de Souza Farias ◽

...

Keyword(s):

Total Energy ◽

Piezoelectric Properties ◽

Piezoelectric Effect ◽

Basis Set ◽

Basis Sets ◽

Gaussian Basis Sets ◽

Hartree Fock ◽

Generator Coordinate ◽

Mechanical Study ◽

Quantum Mechanical Study

In previous articles we reported through theoretical studies the piezoelectric effect in BaTiO3, SmTiO3, and YFeO3. In this paper, we used the Douglas-Kroll-Hess (DKH) second-order scalar relativistic method to investigate the piezoelectricity in YTiO3. In the calculations we used the [6s4p] and [10s5p4d] Gaussian basis sets for the O (3P) and Ti (5S) atoms, respectively, from the literature in combination with the (30s21p16d)/[15s9p6d] basis set for the Y (3D) atom, obtained by generator coordinate Hartree-Fock (GCHF) method, and they had their quality evaluated using calculations of total energy and orbital energies (HOMO and HOMO-1) of the 2TiO+1 and 1YO+1 fragments. The dipole moment, the total energy, and the total atomic charges in YTiO3 in Cs space group were calculated. When we analyze those properties we verify that it is reasonable to believe that YTiO3 does not present piezoelectric properties.

Download Full-text

Relativistic AB Initio calculations of interaction energies: formulation and application to ionic solids

Philosophical Transactions of the Royal Society of London. Series A, Mathematical and Physical Sciences ◽

10.1098/rsta.1986.0105 ◽

1986 ◽

Vol 320 (1553) ◽

pp. 71-105 ◽

Cited By ~ 34

Keyword(s):

Ab Initio ◽

Inner Core ◽

Basis Set ◽

Basis Sets ◽

Computational Techniques ◽

Central Field ◽

Atomic Orbitals ◽

Molecule Formation ◽

Ionic Solids ◽

Free Atoms

The theory and computational techniques used in a computer program capable of performing fully relativistic ab initio electronic structure calculations for pairs of interacting atomic species are presented. If the species are ions in a crystal, a description of an ionic solid is obtained. If the two species are otherwise free, the program yields a wavefunction for a diatomic molecule. The molecular wavefunction is an antisymmetrized product of core and valence parts. The core is a Hartree product of the Dirac—Fock atomic orbitals of the free atoms. The largest contribution to the energy arises from the inner-core orbitals, each having negligible overlap with all other orbitals. The purely atomic inner-core energy does not contribute to the binding energy of the molecule, thus obviating the need to calculate the largest part of the molecular energy. The outer core consists of those remaining closed subshells of the isolated atoms that are not significantly affected on molecule formation. All the remaining orbitals, including at least the valence Dirac—Fock atomic orbitals of the free atoms plus further atomic functions needed to describe charge density changes upon molecule formation, are used to construct the valence wavefunction. This can be constructed to take account of correlation between the valence electrons. All atomic functions have central field form with the radial parts defined numerically. This method of constructing the molecular wavefunction avoids the need for large basis sets, ensures that the Dirac small components bear the correct relation to the large components and avoids basis set superposition errors. This program is used to initiate a non-empirical study of the properties of ionic solids. The results show that these properties cannot be reliably predicted by using free ion wavefunctions and that the Watson shell model for describing the non-negligible differences between free and in-crystal ion wavefunctions is not satisfactory. The results demonstrate the importance of inter-ionic dispersive attractions but show that it is not satisfactory to neglect the part quenching of the standard long-range form of these attractions arising from overlap of the ion wavefunctions.

Download Full-text

Property-Optimized Gaussian Basis Sets for Lanthanides

10.33774/chemrxiv-2021-qnjnr-v2 ◽

2021 ◽

Author(s):

Dmitrij Rappoport

Keyword(s):

Basis Set ◽

Oxidation States ◽

Basis Sets ◽

Gaussian Basis Sets ◽

Test Set ◽

Valence Basis Sets ◽

Triple Zeta ◽

Lanthanide Atoms ◽

Split Valence ◽

Quadruple Zeta

Property-optimized Gaussian basis sets of split-valence, triple-zeta and quadruple-zeta valence quality are developed for the lanthanides Ce–Lu for use with small-core relativistic effective core potentials. They are constructed in a systematic fashion by augmenting def2 orbital basis sets with diffuse basis functions and minimizing negative static isotropic polarizabilities of lanthanide atoms with respect to basis set exponents within the unrestricted Hartree–Fock method. The basis set quality is assessed using a test set of 70 molecules containing the lanthanides in their common oxidation states and f electron occupations. 5d orbital occupation turns out to be the determining factor for the basis set convergence of polarizabilities in lanthanide atoms and the molecular test set. Therefore, two series of property-optimized basis sets are defined. The augmented def2-SVPD, def2-TZVPPD, and def2-QZVPPD basis sets balance the accuracy of polarizabilities across lanthanide oxidation states. The relative errors in atomic and molecular polarizability calculations are ≤8% for augmented split-valence basis sets, ≤2.5% for augmented triple-zeta valence basis sets, and ≤1% for augmented quadruple-zeta valence basis sets. In addition, extended def2-TZVPPDD and def2-QZVPPDD are provided for accurate calculations of lanthanide atoms and neutral clusters. The property-optimized basis sets developed in this work are shown to accurately reproduce electronic absorption spectra of a series of LnCp'3- complexes (Cp' = C5H4SiMe3, Ln = Ce–Nd, Sm) with time-dependent density functional theory.

Download Full-text

Basis Set Effects in Density Functional Theory Calculation of Muoniated Cytosine Nucleobase

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.860.282 ◽

2020 ◽

Vol 860 ◽

pp. 282-287

Author(s):

Wan Nurfadhilah Zaharim ◽

Shukri Sulaiman ◽

Saidah Sakinah Mohd Tajudin ◽

Siti Nuramira Abu Bakar ◽

Nur Eliana Ismail ◽

...

Keyword(s):

Density Functional Theory ◽

Total Energy ◽

Density Functional ◽

Density Functional Theory Calculation ◽

Geometry Optimization ◽

Density Functional Theory Method ◽

Basis Set ◽

Basis Sets ◽

Functional Theory ◽

Muonium Hyperfine

The Density Functional Theory method was employed to investigate the electronic structure and muonium hyperfine interaction of muonium trapped near carbon atom labelled as '5' in cytosine nucleobase. Eighteen different basis sets in combination with B3LYP functional were examined in geometry optimization calculations on the muoniated radical. There are significant quantitative differences in the calculated total energy. The employment of basis set that does not include polarization function produces an optimized structure with high total energy. The 6-311++G(d,p) basis set yielded the lowest total energy as compared to other basis sets. The bond order of muonium trapped at C5 atom is in the range of 0.841 to 0.862. The 6-31G basis set produced the muonium Fermi contact coupling constant that is the closest to the experimental value.

Download Full-text

A Systematic DFT Study of Two Elementary Steps Involving Hydrogen Peroxide and the Hydroxyl Radical in the Fenton Reaction

10.26434/chemrxiv.6160142 ◽

2018 ◽

Author(s):

Danilo Carmona ◽

David Contreras ◽

Oscar A. Douglas-Gallardo ◽

Stefan Vogt-Geisse ◽

Pablo Jaque ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Hydroxyl Radical ◽

Ab Initio ◽

Fenton Reaction ◽

Basis Set ◽

Basis Sets ◽

Dft Methods ◽

Elementary Steps ◽

Oxygen Oxygen ◽

Complete Basis Set

The Fenton reaction plays a central role in many chemical and biological processes and has various applications as e.g. water remediation. The reaction consists of the iron-catalyzed homolytic cleavage of the oxygen-oxygen bond in the hydrogen peroxide molecule and the reduction of the hydroxyl radical. Here, we study these two elementary steps with high-level ab-initio calculations at the complete basis set limit and address the performance of different DFT methods following a specific classification based on the Jacob´s ladder in combination with various Pople's basis sets. Ab-initio calculations at the complete basis set limit are in agreement to experimental reference data and identified a significant contribution of the electron correlation energy to the bond dissociation energy (BDE) of the oxygen-oxygen bond in hydrogen peroxide and the electron affinity (EA) of the hydroxyl radical. The studied DFT methods were able to reproduce the ab-initio reference values, although no functional was particularly better for both reactions. The inclusion of HF exchange in the DFT functionals lead in most cases to larger deviations, which might be related to the poor description of the two reactions by the HF method. Considering the computational cost, DFT methods provide better BDE and EA values than HF and post--HF methods with an almost MP2 or CCSD level of accuracy. However, no systematic general prediction of the error based on the employed functional could be established and no systematic improvement with increasing the size in the Pople's basis set was found, although for BDE values certain systematic basis set dependence was observed. Moreover, the quality of the hydrogen peroxide, hydroxyl radical and hydroxyl anion structures obtained from these functionals was compared to experimental reference data. In general, bond lengths were well reproduced and the error in the angles were between one and two degrees with some systematic trend with the basis sets. From our results we conclude that DFT methods present a computationally less expensive alternative to describe the two elementary steps of the Fenton reaction. However, choice of approximated functionals and basis sets must be carefully done and the provided benchmark allows a systematic validation of the electronic structure method to be employed

Download Full-text

DFT Benchmark Study of the O--O Bond Dissociation Energy in Peroxides Validated with High-Level Ab-Initio Calculations

10.26434/chemrxiv.8217221.v1 ◽

2019 ◽

Author(s):

Danilo Carmona ◽

Pablo Jaque ◽

Esteban Vöhringer-Martinez

Keyword(s):

Reference Value ◽

Basis Set ◽

Basis Sets ◽

Mean Deviation ◽

Bond Dissociation ◽

Dissociation Energies ◽

The Mean ◽

Experimental Values ◽

High Level ◽

Almost All

<div><div><div><p>Peroxides play a central role in many chemical and biological pro- cesses such as the Fenton reaction. The relevance of these compounds lies in the low stability of the O–O bond which upon dissociation results in radical species able to initiate various chemical or biological processes. In this work, a set of 64 DFT functional-basis set combinations has been validated in terms of their capability to describe bond dissociation energies (BDE) for the O–O bond in a database of 14 ROOH peroxides for which experimental values ofBDE are available. Moreover, the electronic contributions to the BDE were obtained for four of the peroxides and the anion H2O2− at the CBS limit at CCSD(T) level with Dunning’s basis sets up to triple–ζ quality provid- ing a reference value for the hydrogen peroxide anion as a model. Almost all the functionals considered here yielded mean absolute deviations around 5.0 kcal mol−1. The smallest values were observed for the ωB97 family and the Minnesota M11 functional with a marked basis set dependence. Despite the mean deviation, order relations among BDE experimental values of peroxides were also considered. The ωB97 family was able to reproduce the relations correctly whereas other functionals presented a marked dependence on the chemical nature of the R group. Interestingly, M11 functional did not show a very good agreement with the established order despite its good performance in the mean error. The obtained results support the use of similar validation strategies for proper prediction of BDE or other molecular properties by DF Tmethods in subsequent related studies.</p></div></div></div>

Download Full-text

Benchmark of Simplified Time-Dependent Density Functional Theory for UV-Vis Spectral Properties of Porphyrinoids

10.26434/chemrxiv.9912860 ◽

2019 ◽

Author(s):

Kamal Batra ◽

Stefan Zahn ◽

Thomas Heine

Keyword(s):

Density Functional Theory ◽

Density Functional ◽

Large Scale ◽

Absolute Error ◽

Time Dependent ◽

Basis Set ◽

Basis Sets ◽

Functional Theory ◽

Framework Materials ◽

Dependent Density

<p>We thoroughly benchmark time-dependent density- functional theory for the predictive calculation of UV/Vis spectra of porphyrin derivatives. With the aim to provide an approach that is computationally feasible for large-scale applications such as biological systems or molecular framework materials, albeit performing with high accuracy for the Q-bands, we compare the results given by various computational protocols, including basis sets, density-functionals (including gradient corrected local functionals, hybrids, double hybrids and range-separated functionals), and various variants of time-dependent density-functional theory, including the simplified Tamm-Dancoff approximation. An excellent choice for these calculations is the range-separated functional CAM-B3LYP in combination with the simplified Tamm-Dancoff approximation and a basis set of double-ζ quality def2-SVP (mean absolute error [MAE] of ~0.05 eV). This is not surpassed by more expensive approaches, not even by double hybrid functionals, and solely systematic excitation energy scaling slightly improves the results (MAE ~0.04 eV). </p>

Download Full-text

AlN Nanotubes: A DFT Study of Al-27 and N-14 Electric Field Gradient Tensors

Zeitschrift für Naturforschung A ◽

10.1515/zna-2007-1206 ◽

2007 ◽

Vol 62 (12) ◽

pp. 711-715 ◽

Cited By ~ 2

Author(s):

Ahmad Seif ◽

Mahmoud Mirzaei ◽

Mehran Aghaie ◽

Asadollah Boshra

Keyword(s):

Electric Field ◽

Electric Field Gradient ◽

Field Gradient ◽

Density Functional ◽

Quadrupole Coupling Constant ◽

Basis Set ◽

Basis Sets ◽

B3lyp Method ◽

Package Program ◽

Nqr Parameters

Density functional theory (DFT) calculations were performed to calculate the electric field gradient (EFG) tensors at the sites of aliminium (27Al) and nitrogen (14N) nuclei in an 1 nm of length (6,0) single-walled aliminium nitride nanotube (AlNNT) in three forms of the tubes, i. e. hydrogencapped, aliminium-terminated and nitrogen-terminated as representatives of zigzag AlNNTs. At first, each form was optimized at the level of the Becke3,Lee-Yang-Parr (B3LYP) method, 6-311G∗∗ basis set. After, the EFG tensors were calculated at the level of the B3LYP method, 6-311++G∗∗ and individual gauge for localized orbitals (IGLO-II and IGLO-III) types of basis sets in each of the three optimized forms and were converted to experimentally measurable nuclear quadrupole resonance (NQR) parameters, i. e. quadrupole coupling constant (qcc) and asymmetry parameter (ηQ). The evaluated NQR parameters revealed that the considered model of AlNNT can be divided into four equivalent layers with similar electrostatic properties.With the exception of Al-1, all of the three other Al layers have almost the same properties, however, N layers show significant differences in the magnitudes of the NQR parameters in the length of the nanotube. Furthermore, the evaluated NQR parameters of Al-1 in the Al-terminated form and N-1 in the N-terminated form revealed the different roles of Al (base agent) and of N (acid agent) in AlNNT. All the calculations were carried out using the GAUSSIAN 98 package program.

Download Full-text