All-electron Basis Sets Research Articles

DFT investigations on the influence of stacking on the electronic structure, absorption, and non-linear optical properties of 3,5-bis[4-(4-methylphenylcarbonyloxy)phenyl]-1,2,4-oxadiazole.

1,2,4-Oxadiazole serves as a fundamental building block driving advancements across diverse scientific and technological arenas, contributing to the creation of innovative materials for various applications including devices, sensors, medications, agrochemicals, and biomedical instruments. Employing density functional theory (DFT) methods, we investigate the impact of different conformers of an oxadiazole substituted derivative, specifically 3,5-bis[4-(4-methylphenylcarbonyloxy)phenyl]-1,2,4-oxadiazole, in both monomeric and stacked configurations (dimeric and tetrameric). We analyze the electronic structures of various conformers, including assessment of HOMO-LUMO energy gaps, to detect the influence of diverse substituents and stacking arrangements. We have also explored the stability of stacked structure in explicit solvent environment. Additionally, we examine absorption spectra, non-linear optical properties, and electronic circular dichroism to evaluate the potential applications of these molecules in optoelectronic devices. Our calculations showed that all the conformers were thermodynamically stable within an energy difference of 2.64kcalmol-1. The study also suggests possible application of the material in optical and electronic devices. DFT calculations were carried out using the CAM-B3LYP and wB97XD functionals with a 6-31 + G* all-electron basis set, paired with the SCRF/PCM solvation model, implemented in the Gaussian 09 package. Equilibrium structure was achieved by performing NPT and NVT simulations using the Gromacs package.

Synthesis, Structural, DFT studies, Biological Effectiveness, and Molecular Docking Aspects of Multitarget Novel N-(4-Phenylthiazol-2-yl)hydrazine carboxamide Hybrids as COX inhibitors, Anti-TB, and Anti-oxidant activity

We herein report, a series of N-(4-phenylthiazol-2-yl)hydrazinecarboxamide based multitarget compounds 3(a-i) were designed and synthesized. Ten compounds 2, and 3(a-i) were characterized by FTIR, NMR (1H and 13C), and mass analysis and subsequently, tested for their potential COX inhibitors, anti-TB, and anti-oxidant activities. The physicochemical and ADME studies for newly synthesized compounds were disclosed. The DFT calculations were taken for the selected molecules using CAM-B3LYP hybrid functional with a 6–31+g(d) all-electron basis set using the Gaussian 09 package. The compounds 3d, 3e, and 3f recognized outstanding COX-II inhibitions with IC50 values of 0.62, 0.78, and 0.72 μM compared to standard drugs. The compounds 3d, 3e, and 3f showed outstanding anti-TB activity with a MIC value of 0.78μg/mL. The compound 3d, and 3f attested outstanding antioxidant activity at 10 μg/mL with a rate of inhibition of 68.12%, and 68.85% respectively. Finally, the molecular docking studies carried out with cyclooxygenase-2 (PDB ID: 6COX), M. tuberculosis enoyl reductase (INHA) (PDB ID: 4TZK), and cytochrome c peroxidase (PDB ID: 2×08), for all the newly synthesized derivatives. Finally, selected compounds were taken for their molecular dynamic studies.

Extensive reference set and refined computational protocol for calculations of 57Fe Mössbauer parameters.

Mössbauer spectroscopy is a powerful technique for probing the local electronic structure of iron compounds, because it reports in an element-selective manner on both the oxidation state and coordination environment of the Fe ion. Computational prediction of the two main Mössbauer parameters, isomer shift (δ) and quadrupole splitting (ΔEQ), has long been targeted by quantum chemical studies, and useful protocols based on density functional theory have been proposed. Here we present an extensive curated reference set of Fe compounds that is considerably larger and more diverse than literature precedents. We make a distinction between low-temperature and high-temperature experimental subgroups. This set is employed for optimizing a refined computational protocol utilizing the scalar version of the exact 2-component (X2C) Hamiltonian with the finite nucleus approximation. Attention is devoted to having an accurate and flexible all-electron basis set for Fe. We assess the performance of several DFT methods that cover all representative families and rungs of functionals and find that hybrid functionals with ca. 25-30% exact exchange offer the best accuracy for isomer shifts. The work establishes a refined general protocol of wide applicability that achieves good performance for the prediction of isomer shifts in a wider variety of systems than before, but the limitations of DFT for quadrupole splittings are also highlighted. Finally, comparison of calculated values with high-temperature experimental results shows that the use of an empirical correction factor is required to account for the second-order Doppler shift and to achieve the same quality of correlation as with the low-temperature data.

Molecular structure and spectra of ytterbium dihalides from first principles

The molecular structure, vibrational frequencies, infrared intensities and electric dipole moments of ytterbium dihalides YbX2 (X = F, Cl, Br, I) in their ground electronic state are studied at the coupled-cluster singles, doubles and perturbative triples CCSD(T) level using a series of large all-electron basis sets together with the complete basis set (CBS) extrapolation procedure, and with both scalar-relativistic and spin–orbit coupling effects taken into account. Excitation energies of low-lying electronic states are calculated at the multireference configuration interaction, equation-of-motion CCSD and single-reference CCSD(T) levels of theory. For all of the molecules under study, the CCSD(T)/CBS equilibrium geometries are found to be non-linear (C2v symmetry). There is a rapid decrease in heights of the barriers to linearity on passing through the YbX2 molecular series from fluoride to iodide: 1587 → 261 → 110 → 7 (all in cm−1) for YbF2 → YbCl2 → YbBr2 → YbI2, respectively. The uncertainties in the molecular structure data published to date are discussed and resolved in the light of the present results.

The Use of Effective Core Potentials with Multiconfiguration Pair-Density Functional Theory.

The reliable and accurate prediction of chemical properties is a key goal in quantum chemistry. Transition-metal-containing complexes can often pose difficulties to quantum mechanical methods for multiple reasons, including many electron configurations contributing to the overall electronic description of the system and the large number of electrons significantly increasing the amount of computational resources required. Often, multiconfigurational electronic structure methods are employed for such systems, and the cost of these calculations can be reduced by the use of an effective core potential (ECP). In this work, we explore both theoretical considerations and performances of ECPs applied in the context of multiconfiguration pair-density functional theory (MC-PDFT). A mixed-basis set approach is used, using ECP basis sets for transition metals and all-electron basis sets for nonmetal atoms. We illustrate the effects that an ECP has on the key parameters used in the computation of MC-PDFT energies, and we explore how ECPs affect the prediction of physical observables for chemical systems. The dissociation curve for a metal dimer was explored, and ionization energies for transition metal-containing diatomic systems were computed and compared to experimental values. In general, we find that ECP approaches employed with MC-PDFT are able to predict ionization energies with improved accuracy compared to traditional Kohn-Sham density functional theory approaches.

Accurate and efficient prediction of optical gaps in silicon and germanium nanoparticles using a high-local-exchange density functional

We investigated the HOMO-LUMO gaps and the optical gaps of Si and Ge nanoparticles (NPs) with various terminations and sizes using different functionals (HLE16, B3LYP, HSE-HJS) and basis sets (CRENBL, def2-SVP, def2-TZVP). The high-local-exchange functional HLE16, without Hartree–Fock exchange, effectively reproduces optical gaps using HOMO−LUMO gaps, offering a cost-effective alternative to hybrid functionals and TDDFT in nanoscale systems. Size (quantum confinement effects) and termination ligands (surface effects) significantly impact energy gaps: nonpolar CH3 had minimal effects, while polar ligands reduced gaps notably. Finally, ECP basis sets like CRENBL are better suited for NP electronic structures than all-electron basis sets.

Performance of density-functional-theory and random-phase-approximation methods on the study of transition-metal clusters: the Tan clusters as an example

Recently developed density-functional-theory (DFT) and random-phase-approximation (RPA) methods are used to study competing isomers of some negatively charged Ta clusters, namely Ta12 - and Ta10 -, in an attempt to find a suitable strategy towards accurate studies of transition-metal clusters based on DFT. Also the neutral and cationic forms Ta12 (0,+) of the twelve-atom cluster are studied. The results are compared with experimental information obtained by several methods that differ in the property under study and the total electric charge of the clusters. We find that a careful choice of the density functional, the use of relativistic two-component methods, eventually in combination with all-electron basis sets, and the application of RPA-type methods, may all be necessary steps for a good assessment. Such an assessment should be made in relation to several experimental properties as much as possible.

All-electron basis sets for H to Xe specific for ZORA calculations: Applications in atoms and molecules

Abstract A segmented basis set of quadruple zeta valence quality plus polarization functions (QZP) for H through Xe was developed to be used in conjunction with the ZORA Hamiltonian. This set was augmented with diffuse functions to describe electrons farther away from the nuclei adequately. Using the ZORA-CCSD(T)/QZP-ZORA theoretical model, atomic ionization energies and bond lengths, harmonic vibrational frequencies, and atomization energies of some molecules were calculated. The addition of core-valence corrections has been shown to improve the agreement between theoretical and experimental results for molecular properties. For atomization energies, a similar observation emerges when considering spin-orbit couplings. With the augmented QZP-ZORA set, static mean dipole polarizabilities of a set of atoms were calculated and compared with previously published recommended and experimental values. Performance evaluations of the ZORA and Douglas–Kroll–Hess Hamiltonians were made for each property studied.

Investigating the molecular interactions of 11-substituted-1-(4-chlorophenyl)-8H-indolo[3,2-c][1,2,4]triazolo[3,4-a]isoquinolines for Antimicrobial Potential: Synthesis, Spectral, In vitro and In silico study interpretations

Indole molecules are one of the important scaffolds in the discovery and development of new drugs. We herein described a synthesis of new 11-substituted-1-(4-chlorophenyl)-8H-indolo[3,2-c][1,2,4]triazolo[3,4-a]isoquinoline 6 (a-h). Structures of the newly synthesized compounds were confirmed by making use of spectroscopic techniques like IR, NMR and mass. The DFT calculations were taken for the selected molecules using CAM-B3LYP hybrid functional with a 6–31+g(d) all-electron basis set using the Gaussian 09 package. The drug-likeness calculations were explained for the synthesized derivatives. The compounds 6b, 6c and 6 g exhibited excellent antibacterial, antifungal and anti-TB activities against tested pathogens at MIC 3.125 μg/ml. Furthermore, molecular docking studies of these compounds against S. aureus Gyrase (PDB ID:2XCT), Staphylococcus aureus tyrosyl-tRNA synthetase (PDB ID:1JIJ), and Mycobacterium tuberculosis enoyl reductase (INHA) (PDB ID:4TZK), revealed the potential binding mode of the ligands to the site of the appropriate targets. Finally, drug likeness and SAR studies were disclosed. Lastly, the protein stability, fluctuations of APO-Protein, and protein-ligand complexes were investigated through molecular dynamics simulations studies using Desmond Maestro 11.3 and potential lead molecules were identified.

Inverse Hypercorroles.

Ground-state and time-dependent density functional theory (TDDFT) calculations with the long-range-corrected, Coulomb-attenuating CAMY-B3LYP exchange-correlation functional and large, all-electron STO-TZ2P basis sets have been used to examine the potential "inverse hypercorrole" character of meso-p-nitrophenyl-appended dicyanidocobalt(III) corrole dianions. The effect is most dramatic for 5,15-bis(p-nitrophenyl) derivatives, where it manifests itself in intense NIR absorptions. The 10-aryl groups in these complexes play a modulatory role, as evinced by experimental UV-visible spectroscopic and electrochemical data for a series of 5,15-bis(p-nitrophenyl) dicyanidocobalt(III) corroles. TDDFT (CAMY-B3LYP) calculations ascribe these features clearly to a transition from the corrole's a2u-like HOMO (retaining the D4h irrep used for metalloporphyrins) to a nitrophenyl-based LUMO. The outward nature of this transition contrasts with the usual phenyl-to-macrocycle direction of charge transfer transitions in many hyperporphyrins and hypercorroles; thus, the complexes studied are aptly described as inverse hypercorroles.

Theoretical prediction of low-energy photoelectron spectra of AlnNi- clusters (n = 1-13).

Mixed-metal clusters have long been studied because of their peculiar properties and how they change with cluster size, composition, and charge state and their potential roles in catalysis. The characterization of these clusters is therefore a very important issue. One of the main experimental tools for characterizing their electronic structure is photoelectron spectroscopy. Theoretical computation completes the task by fully determining the structural properties and matching the theoretical predictions to the measured spectra. We present density functional theory computations of the structural, magnetic, and electronic properties of negatively charged mixed AlnNi- clusters with up to 13 Al atoms. The lowest energy structures of the anionic clusters with up to 7 atoms are also found to be low-energy isomers of the neutral counterparts found in the literature. The 13-atom cluster is found to be a quartet and a perfect icosahedron. The predicted photoelectron spectra are also presented and can be used to interpret future experimental data. We also presented indicators that can be used to determine the potential of these systems for single-atom catalysis. These indicators point to smaller clusters to be more reactive as the gap between the Fermi energy and the center of the d-band increases with cluster size and that Ni occupies an internal site for n = 11-13. We speculate that reactivity can be enhanced if one adds an additional Ni atom. The DFT calculations were performed using the Becke exchange and Perdew-Wang/91 correlation functionals (BPW91), a DFT-optimized all-electron basis set for the aluminum atom, and the Stuttgart small core pseudopotential for the Ni atom. All of the computations used the Gaussian 03 software.

Ab initio multireference calculation of electronic spectra of the osmium complexes, [Os(bpy) ] and [Os(phen) ] .

The spin-orbit coupling corrected absorption spectra of osmium complexes, [Os(bpy) ] and [Os(phen) ] , were calculated by using ab initio multireference perturbation method (NEVPT2) with relativistic effects taken into account throughout ZORA approximation and corresponding all-electron basis sets. For the same purpose, the time-dependent DFT techniques were used. A very good agreement between NEVPT2 and experimental spectra should be highlighted, especially for the MLCT transitions that occur in visible and near-UV regions ( cm ). Moreover, the present study offers description of excited states of titled osmium complexes and their spectra interpretation using molecular orbitals.

Four-component full relativistic study on the spectroscopic properties and direct laser cooling schemes for the PbH, PoH, BiH+, and AtH+ molecules

The pseudo-closed transition with enough large Frank-Condon factor (FCF) is a necessary condition for direct laser cooling molecules, which means that only a few molecules with the appropriate ground and excited electronic states can be considered as potential candidates. The electronic and spectroscopic properties of five Ω states are evaluated for the PbH, PoH, BiH+, and AtH+ molecules based on the four-component full relativistic calculations with all-electron basis sets, by which we construct optical schemes for these molecules by using the X12Π1/2 (ν'') ↔ X22Π3/2 (ν') transitions for PbH and BiH+ or the X12Π3/2 (ν'') ↔ X22Π1/2 (ν') ones for PoH and AtH+. The built schemes can provide 104 ∼ 105 scattering phonons with three or five pumping lasers. Moreover, the Doppler/recoil temperatures are 2.08 × 10−3/0.04, 2.91 × 10−3/0.11, 7.48 × 10−3/0.08 and 0.01/0.18 μK, respectively, which means that the temperature of the order of nanokelvin for the PbH and PoH and microkelvin for the BiH+ and AtH+ molecules may be cooled based on the present optical schemes.

Ab Initio Study on the Vibrational and Electronic Properties of Radiation-Induced Defects in Potassium Bromide

The vibrational and electronic properties of several basic radiation defects in potassium bromide are computed at the quantum mechanical level using a periodic supercell approach based on hybrid functionals, an all-electron Gaussian-type basis set, and the Crystalcomputer code. The exciton energy in alkali halides is sufficient to create lattice defects, such as F–H Frenkel defect pairs, resulting in a relatively high concentration of single defects and their complexes. Here, we consider eight defects: the electronic F+- and F-centers (bromine vacancy without and with trapped electrons) and their dimers; hole H-center (neutral bromine atom forming the dumbbell ion with a regular Br− ion.); VK-center (Br2− molecular ion consisting of a hole and two regular ions); and two complex Br3− defects, combinations of several simple defects. The local geometry and the charge- and spin-density distributions of all defects are analyzed. Every defect shows its characteristic features in Raman spectra, and their comparison with available experimental data is discussed.

Challenges with relativistic GW calculations in solids and molecules.

For molecules and solids containing heavy elements, accurate electronic-structure calculations require accounting not only for electronic correlations but also for relativistic effects. In molecules, relativity can lead to severe changes in the ground-state description. In solids, the interplay between both correlation and relativity can change the stability of phases or it can lead to an emergence of completely new phases. Traditionally, the simplest illustration of relativistic effects can be done either by including pseudopotentials in non-relativistic calculations or alternatively by employing large all-electron basis sets in relativistic methods. By analyzing different electronic properties (band structure, equilibrium lattice constant and bulk modulus) in semiconductors and insulators, we show that capturing the interplay of relativity and electron correlation can be rather challenging in Green's function methods. For molecular problems with heavy elements, we also observe that similar problems persist. We trace these challenges to three major problems: deficiencies in pseudopotential treatment as applied to Green's function methods, the scarcity of accurate and compact all-electron basis sets that can be converged with respect to the basis-set size, and linear dependencies arising in all-electron basis sets, particularly when employing Gaussian orbitals. Our analysis provides detailed insight into these problems and opens a discussion about potential approaches to mitigate them.

Theoretical investigations into the bonding and separation properties of non-rigid, partially rigid, and rigid ligands derived from Et-Tol-PTA with trivalent lanthanides and actinides.

The separation of trivalent actinide elements from lanthanide elements represents one of the most formidable challenges within the context of nuclear waste partitioning and transmutation (P&T) processes. Consequently, we embarked on a systematic investigation aimed at elucidating the bonding properties and thermodynamic behavior of a N-ethyl-N-tolyl-2-amide-1,10-phenanthroline (Et-Tol-PTA) ligand in conjunction with trivalent actinide and lanthanide elements. This investigation involved the utilization of various density functional theory (DFT) methods and a comparative analysis between small-core pseudopotential basis sets and all-electron basis sets. It was found that well-performing results were achieved using the PBE0 functional in both bond length and thermodynamic energy calculations, with minimal impact being exerted by the basis set on the results. Furthermore, an exploration was carried out into the bonding and thermodynamic properties of trivalent actinides and lanthanides with ligands derived from Et-Tol-PTA, encompassing non-rigid (La), partially rigid (Lb, Lc), and rigid (Ld) ligands. Thermodynamically, advantages in the separation of Am(III)/Eu(III) were exhibited by Lb and Lc ligands, while excellent performance in the separation of Am(III)/Cm(III) was demonstrated by the La ligand. Analyses conducted using quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), and natural bond orbital (NBO) methodologies revealed the presence of partial covalent character in the bonds between oxygen (O) and metal (M), as well as between nitrogen (N) and metal (M), with a higher degree of covalent character being observed in O-Am and N-Am bonds compared to O-Cm/Eu and N-Cm/Eu interactions.

Nitrogen Reduction to Ammonia on a Fe16 Nanocluster: A Computational Study of Catalysis.

The sequence of elementary steps leading to reductive ammonia formation from N2 and H2 catalyzed by a Fe16 cluster is studied using generalized gradient approximation density functional theory and an all-electron basis set of triple-ζ quality. The computational methods are validated by comparison to experimental data such as binding energies where possible. First, the associative and dissociative attachment of N2 to Fe16 is considered, followed by exploration of the pathways leading to distal (Fe16-N-NH2) and enzymatic (NFe16-NH2) formation of an amino group. Next, the pathways leading to NH3 formation in both distal and enzymatic cases are examined. Two mechanisms for NH3 detachment have been discovered. An interesting peculiarity of the pathways is that they often proceed with total spin fluctuations, which are related to the rupture and formation of bonds on the surface of the catalyst over the course of the reactions. The reaction Fe16 + N2 + 2H2 → Fe16NH + NH3 is found to be exothermic by 1.02 eV (93.8 kJ/mol).

Investigation of the Effect of Solvents on the Synthesis of Aza-flavanone from Aminochalcone Facilitated by Halogen Bonding.

It has been recognized that CBr4 can give rise to a noncovalent interaction known as halogen bond (XB). CBr4 was found to catalyze, in terms of XB formation, the transformation of 2'-aminochalcone to aza-flavanone through an intramolecular Michael addition reaction. The impact of XB and the resulting yield of aza-flavanone exhibited a pronounced dependence on the characteristics of the solvent. Notably, yields of 88% in ethanol and 33% in DMSO were achieved, while merely a trace amount of the product was detected in benzene. In this work, we use a computational modeling study to understand this variance in yield. The reaction is modeled at the level of density functional theory (based on the M06-2X exchange-correlation functional) with all-electron basis sets of triple-ζ quality. Grimme's dispersion correction is incorporated to account for the noncovalent interactions accurately. Harmonic frequency calculations are carried out to establish the character of the optimized structures (minimum or saddle point). Our calculations confirm the formation of an XB between CBr4 and the reacting species and its role in lowering the activation energy barrier. Stronger orbital interactions and significant lowering of the steric repulsion were found to be important in lowering the activation barrier. The negligible yield in the nonpolar solvent benzene may be attributed to the high activation energy as well as the inadequate stabilization of the zwitterionic intermediate. In ethanol, a protic solvent, additional H-bonding contributes to further lowering of the activation barrier and better stabilization of the zwitterionic intermediate. The combined effects of solvent polarity, XB, and H-bond are likely to give rise to an excellent yield of aza-flavanone in ethanol.

Modeling stoichiometric and oxygen defective TiO2 anatase bulk and (101) surface: structural and electronic properties from hybrid DFT.

We present a periodic hybrid DFT investigation of the structural and electronic properties of both stoichiometric and oxygen-defective TiO2 anatase bulk and (101) surface, in singlet and triplet spin states. In all cases, an excellent agreement with available photoelectron spectroscopy data has been obtained, reproducing the offsets of the deep defect levels positions from the conduction band minimum of TiO2 created upon oxygen vacancy (VO) formation. For the bulk, different local structural polaronic distortions around the VO site have been evidenced depending on the spin state considered. Although a similar conclusion has been drawn for the defective surface for the nine different vacancy positions which have been considered, large migration of the twofold coordinated surface O atom has also been evidenced, up to the initial vacancy site in some cases. The very good agreement obtained with available experimental data regarding the offsets from the conduction band minimum of the deep defect levels positions both for the bulk and the (101) surface of TiO2 anatase is encouraging for the application of the proposed hybrid-based computational strategy to TiO2 surface-related processes such as TiO2-based photocatalysis in which oxygen vacancies are known to play a key role. All calculations have been performed with Crystal17, considering different hybrid functionals with both effective core pseudopotentials and all-electron atom-centered basis sets, as well as additional empirical dispersion effects with the D2 and D3 models.

Exploration of Indolo[3,2c]isoquinoline derived triazoles as potential antimicrobial and DNA cleavage agents: Synthesis, DFT calculations, and molecular modeling studies

Indole and its derivatives are well-known assorted motif in drug design and development. We here in reporting synthesis of new 9-chloro-1-(4-substituted phenyl)-12H-indolo[2,3-c][1,2,4]triazolo[3,4-a]isoquinolines 7 (a-h). Structures of the newly synthesized compounds were confirmed by making use of spectroscopic techniques like IR, NMR and Mass. The DFT calculations were taken for the selected molecules using CAM-B3LYP hybrid functional with a 6–31 + g(d) all-electron basis set using the Gaussian 09 package. The drug-likeness predictions were described for the synthesized derivatives. The In vitro antimicrobial and DNA cleavage activities were reported for all compounds 7 (a-h). The compounds 7a, 7b, and 7h showed excellent microbial inhibition and DNA cleavage activity as compared to standard drugs. Furthermore, the docking studies for the newly synthesized molecules were carried out by Auto dock software with two molecular targets Epidermal Growth Factor Receptor tyrosine kinase (1 M17) and C-kit Tyrosine Kinase (1 T46) exhibited better binding affinity of all synthesized compounds. In addition, the docking results were observed to be in full agreement with the in vitro DNA cleavage assay suggesting the potential of synthesized metal complexes in biological applications. Lastly, the protein stability, fluctuations of APO-Protein, and protein–ligand complexes were investigated through Molecular Dynamics (MD) simulations studies using Desmond Maestro 11.3 and potential lead molecules were identified.