Double-zeta Basis Set Research Articles

Role of Dark States and Stokes Shift Simulations for Tetraphenylpyrazine Compared to Other Donor-Acceptor Photosensitizers.

An excellent agreement for simulated and measured absorption and emission spectra is found for four donor-acceptor aromatic molecules (tetraphenylpyrazine, tetraphenylethene, distirylanthracene and hexaphenylsilole) whose derivatives serve as solid state photosensitizers. After comparing several hybrid TDDFT functionals, EOM-CCSD, and experiments, the best agreement was found with TD-B3LYP and double zeta basis sets (6-31G** and def2-SVP) for one molecule in gas phase. A full characterisation of twelve to twenty electronic excited states was performed in every system. Symmetry-forbidden bands are found in the absorption spectra by sampling fifty to hundred geometries from a Wigner distribution. The density of states in the region 2-6 eV was also analysed, showing a very packed region of excited states and suggesting that dark electronic states may play a role in the dynamics of some of the photoexcited systems. Further calculations were done with QM/xTB at geometries extracted from previously published X-ray data to evaluate the influence of the environment on the excitations of the four aggregated molecular crystals.

Accurate structures and rotational constants of bicyclic monoterpenes at DFT cost by means of the bond-corrected Pisa composite scheme (BPCS).

The structural, conformational, and spectroscopic properties in the gas phase of 20 bicyclic monoterpenes and monoterpenoids have been analyzed by a new accurate, reduced-cost computational strategy. In detail, the revDSD-PBEP86 double-hybrid functional in conjunction with the D3BJ empirical dispersion corrections and a suitable triple-zeta basis set provides accurate geometrical parameters, whence equilibrium rotational constants, which are further improved by proper account of core-valence correlation. Average deviations within 0.1% between computed and experimental rotational constants are reached when taking into account the vibrational corrections obtained by the B3LYP functional in conjunction with a double-zeta basis set in the framework of second-order vibrational perturbation theory. In addition to their intrinsic interest, the studied terpenes further extend the panel of systems for which the proposed strategy has provided accurate results at density functional theory cost. Therefore, a very accurate yet robust and user-friendly tool is now available for systematic investigations of the role of stereo-electronic effects on the properties of large systems of current technological and/or biological interest by experimentally oriented researchers.

A neural network-based four-body potential energy surface for parahydrogen.

We present an isotropic abinitio (para-H2)4 four-body interaction potential energy surface (PES). The electronic structure calculations are performed at the correlated coupled-cluster theory level, with single, double, and perturbative triple excitations. They use an atom-centered augmented correlation-consistent double zeta basis set, supplemented by a (3s3p2d) midbond function. We use a multilayer perceptron to construct the PES. We apply a rescaling transformation to the output energies during training to improve the prediction of weaker energies in the sample data. At long distances, the interaction energies are adjusted to match the empirically derived four-body dispersion interaction. The four-body interaction energy at short intermolecular separations is net repulsive. The use of this four-body PES, in combination with a first principles pair potential for para-H2 [J. Chem. Phys. 119, 12551 (2015)] and an isotropic abinitio three-body potential for para-H2 [J. Chem. Phys. 156, 044301 (2022)], is expected to provide closer agreement with experimental results.

On the CO[Formula: see text] adsorption in a boron nitride analog for the recently synthesized biphenylene network: a DFT study.

Recent advances in nanomaterial synthesis and characterization have led to exploring novel 2D materials. The biphenylene network (BPN) is a notable achievement in current fabrication efforts. Numerical studies have indicated the stability of its boron nitride counterpart, known as BN-BPN. In this study, we employ computational simulations to investigate the electronic and structural properties of pristine and doped BN-BPN monolayers upon CO[Formula: see text] adsorption. Our findings demonstrate that pristine BN-BPN layers exhibit moderate adsorption energies for CO[Formula: see text] molecules, approximately [Formula: see text]0.16 eV, indicating physisorption. However, introducing one-atom doping with silver, germanium, nickel, palladium, platinum, or silicon significantly enhances CO[Formula: see text] adsorption, leading to adsorption energies ranging from [Formula: see text]0.13 to [Formula: see text]0.65 eV. This enhancement indicates the presence of both physisorption and chemisorption mechanisms. BN-BPN does not show precise CO[Formula: see text] sensing and selectivity. Furthermore, our investigation of the recovery time for adsorbed CO[Formula: see text] molecules suggests that the interaction between BN-BPN and CO[Formula: see text] cannot modify the electronic properties of BN-BPN before the CO[Formula: see text] molecules escape. We performed density functional theory (DFT) simulations using the DMol3 code in the Biovia Materials Studio software. We incorporated Van der Waals corrections (DFT-D) within the Grimme scheme for an accurate representation. The exchange and correlation functions were treated using the Perdew-Burke-Ernzerhof (PBE) functional within the generalized gradient approximation (GGA). We used a double-zeta plus polarization (DZP) basis set to describe the electronic structure. Additionally, we accounted for the basis set superposition error (BSSE) through the counterpoise method. We included semicore DFT pseudopotentials to accurately model the interactions between the nuclei and valence electrons.

Basis Set Effects on the Stabilities and Interaction Energies of Small Amide Molecules Adsorbed on Kaolinite Surface

Adsorptions of small amide molecules, acetamide (AA) and N-methyl-acetamide (NMA) on the surface of kaolinite are investigated in this study. The focus is on the basis set effects towards the stabilities and the interaction energies of the molecules on the Al–O surface. With a fixed B3LYP functional, we increased the size of the basis sets for the single-point calculations, to find the converged interaction energies and obtain the relative stabilities. We found that, under the direct usage of Pople-type and Dunning’s correlation consistent basis sets, it is not possible to achieve the pattern of convergence for the interaction energies and the relative stabilities. Compared to the complete basis set (CBS) extrapolation scheme, the double zeta basis sets deviated the most, in the range of 21 to 27%, while it is from 1 to 7% for the triple zeta basis sets. Based on the results, we suggest using 6-311++G(2df,2pd) or cc-pVQZ for energy-related quantities. Compared to AA, NMA attached more strongly by 0.5 eV on the surface of Al–O.

Transfer-learned potential energy surfaces: Toward microsecond-scale molecular dynamics simulations in the gas phase at CCSD(T) quality.

The rise of machine learning has greatly influenced the field of computational chemistry and atomistic molecular dynamics simulations in particular. One of its most exciting prospects is the development of accurate, full-dimensional potential energy surfaces (PESs) for molecules and clusters, which, however, often require thousands to tens of thousands of abinitio data points restricting the community to medium sized molecules and/or lower levels of theory (e.g., density functional theory). Transfer learning, which improves a global PES from a lower to a higher level of theory, offers a data efficient alternative requiring only a fraction of the high-level data (on the order of 100 are found to be sufficient for malonaldehyde). This work demonstrates that even with Hartree-Fock theory and a double-zeta basis set as the lower level model, transfer learning yields coupled-cluster single double triple [CCSD(T)]-level quality for H-transfer barrier energies, harmonic frequencies, and H-transfer tunneling splittings. Most importantly, finite-temperature molecular dynamics simulations on the sub-μs time scale in the gas phase are possible and the infrared spectra determined from the transfer-learned PESs are in good agreement with the experiment. It is concluded that routine, long-time atomistic simulations on PESs fulfilling CCSD(T)-standards become possible.

Electronically excited states of closed-shell azabenzene and purine anion structures: Is 2D enough for dipole-bound excited states?

Deprotonated azabenzene anions require dipole moments in their corresponding neutral radicals of more than 3.5D in order to exhibit dipole-bound excited states (DBXSs). This is notably larger than the typical 2.0-2.5D associated with such behavior. Similar computational analysis on deprotonated purine derivatives also conducted herein only requires the more traditional 2.5D dipole moment, implying that the single six-membered azabenzene rings have additional factors at play in binding diffuse electrons. The present study also shows that the use of coupled cluster singles and doubles with a double-zeta correlation consistent basis set and additional diffuse functions originating from the center-of-charge for all aspects of the computations decreases the error in predicting DBXSs to less than 0.006eV at worst and likely less than 0.003eV for most cases. These results can influence the modeling of molecular spectra beyond fundamental chemical curiosity with application to astrochemistry, solar energy harvesting, and combustion chemistry among others.

A non-self-consistent tight-binding electronic structure potential in a polarized double-ζ basis set for all spd-block elements up to Z = 86.

Existing semiempirical molecular orbital methods suffer from the usually minimal atomic-orbital (AO) basis set used to simplify the calculations. Here, a completely new and consistently parameterized tight-binding electronic structure Hamiltonian evaluated in a deeply contracted, properly polarized valence double-zeta basis set (vDZP) is described. The inner-shell electrons are accounted for by standard, large-core effective potentials and approximations to them. The primary target of this so-called density matrix tight-binding method is to reproduce the one-particle density matrix P of a molecular ωB97X-V range-separated hybrid density functional theory (DFT) calculation in exactly the same basis set. Additional properties considered are orbital energies, dipole polarizabilities and dipole moments, and dipole polarizability derivatives. The key features of the method are as follows: (a) it is non-self-consistent with an overall fixed number of only three required matrix diagonalizations; (b) only AO overlap integrals are needed to construct the effective Hamiltonian matrix; (c) new P-dependent terms emulating non-local exchange are included; and (d) only element-specific empirical parameters (about 50 per element) need to be determined. The method globally achieves a high accuracy for the target properties at a speedup compared to the ωB97X-V/vDZP reference of about 3-4 orders of magnitude. It performs robustly for difficult transition metal complexes, for highly charged or zwitterionic systems, and for chemically unusual bonding situations, indicating a generally robust approximation of the (self-consistent) Kohn-Sham potential. As an example application, the vibrational Raman spectrum of an entire protein with 327 atoms with respect to the DFT reference calculation is shown. This method may be used out-of-the-box to generate molecular/atomic features for machine learning applications or as the basis for accurate high-speed DFT methods.

Electronic transport on the two state “ON–OFF” of 1,3,3-trimethylindolino-6′-nitrobenzopyrylospiran as a light-driven molecular optical switch: A first-principle study

Here, the electronic transport characteristics of the 1,3,3-trimethylindolino-6′-nitrobenzopyrylospiran were studied by using NEGF and DFT methods. By being exposed to UV or visible light, this molecule can change from its MC to SP states. The titled structure was optimized at B3LYP/6–311++G(d,p) level of theory. To obtain conductivity results, the electrons of metal and organic atoms were approached by the single-plus polarization (SZP) for single-zeta and double-plus polarization (DZP) for double zeta basis sets, respectively. We examined some factors in this study, including various molecule geometries, the type of surface materials (Platinum, gold, and silver), the switching ratio, the gap between HOMO and LUMO levels, and the transmission spectra, at different bias voltages. The outcomes show that conductivity transforms from an off-state (high resistance) to an on-state as the molecule switches from MC to SP form (low resistance).

Electron Correlation in the Iron(II) Porphyrin by Natural Orbital Functional Approximations.

The relative stability of the singlet, triplet, and quintet spin states of iron(II) porphyrin (FeP) represents a challenging problem for electronic structure methods. While it is currently accepted that the ground state is a triplet, multiconfigurational wave function-based methods predict a quintet, and density functional approximations vary between triplet and quintet states, leading to a prediction that highly depends on the features of the method employed. The recently proposed Global Natural Orbital Functional (GNOF) aims to provide a balanced treatment between static and dynamic correlation, and together with the previous Piris Natural Orbital Functionals (PNOFs), allowed us to explore the importance of each type of correlation in the stability order of the states of FeP with a method that conserves the spin of the system. It is noteworthy that GNOF correlates all electrons in all available orbitals for a given basis set; in the case of the FeP with a double-ζ basis set as used in this work, this means that GNOF can properly correlate 186 electrons in 465 orbitals, significantly increasing the sizes of systems amenable to multiconfigurational treatment. Results show that PNOF5, PNOF7s, and PNOF7 predict the quintet to have a lower energy than the triplet state; however, the addition of dynamic correlation via second-order Møller-Plesset corrections (NOF-MP2) turns the triplet state to be lower than the quintet state, a prediction also reproduced by GNOF that incorporates much more dynamic correlation than its predecessors.

Band Gap Opening in Borophene/GaN and Borophene/ZnO Van der Waals Heterostructures Using Axial Deformation: First-Principles Study.

One of the topical problems of materials science is the production of van der Waals heterostructures with the desired properties. Borophene is considered to be among the promising 2D materials for the design of van der Waals heterostructures and their application in electronic nanodevices. In this paper, we considered new atomic configurations of van der Waals heterostructures for a potential application in nano- and optoelectronics: (1) a configuration based on buckled triangular borophene and gallium nitride (GaN) 2D monolayers; and (2) a configuration based on buckled triangular borophene and zinc oxide (ZnO) 2D monolayers. The influence of mechanical deformations on the electronic structure of borophene/GaN and borophene/ZnO van der Waals heterostructures are studied using the first-principles calculations based on density functional theory (DFT) within a double zeta plus polarization (DZP) basis set. Four types of deformation are considered: uniaxial (along the Y axis)/biaxial (along the X and Y axes) stretching and uniaxial (along the Y axis)/biaxial (along the X and Y axes) compression. The main objective of this study is to identify the most effective types of deformation from the standpoint of tuning the electronic properties of the material, namely the possibility of opening the energy gap in the band structure. For each case of deformation, the band structure and density of the electronic states (DOS) are calculated. It is found that the borophene/GaN heterostructure is more sensitive to axial compression while the borophene/ZnO heterostructure is more sensitive to axial stretching. The energy gap appears in the band structure of borophene/GaN heterostructure at uniaxial compression by 14% (gap size of 0.028 eV) and at biaxial compression by 4% (gap size of 0.018 eV). The energy gap appears in the band structure of a borophene/ZnO heterostructure at uniaxial stretching by 10% (gap size 0.063 eV) and at biaxial compression by 6% (0.012 eV). It is predicted that similar heterostructures with an emerging energy gap can be used for various nano- and optoelectronic applications, including Schottky barrier photodetectors.

Ab initio relativistic potential energy surface with analytical long-range part of benzene-Rn complex and its application to intermolecular vibrations

We study the benzene-Rn (BzRn) complex in its electronic ground state using an ab initio scalar relativistic method in the framework of the coupled-cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)]. Two different approaches to treat the scalar relativistic effects have been tested — the small-core pseudopotential (PP) and the Douglas–Kroll–Hess (DKH) Hamiltonian. These methods were used with the augmented Dunning’s double zeta basis set for C and H atoms, and the augmented triple PP basis set for Rn supplemented by midbond functions. Additionally, the effects of the basis extension for C and H atoms and the extension of the correlation space to include the internal orbitals of Rn and C have been tested. The comparison of the binding energy De and the equilibrium coordinate ze found with different methods has allowed to choose the optimal one based on PP for the construction of the analytical potential energy surface (PES). The long-range part of the potential has been fitted separately and the obtained long-range coefficients have been compared to their counterparts calculated from the first principles using the CCSD polarization propagator. The vibrational energy level pattern of BzRn has been studied, and the revealed polyad structure of the complex has been compared to the previously studied benzene-Kr and benzene-Xe complexes. A Python code that yields the interaction energy at any Rn position is provided.

Theoretical calculations for new coumarin Schiff base complexes as candidates for in vitro and in silico biological applications

The Schiff base (Sb) formed by the condensation of 8‐acetyl‐7‐hydroxy‐4‐methyl coumarin and sulfaclozine was used for the preparation of [Cu2(CH3COO)3(Sb)(H2O)] (Cu2‐Sb) and [Pd2(OH)3(Sb)(H2O)]·2H2O (Pd2‐Sb) complexes. Also, the mixed ligand zinc complex, [(Sb)Zn(Cipro)]·4H2O, (Sb‐Zn‐Cipro) was prepared from (Sb) and ciprofloxacin. Many tools of analysis as elemental and spectral studies, in addition to thermogravimetry (TG), molar conductance, magnetic moment, X‐ray diffraction (XRD), energy dispersive X‐ray (EDX), scanning electron microscope (SEM), and electron spin resonance (ESR) measurements, were used to prove the complexes' composition. The morphology studies confirm the nanostructure of copper and palladium complexes. At the B3LYP/GENECP level, the optimal structure of the complexes was estimated using the 6‐31G++(d, p) basis set for C, H, N, S, and O atoms and the Los Alamos National Laboratory double zeta (LANL2DZ) basis set for metal atoms. A distorted square planar geometry is presumed for (Pd2‐Sb), and distorted tetrahedral geometry is presumed for (Cu2‐Sb) and (Sb‐Zn‐Cipro). The in vitro examination of the antimicrobial activity of the complexes was performed. The cytotoxic effects of the (Pd2‐Sb) and (Sb‐Zn‐Cipro) against MCF‐7 (breast cancer) and HCT‐116 (colon cancer) cell lines were achieved in vitro. The results showed that (Sb‐Zn‐Cipro) has the best biological activity. In view of this, the in silico binding mode of (Sb‐Zn‐Cipro) complex with Escherichia coli (KAS I‐PDB ID‐1FJ4), Staphylococcus aureus tyrosyl‐tRNA synthetase (PDB id: 1JIJ), yeast‐specific serine/threonine protein phosphatase (PPZ1) of Candida albicans (PDB ID: 5JPE), breast cancer mutant oxidoreductase (PDB ID: 3HB5), and colon cancer human cyclin‐dependent kinase 2; CDK2 (PDB ID: 6GUE) was performed using molecular docking.

The role of intermolecular interactions of aromatic sandwich dimer ligands for the half-titanocene catalysts: Theoretical study

Visualization of intermolecular interaction of half-titanocene complex modified by sandwich dimers. (a) reduced density gradient function (RDG); (b) dispersion point isosurface diagram of weak intermolecular interaction. • Ab initio calculations on the influences of intermolecular interactions in ligands on the half-titanocenes. • A set of model ligands and their sandwich dimers optimized at 12 levels of theory. • Suitability in various occasions explored based on statistical analyses. • Intermolecular interactions visualized by wave function analyses and correlational analyses after feature extraction. • Types and intermolecular interactions of ligands in affecting the conformation of catalysts was discussed. The successful design of an efficient half-titanocenes could strongly benefit from a conceptual understanding of how intermolecular forces lead to structure formation on the atomistic level. This work reports density functional theory calculations on the influences of intermolecular interactions in aromatic ligands on the half-titanocenes. For this purpose, a set of model aromatic ligands R, in which R = benzene, naphthalene, anthracene, pyrene, hexafluorobenzene and their sandwich dimers, were chosen and optimized at 12 levels of theory including three kinds of hybrid functionals with different contents of HF functions combined with double or triple zeta basis sets with or without diffusion functions. The practicality and reliability of the assorted methods to predict geometric parameters were explored based on multivariable linear regression analysis and correlation analysis. Intermolecular interactions were visualized by wave function analyses and correlational analyses after feature extraction were conducted to discuss the possible role of types and intermolecular interactions of aromatic ligands in affecting the conformation of catalysts.

Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching.

A fragmentation approach referred to as a simple overlapping region method for force matching (SORForM) is presented. SORForM is designed to enable efficient computation of quantum mechanical (QM) forces for large molecules and is validated in the framework of adaptive force matching (AFM) to develop solute models in water. The SORForM method divides a molecule into overlapping QM regions with each region containing a gradient zone and a buffer zone. The buffer zone ensures that the atoms in the gradient zone have their surroundings unchanged with fragmentation. The performance of the method is validated with mefenamic acid and linalyl acetate by comparing the hydration free energies of AFM models developed with and without SORForM. The AFM hydration free energies are also compared with that of the experiments. The models developed with B3LYP-D3(BJ) and def2-TZVP are in excellent agreement with experiments. Our work shows that PBE-D3(BJ) provides less satisfactory results when compared to B3LYP-D3(BJ). The def2-TZVP basis set is found to greatly improve the agreement with experiments when compared to a double-zeta quality basis set.

Metal-organic frameworks properties from hybrid density functional approximations.

The chemical versatility and modular nature of Metal-Organic Frameworks (MOFs) make them unique hybrid inorganic-organic materials for several important applications. From a computational point of view, ab initio modeling of MOFs is a challenging and demanding task, in particular, when the system reaches the size of gigantic MOFs as MIL-100 and MIL-101 (where MIL stands for Materials Institute Lavoisier) with several thousand atoms in the unit cell. Here, we show how such complex systems can be successfully tackled by a recently proposed class of composite electronic structure methods revised for solid-state calculations. These methods rely on HF/density functional theory hybrid functionals (i.e., PBEsol0 and HSEsol) combined with a double-zeta quality basis set. They are augmented with semi-classical corrections to take into account dispersive interactions (D3 scheme) and the basis set superposition error (gCP). The resulting methodologies, dubbed "sol-3c," are cost-effective yet reach the hybrid functional accuracy. Here, sol-3c methods are effectively applied to predict the structural, vibrational, electronic, and adsorption properties of some of the most common MOFs. Calculations are feasible even on very large MOFs containing more than 2500 atoms in the unit cell as MIL-100 and MIL-101 with reasonable computing resources. We propose to use our composite methods for the routine in silico screening of MOFs targeting properties beyond plain structural features.

Synthesis, spectroscopic, DFT calculations, biological activities and molecular docking studies of new isoxazolone, pyrazolone, triazine, triazole and amide derivatives

Ethyl-2-cyano-2-(2-(3-nitrophenyl)hydrazono)acetate was synthesized and used as a versatile reagent for the synthesis of different heterocyclic compounds such as isoxazolone, pyrazolone, triazine, triazole and amide derivatives via its reactions with different nucleophiles. Conventional, microwave and grinding techniques were used for synthesis of the newly isolated derivatives. Various physical parameters were calculated from the percentage yield and reaction time in order to compare between the three techniques. The reported compounds were characterized by elemental analyses and different spectroscopic tools such as IR, 1H NMR, 13C NMR and mass spectrometry. The optimized molecular geometries of some selected compounds were investigated using the density functional theory (DFT/B3LYP) method with the use of double zeta plus polarization basis set 6–31 G (d,p) for the C, H, N, O and S atoms. The quantum global reactivity descriptors were also calculated and discussed. The antibacterial and cytotoxicity screening of those compounds were performed to determine their therapeutic potential. Molecular docking of the compounds was also examined. The different biological studies as well as the molecular docking were correlated to each other, and supported that the compounds could bind to DNA, possibly, via intercalative mode and showed a various DNA binding potency.

ZORA double zeta basis sets for fifth row elements: Application in studies of electronic structures of atoms and molecules

Segmented all-electron basis set of double zeta valence quality plus polarization functions (DZP) to be used with the zero-order regular approximation (ZORA) scalar relativistic Hamiltonian was developed for the elements Cs, Ba, La, and from Hf to Rn. This set was augmented with diffuse functions for the purpose of describing electrons distant from atomic nuclei. Using the ZORA-B3LYP method, some atomic and molecular properties are computed. Benchmark theoretical results and experimental data were used to evaluate the performance of the DZP-ZORA and ADZP-ZORA basis sets. Despite their small sizes, these sets have proven to be accurate and reliable and can also be used in property calculations involving electrons not only from the outer shells, but also from the inner shells. Comparison of second order Douglas-Kroll-Hess and ZORA results was made.

Synthesis and elucidation of binuclear thiazole-based complexes from Co(II) and Cu(II) ions: Conductometry, cytotoxicity and computational implementations for various verifications

A new thiazole-based ligand was prepared and investigated then used to preparing its Co(II) and Cu(II) complexes. All available analytical (CHN analysis & TGA) and spectral (IR, UV–Vis, 1H NMR, Mass, SEM, XRD & EDX) techniques were applied to elucidate the chemical formulae of new compounds. The ligand behaved as a neutral tetradentate towards binuclear metal ions in the two complex via N-H, two C = N and C-S groups. A tetrahedral geometry was suggested for Co(II) complex according to 4A2(F)→4T1(F)(ʋ3) transition at 15,873 cm−1. While, a square-planer geometry was suggested for Cu(II) complex according to 2B1g →2B2g (ʋ1) and 2B1g → 2Eg transitions. The magnetic moment values of the two complexes were appeared lower than the normal values, due to binuclear presence minimized electron spinning. The mass spectra of the complexes recorded their molecular ion peaks that match to the molecular formula after expel of crystal water molecules. A conductometry study was executed for the complex formed from nano-sized CuCl2 and the ligand in solution to extract the association and formation constants as well as the M : L molar ratio. The stereo structures of the ligand and its binuclear complexes were optimized by DFT method under valence double-zeta basis set. The distribution of N(1)-N(10), C(11)-S(12) and C(15)-N(13) groups is suitable for their coordination with the two metal ions without bond strain. The in vitro assay was performed for the new compounds against HePG2, PC3 and MCF-7 cancer cell lines. The two complexes exhibited high toxicity against breast cancer cells. This result was confirmed interestingly via in silico ways as pharmacophore query and MOE-docking. The interaction parameters and docking patterns reflect the superiority of Co(II) and Cu(II) complexes in controlling breast cancer cell which agree with that obtained in vitro.

Assessment of the Accuracy of DFT-Predicted Li+-Nucleic Acid Binding Energies.

Understanding how lithium interacts with complex biosystems is crucial for uncovering the roles of this alkali metal in biology and designing extraction techniques for battery production and environmental remediation. In this light, fundamental information about Li+ binding to nucleic acids is required. Herein, a new database of Li+-nucleic acid interactions is presented that contains CCSD(T)/CBS benchmark energies for all nucleobase and phosphate binding locations. Furthermore, the performance of 54 DFT functionals in combination with three triple-zeta (TZ) basis sets (6-311+G(3df,2p), aug-cc-pVTZ, and def2-TZVPP) is tested. The results identify a range of functionals across different families (B2-PLYP, PBE-QIDH, ωB97, ωB97X-D, MN15, B3PW91, B97-2, TPSS, BP86-D3(BJ), and PBE) that can accurately describe coordinated Li+-nucleic acid interactions, with the average mean percent error (AMPE) across binding positions and basis sets being below 2%. Nevertheless, only three functionals tested (B2-PLYP, PBE-QIDH, and ωB97X-D) preserve this accuracy for metal cation-π interactions, suggesting that caution is warranted when choosing a functional to describe a diverse range of Li+-nucleic acid complexes. Removal of counterpoise corrections has very little impact on the reliability of most functionals, while the effect of empirical dispersion corrections varies depending on the functional choice and interaction type. While increasing the basis set to quadruple-zeta quality had little impact on the AMPE, the accuracy of double-zeta basis sets varies with family. Importantly, DFT methods reproduce the CCSD(T)/CBS trend in the preferred binding position for a given nucleic acid component and the global trend across components (phosphate ≫ G > C ≫ A ∼ T = U), as well as the geometries of the metal-nucleic acid complexes. The overall top performing functional is PBE-QIDH, which results in deviations from CCSD(T)/CBS values as small as ∼0.1 kcal/mol for nucleobase contacts and ∼1 kcal/mol for phosphate interactions. The most accurate DFT methods identified in the present work are recommended for future investigations of lithium interactions in larger nucleic acid systems to provide insights into the biological roles of this metal and the design of novel biosensing strategies.